############# Output Dietary#########
> ################# Survey Weighted NHANES Geaneralized Mixed Linear Models  #####################################################
> ### Download  data from NHANES
> ### SPSS--> Excel--> Code data on Excel
> ### see https://www.extendoffice.com/documents/excel/5168-excel-categorize-data-based-on-values.html
> 
> #### For References on the Script, see paper
> ### Library packages are uploaded as needed 
> #### For general coding and plotting graphs
> 
> library("tidyverse")
> library("dbplyr")
> library("ggplot2")
> library("caret")
> library('dplyr')
> library("gtsummary")
> library("jtools")
> library("survey")
> library("interactions")
> ####> #######################################################################################################################
> ### Final Script 2b
> #####################################################################################################################
> nhanes1 <- q123_1 %>% mutate_if(is.character,as.factor)
> class(nhanes1)
[1] "tbl_df"     "tbl"        "data.frame"
> print(nhanes1)
# A tibble: 4,415 x 28
    SEQN Fasting    Fasting_R HSCRP_R HSCRP Age    Age_R SDMVPSU    WT4 SDMVSTRA Gender Ethnicity    BMI   WBC Kcal  Kcal_R
   <dbl> <fct>          <dbl>   <dbl> <dbl> <fct>  <dbl>   <dbl>  <dbl>    <dbl> <fct>  <fct>      <dbl> <dbl> <fct>  <dbl>
 1 83732 Not Fasted         3     0.6 0.817 Middl~    62       1 34973.      125 Male   White       27.8   9.8 High~  2262.
 2 83733 Fasted            12     1.4 1.51  Middl~    53       1  6595.      125 Male   White       30.8   7.3 High~  3468.
 3 83734 Fasted            10     0.6 0.817 Older~    78       1  2464.      131 Male   White       28.8   4.4 High~  2205 
 4 83736 Fasted            10     0.5 0.730 Adult     42       2  4907.      126 Female Black       20.3   4.2 Low ~   853 
 5 83737 Fasted            12     2.5 2.47  Older~    72       1  2157.      128 Female Mexican A~  28.6   6.1 Low ~   984.
 6 83741 Fasted             9     1.3 1.43  Young~    22       2  9772.      128 Male   Black       28     3.5 Mode~  1771 
 7 83742 Not Fasted         3     3   2.90  Young~    32       1  7205.      125 Female Mexican A~  28.2   8.3 Mode~  2034.
 8 83744 Not Fasted         3     0.4 0.643 Middl~    56       2 21383.      126 Male   Black       33.6   6.1 Low ~   746.
 9 83747 Not Fasted         3     3.2 3.08  Adult     46       1  8230.      121 Male   White       27.6   8.3 Mode~  1528.
10 83752 Not Fasted         1     0.9 1.08  Young~    30       1 11830.      124 Female Other His~  26.6   9.8 High~  3114.
# ... with 4,405 more rows, and 12 more variables: Protein <dbl>, Carbohydrate <fct>, Carbohydrate_R <dbl>, Sugar <dbl>,
#   Zinc <fct>, Zinc_R <dbl>, Choline <dbl>, Folate <dbl>, Copper <dbl>, S.Fat <dbl>, M.Fat <dbl>, P.Fat <dbl>
> 
> ######### Summary of Data################
> summary(nhanes1)
      SEQN              Fasting       Fasting_R         HSCRP_R           HSCRP                       Age      
 Min.   : 83732   Fasted    :1950   Min.   : 0.000   Min.   : 0.080   Min.   : 0.0053   Adult           :1032  
 1st Qu.: 88802   Not Fasted:2465   1st Qu.: 2.000   1st Qu.: 0.500   1st Qu.: 0.5563   Middle Age Adult:1116  
 Median : 93437                     Median : 5.000   Median : 1.360   Median : 1.3388   Older Adult     :1056  
 Mean   : 93376                     Mean   : 7.054   Mean   : 3.354   Mean   : 3.3632   Young Adult     :1211  
 3rd Qu.: 98108                     3rd Qu.:11.000   3rd Qu.: 3.535   3rd Qu.: 3.5415                          
 Max.   :102956                     Max.   :37.000   Max.   :94.210   Max.   :94.2100                          
     Age_R          SDMVPSU           WT4            SDMVSTRA        Gender                Ethnicity         BMI       
 Min.   :19.00   Min.   :1.000   Min.   :  1431   Min.   :119.0   Female:2269   Asian           : 613   Min.   :17.00  
 1st Qu.:34.00   1st Qu.:1.000   1st Qu.:  6842   1st Qu.:126.0   Male  :2146   Black           : 981   1st Qu.:21.90  
 Median :50.00   Median :1.000   Median : 13909   Median :133.0                 Mexican American: 672   Median :25.70  
 Mean   :49.55   Mean   :1.497   Mean   : 25084   Mean   :133.4                 Other Hispanic  : 514   Mean   :25.75  
 3rd Qu.:64.00   3rd Qu.:2.000   3rd Qu.: 29994   3rd Qu.:141.0                 Other Race      : 192   3rd Qu.:29.50  
 Max.   :80.00   Max.   :2.000   Max.   :450998   Max.   :148.0                 White           :1443   Max.   :34.90  
      WBC                             Kcal          Kcal_R          Protein                Carbohydrate  Carbohydrate_R   
 Min.   :  2.000   High Calorie Diet    :1619   Min.   : 227.5   Min.   :  2.58   High Intake    :2743   Min.   :  12.48  
 1st Qu.:  5.800   Low Calorie Diet     :1265   1st Qu.:1434.0   1st Qu.: 53.27   Low Intake     : 743   1st Qu.: 169.61  
 Median :  7.100   Moderate Calorie Diet:1531   Median :1861.0   Median : 69.94   Moderate Intake: 929   Median : 224.59  
 Mean   :  7.492                                Mean   :1965.0   Mean   : 75.22                          Mean   : 238.63  
 3rd Qu.:  8.500                                3rd Qu.:2382.5   3rd Qu.: 91.79                          3rd Qu.: 289.74  
 Max.   :400.000                                Max.   :8356.5   Max.   :305.08                          Max.   :1063.07  
     Sugar                        Zinc          Zinc_R          Choline           Folate           Copper      
 Min.   :  0.335   Adequate Intake  :2785   Min.   : 0.325   Min.   :   4.9   Min.   :  14.0   Min.   : 0.145  
 1st Qu.: 62.685   Inadequate Intake:1630   1st Qu.: 6.820   1st Qu.: 196.9   1st Qu.: 303.5   1st Qu.: 0.720  
 Median : 91.445                            Median : 9.350   Median : 275.9   Median : 430.5   Median : 0.975  
 Mean   :102.192                            Mean   :10.246   Mean   : 305.5   Mean   : 495.2   Mean   : 1.094  
 3rd Qu.:129.425                            3rd Qu.:12.648   3rd Qu.: 382.4   3rd Qu.: 619.0   3rd Qu.: 1.300  
 Max.   :680.345                            Max.   :39.910   Max.   :1391.2   Max.   :3851.5   Max.   :17.800  
     S.Fat             M.Fat             P.Fat      
 Min.   :  1.609   Min.   :  1.635   Min.   : 0.69  
 1st Qu.: 16.291   1st Qu.: 17.509   1st Qu.:11.27  
 Median : 23.143   Median : 24.477   Median :16.30  
 Mean   : 25.327   Mean   : 26.632   Mean   :17.95  
 3rd Qu.: 31.804   3rd Qu.: 33.205   3rd Qu.:22.52  
 Max.   :127.370   Max.   :133.245   Max.   :88.96  
> 
> ###########Structure of the Data############
> str(nhanes1)
tibble [4,415 x 28] (S3: tbl_df/tbl/data.frame)
 $ SEQN          : num [1:4415] 83732 83733 83734 83736 83737 ...
 $ Fasting       : Factor w/ 2 levels "Fasted","Not Fasted": 2 1 1 1 1 1 2 2 2 2 ...
 $ Fasting_R     : num [1:4415] 3 12 10 10 12 9 3 3 3 1 ...
 $ HSCRP_R       : num [1:4415] 0.6 1.4 0.6 0.5 2.5 1.3 3 0.4 3.2 0.9 ...
 $ HSCRP         : num [1:4415] 0.817 1.513 0.817 0.73 2.469 ...
 $ Age           : Factor w/ 4 levels "Adult","Middle Age Adult",..: 2 2 3 1 3 4 4 2 1 4 ...
 $ Age_R         : num [1:4415] 62 53 78 42 72 22 32 56 46 30 ...
 $ SDMVPSU       : num [1:4415] 1 1 1 2 1 2 1 2 1 1 ...
 $ WT4           : num [1:4415] 34973 6595 2464 4907 2157 ...
 $ SDMVSTRA      : num [1:4415] 125 125 131 126 128 128 125 126 121 124 ...
 $ Gender        : Factor w/ 2 levels "Female","Male": 2 2 2 1 1 2 1 2 2 1 ...
 $ Ethnicity     : Factor w/ 6 levels "Asian","Black",..: 6 6 6 2 3 2 3 2 6 4 ...
 $ BMI           : num [1:4415] 27.8 30.8 28.8 20.3 28.6 28 28.2 33.6 27.6 26.6 ...
 $ WBC           : num [1:4415] 9.8 7.3 4.4 4.2 6.1 3.5 8.3 6.1 8.3 9.8 ...
 $ Kcal          : Factor w/ 3 levels "High Calorie Diet",..: 1 1 1 2 2 3 3 2 3 1 ...
 $ Kcal_R        : num [1:4415] 2262 3468 2205 853 984 ...
 $ Protein       : num [1:4415] 104.8 114.1 105.1 25.3 52.9 ...
 $ Carbohydrate  : Factor w/ 3 levels "High Intake",..: 1 1 1 2 2 1 1 2 2 1 ...
 $ Carbohydrate_R: num [1:4415] 237 290 249 111 127 ...
 $ Sugar         : num [1:4415] 80.4 107.7 78.7 72.7 23.1 ...
 $ Zinc          : Factor w/ 2 levels "Adequate Intake",..: 1 2 1 2 2 1 1 2 2 1 ...
 $ Zinc_R        : num [1:4415] 11.91 7.06 15.37 2.29 5.67 ...
 $ Choline       : num [1:4415] 415.5 889.2 514.8 82.2 192.8 ...
 $ Folate        : num [1:4415] 536 586 428 128 362 ...
 $ Copper        : num [1:4415] 1.185 0.89 2.005 0.255 0.8 ...
 $ S.Fat         : num [1:4415] 31.92 29.35 31.48 13.26 8.23 ...
 $ M.Fat         : num [1:4415] 37.2 40.1 29.4 13.2 11.3 ...
 $ P.Fat         : num [1:4415] 22.67 33.12 21.51 4.92 8.38 ...
> 
> ######## Head of structure################
> head(nhanes1)
# A tibble: 6 x 28
   SEQN Fasting    Fasting_R HSCRP_R HSCRP Age    Age_R SDMVPSU    WT4 SDMVSTRA Gender Ethnicity    BMI   WBC Kcal   Kcal_R
  <dbl> <fct>          <dbl>   <dbl> <dbl> <fct>  <dbl>   <dbl>  <dbl>    <dbl> <fct>  <fct>      <dbl> <dbl> <fct>   <dbl>
1 83732 Not Fasted         3     0.6 0.817 Middl~    62       1 34973.      125 Male   White       27.8   9.8 High ~  2262.
2 83733 Fasted            12     1.4 1.51  Middl~    53       1  6595.      125 Male   White       30.8   7.3 High ~  3468.
3 83734 Fasted            10     0.6 0.817 Older~    78       1  2464.      131 Male   White       28.8   4.4 High ~  2205 
4 83736 Fasted            10     0.5 0.730 Adult     42       2  4907.      126 Female Black       20.3   4.2 Low C~   853 
5 83737 Fasted            12     2.5 2.47  Older~    72       1  2157.      128 Female Mexican A~  28.6   6.1 Low C~   984.
6 83741 Fasted             9     1.3 1.43  Young~    22       2  9772.      128 Male   Black       28     3.5 Moder~  1771 
# ... with 12 more variables: Protein <dbl>, Carbohydrate <fct>, Carbohydrate_R <dbl>, Sugar <dbl>, Zinc <fct>,
#   Zinc_R <dbl>, Choline <dbl>, Folate <dbl>, Copper <dbl>, S.Fat <dbl>, M.Fat <dbl>, P.Fat <dbl>
> 
> ############Tail of structure############
> tail(nhanes1)
# A tibble: 6 x 28
    SEQN Fasting    Fasting_R HSCRP_R  HSCRP Age    Age_R SDMVPSU    WT4 SDMVSTRA Gender Ethnicity   BMI   WBC Kcal  Kcal_R
   <dbl> <fct>          <dbl>   <dbl>  <dbl> <fct>  <dbl>   <dbl>  <dbl>    <dbl> <fct>  <fct>     <dbl> <dbl> <fct>  <dbl>
1 102930 Not Fasted         3    0.51 0.247  Young~    32       1 15944.      138 Female Asian      29.7   5.8 High~  2119 
2 102932 Not Fasted         0    0.37 0.0858 Middl~    62       2 31503.      135 Female Other Hi~  30.5   6.3 Low ~  1482.
3 102941 Not Fasted         2    0.6  0.350  Older~    69       1  6532.      135 Female White      21.7   7   High~  2574.
4 102947 Fasted            16    0.5  0.235  Older~    80       1 23114.      142 Female White      29.9   3.6 Mode~  1852.
5 102952 Fasted            14    0.45 0.178  Young~    35       2 12533.      135 Female Mexican ~  27.6   5.1 High~  2292 
6 102956 Fasted            11    3.7  3.92   Older~    65       2  6327.      141 Female Asian      21     9   High~  2600.
# ... with 12 more variables: Protein <dbl>, Carbohydrate <fct>, Carbohydrate_R <dbl>, Sugar <dbl>, Zinc <fct>,
#   Zinc_R <dbl>, Choline <dbl>, Folate <dbl>, Copper <dbl>, S.Fat <dbl>, M.Fat <dbl>, P.Fat <dbl>
> 
> ######Determine Column Names###############
> 
> colnames(nhanes1)
 [1] "SEQN"           "Fasting"        "Fasting_R"      "HSCRP_R"        "HSCRP"          "Age"            "Age_R"         
 [8] "SDMVPSU"        "WT4"            "SDMVSTRA"       "Gender"         "Ethnicity"      "BMI"            "WBC"           
[15] "Kcal"           "Kcal_R"         "Protein"        "Carbohydrate"   "Carbohydrate_R" "Sugar"          "Zinc"          
[22] "Zinc_R"         "Choline"        "Folate"         "Copper"         "S.Fat"          "M.Fat"          "P.Fat"         
> ###############################################################################################################
> 
> 
> ########################## Create Survey Weight Equation #################################################################################
> nhc2 <- svydesign(id=~SDMVPSU, weights=~WT4, strata=~SDMVSTRA, nest=TRUE, survey.lonely.psu = "adjust", data= nhanes1)
> summary(nhc2)
Stratified 1 - level Cluster Sampling design (with replacement)
With (60) clusters.
svydesign(id = ~SDMVPSU, weights = ~WT4, strata = ~SDMVSTRA, 
    nest = TRUE, survey.lonely.psu = "adjust", data = nhanes1)
Probabilities:
     Min.   1st Qu.    Median      Mean   3rd Qu.      Max. 
2.217e-06 3.334e-05 7.190e-05 1.076e-04 1.461e-04 6.989e-04 
Stratum Sizes: 
           119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146
obs        108 128 157 164 151 160 172 142 136 167 153 136 171 175 145 118 144 162 153 150 128 152 160 147 131 168 143 144
design.PSU   2   2   2   2   2   2   2   2   2   2   2   2   2   2   2   2   2   2   2   2   2   2   2   2   2   2   2   2
actual.PSU   2   2   2   2   2   2   2   2   2   2   2   2   2   2   2   2   2   2   2   2   2   2   2   2   2   2   2   2
           147 148
obs        134 116
design.PSU   2   2
actual.PSU   2   2
Data variables:
 [1] "SEQN"           "Fasting"        "Fasting_R"      "HSCRP_R"        "HSCRP"          "Age"            "Age_R"         
 [8] "SDMVPSU"        "WT4"            "SDMVSTRA"       "Gender"         "Ethnicity"      "BMI"            "WBC"           
[15] "Kcal"           "Kcal_R"         "Protein"        "Carbohydrate"   "Carbohydrate_R" "Sugar"          "Zinc"          
[22] "Zinc_R"         "Choline"        "Folate"         "Copper"         "S.Fat"          "M.Fat"          "P.Fat"         
> str(nhc2)   
List of 9
 $ cluster   :'data.frame':	4415 obs. of  1 variable:
  ..$ SDMVPSU: Factor w/ 60 levels "119.1","119.2",..: 13 13 25 16 19 20 13 16 5 11 ...
  ..- attr(*, "terms")=Classes 'terms', 'formula'  language ~SDMVPSU
  .. .. ..- attr(*, "variables")= language list(SDMVPSU)
  .. .. ..- attr(*, "factors")= int [1, 1] 1
  .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. ..$ : chr "SDMVPSU"
  .. .. .. .. ..$ : chr "SDMVPSU"
  .. .. ..- attr(*, "term.labels")= chr "SDMVPSU"
  .. .. ..- attr(*, "order")= int 1
  .. .. ..- attr(*, "intercept")= int 1
  .. .. ..- attr(*, "response")= int 0
  .. .. ..- attr(*, ".Environment")=<environment: R_GlobalEnv> 
  .. .. ..- attr(*, "predvars")= language list(SDMVPSU)
  .. .. ..- attr(*, "dataClasses")= Named chr "numeric"
  .. .. .. ..- attr(*, "names")= chr "SDMVPSU"
 $ strata    :'data.frame':	4415 obs. of  1 variable:
  ..$ SDMVSTRA: num [1:4415] 125 125 131 126 128 128 125 126 121 124 ...
  ..- attr(*, "terms")=Classes 'terms', 'formula'  language ~SDMVSTRA
  .. .. ..- attr(*, "variables")= language list(SDMVSTRA)
  .. .. ..- attr(*, "factors")= int [1, 1] 1
  .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. ..$ : chr "SDMVSTRA"
  .. .. .. .. ..$ : chr "SDMVSTRA"
  .. .. ..- attr(*, "term.labels")= chr "SDMVSTRA"
  .. .. ..- attr(*, "order")= int 1
  .. .. ..- attr(*, "intercept")= int 1
  .. .. ..- attr(*, "response")= int 0
  .. .. ..- attr(*, ".Environment")=<environment: R_GlobalEnv> 
  .. .. ..- attr(*, "predvars")= language list(SDMVSTRA)
  .. .. ..- attr(*, "dataClasses")= Named chr "numeric"
  .. .. .. ..- attr(*, "names")= chr "SDMVSTRA"
 $ has.strata: logi TRUE
 $ prob      : Named num [1:4415] 2.86e-05 1.52e-04 4.06e-04 2.04e-04 4.64e-04 ...
  ..- attr(*, "names")= chr [1:4415] "1" "2" "3" "4" ...
 $ allprob   :'data.frame':	4415 obs. of  1 variable:
  ..$ WT4: num [1:4415] 2.86e-05 1.52e-04 4.06e-04 2.04e-04 4.64e-04 ...
 $ call      : language svydesign(id = ~SDMVPSU, weights = ~WT4, strata = ~SDMVSTRA, nest = TRUE, survey.lonely.psu = "adjust", data = nhanes1)
 $ variables :'data.frame':	4415 obs. of  28 variables:
  ..$ SEQN          : num [1:4415] 83732 83733 83734 83736 83737 ...
  ..$ Fasting       : Factor w/ 2 levels "Fasted","Not Fasted": 2 1 1 1 1 1 2 2 2 2 ...
  ..$ Fasting_R     : num [1:4415] 3 12 10 10 12 9 3 3 3 1 ...
  ..$ HSCRP_R       : num [1:4415] 0.6 1.4 0.6 0.5 2.5 1.3 3 0.4 3.2 0.9 ...
  ..$ HSCRP         : num [1:4415] 0.817 1.513 0.817 0.73 2.469 ...
  ..$ Age           : Factor w/ 4 levels "Adult","Middle Age Adult",..: 2 2 3 1 3 4 4 2 1 4 ...
  ..$ Age_R         : num [1:4415] 62 53 78 42 72 22 32 56 46 30 ...
  ..$ SDMVPSU       : num [1:4415] 1 1 1 2 1 2 1 2 1 1 ...
  ..$ WT4           : num [1:4415] 34973 6595 2464 4907 2157 ...
  ..$ SDMVSTRA      : num [1:4415] 125 125 131 126 128 128 125 126 121 124 ...
  ..$ Gender        : Factor w/ 2 levels "Female","Male": 2 2 2 1 1 2 1 2 2 1 ...
  ..$ Ethnicity     : Factor w/ 6 levels "Asian","Black",..: 6 6 6 2 3 2 3 2 6 4 ...
  ..$ BMI           : num [1:4415] 27.8 30.8 28.8 20.3 28.6 28 28.2 33.6 27.6 26.6 ...
  ..$ WBC           : num [1:4415] 9.8 7.3 4.4 4.2 6.1 3.5 8.3 6.1 8.3 9.8 ...
  ..$ Kcal          : Factor w/ 3 levels "High Calorie Diet",..: 1 1 1 2 2 3 3 2 3 1 ...
  ..$ Kcal_R        : num [1:4415] 2262 3468 2205 853 984 ...
  ..$ Protein       : num [1:4415] 104.8 114.1 105.1 25.3 52.9 ...
  ..$ Carbohydrate  : Factor w/ 3 levels "High Intake",..: 1 1 1 2 2 1 1 2 2 1 ...
  ..$ Carbohydrate_R: num [1:4415] 237 290 249 111 127 ...
  ..$ Sugar         : num [1:4415] 80.4 107.7 78.7 72.7 23.1 ...
  ..$ Zinc          : Factor w/ 2 levels "Adequate Intake",..: 1 2 1 2 2 1 1 2 2 1 ...
  ..$ Zinc_R        : num [1:4415] 11.91 7.06 15.37 2.29 5.67 ...
  ..$ Choline       : num [1:4415] 415.5 889.2 514.8 82.2 192.8 ...
  ..$ Folate        : num [1:4415] 536 586 428 128 362 ...
  ..$ Copper        : num [1:4415] 1.185 0.89 2.005 0.255 0.8 ...
  ..$ S.Fat         : num [1:4415] 31.92 29.35 31.48 13.26 8.23 ...
  ..$ M.Fat         : num [1:4415] 37.2 40.1 29.4 13.2 11.3 ...
  ..$ P.Fat         : num [1:4415] 22.67 33.12 21.51 4.92 8.38 ...
 $ fpc       :List of 2
  ..$ popsize : NULL
  ..$ sampsize: int [1:4415, 1] 2 2 2 2 2 2 2 2 2 2 ...
  ..- attr(*, "class")= chr "survey_fpc"
 $ pps       : logi FALSE
 - attr(*, "class")= chr [1:2] "survey.design2" "survey.design"
> #########################################################################################################################################################################
> ######################################################################################################################################
> ### Descriptive Stats
> set_gtsummary_theme(theme_gtsummary_compact(set_theme = TRUE))
Setting theme `Compact`
Setting theme `Compact`

> table_three <- svydesign(id=~SDMVPSU, weights=~WT4, strata=~SDMVSTRA, nest=TRUE, survey.lonely.psu = "adjust", data= nhanes1)%>% 
+   
+ tbl_svysummary(by= "Age", # stratification variable.
+                include = c(Age, Zinc,HSCRP, Fasting, Kcal, Carbohydrate,Folate,Choline, WBC, BMI, Ethnicity, Gender), 
+                percent = "column",  #Column or Row percentage, depending on your needs
+                statistic = list(all_continuous() ~ "{mean} ({sd})", # What statistics do you want on your table. 
+                                 #In this case, for all continuous variables it will generate means and standard deviation.
+                                 #For all categorical variables, it will generate weighted percentage, if weight variable is included above.
+                                 all_categorical() ~ "{p}"),
+                digits = list(all_continuous() ~ c(1,1), 
+                              all_categorical() ~ 1),
+                label = list(HSCRP ~ "HSCRP (mg/L)",
+                             Zinc ~ "Zinc (mg)",
+                             Kcal ~ "Kcal (energy)",
+                             Carbohydrate ~"Carbohydrate (g)",
+                             Folate ~ "Folate (mcg)",
+                             Choline ~ "Choline (mg)",
+                             WBC ~" WBC (1000 cells/uL)",
+                             BMI ~ "BMI (kg/m2 in adults)",
+                             Fasting ~ "Fasting (in hrs)",
+                             Ethnicity ~ "Race and Ethnicity",
+                             Gender~ "Gender"))%>%
+                         add_p(
+                         test = list(
+                     all_continuous() ~ "svy.wilcox.test",
+                   all_categorical() ~ "svy.adj.wald.test")) %>%
+   modify_header(update = list(label ~ "",
+                               stat_1 ~ "**Young Adult (19-35)**",
+                               stat_2 ~ "**Adult (36-50)**",
+                               stat_3 ~ "**Middle-Aged Adult (51-65)**",
+                               stat_4 ~ "**Older Adult (66-80)**"))%>%
+   modify_spanning_header(starts_with("stat_") ~ "**Weighted by Age(%)**") %>%
+   modify_caption("**Table 1: Survey Adjusted Demographics and Other Characteristics of the Participants**")%>%
+   modify_footnote(
+     all_stat_cols() ~ " Mean (SD) or Frequency by % reported. N= 4415;Intake data based on per day; Zn: Inadequate Intake = < 8.0 mg ,
+     Adequate Intake >= 8.0 + mg; Kcal: <= 1500.0 kcal= Low Calorie Diet, 1500.1-2100.0 Kcal =  Moderate Calorie Diet, High Calorie Diet> 2100.0 Kcal; Carbohydrate: <= 150.0 g = Low Intake,150.1 - 200.0 g = Moderate Intake,
+     High Intake > 200.0 g +;
+     Fasting: Fasted 9-37 Hours Fasted, Not Fasted; 0-8 Hours;
+     Only 19 year olds used BMI-for age.")
> table_three
>
> ##############################################################################################################################################################################
> ### Young Adults
> ###############################################################################################################################################################################
> ### Fasting 19-35
> d1 <- subset(nhc2,Age_R <36)
> d2 <- na.omit(d1)
> 
> set_gtsummary_theme(theme_gtsummary_compact(set_theme = TRUE))
Setting theme `Compact`
Setting theme `Compact`
> 
> 
> model1am <- svyglm(HSCRP ~ relevel(Zinc, ref = "Inadequate Intake")* relevel(Fasting, ref="Not Fasted")+
+                      WBC + Choline +Folate +BMI+ Gender+ Ethnicity, design = d2, family = gaussian(link='log'))
> 
> 
> 
> ###Summs
> summary(model1am,df= degf(d2))

Call:
svyglm(formula = HSCRP ~ relevel(Zinc, ref = "Inadequate Intake") * 
    relevel(Fasting, ref = "Not Fasted") + WBC + Choline + Folate + 
    BMI + Gender + Ethnicity, design = d2, family = gaussian(link = "log"))

Survey design:
subset(nhc2, Age_R < 36)

Coefficients:
                                                                                                     Estimate Std. Error
(Intercept)                                                                                         1.4909492  0.4218472
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake                                            -0.4684893  0.3130507
relevel(Fasting, ref = "Not Fasted")Fasted                                                          0.5565885  0.2512251
WBC                                                                                                 0.0054971  0.0011266
Choline                                                                                             0.0018572  0.0007181
Folate                                                                                             -0.0005192  0.0003962
BMI                                                                                                -0.0150241  0.0252829
GenderMale                                                                                          0.1399389  0.1718849
EthnicityBlack                                                                                     -0.2075620  0.4433191
EthnicityMexican American                                                                          -0.2459690  0.4540984
EthnicityOther Hispanic                                                                            -0.3432880  0.3695933
EthnicityOther Race                                                                                -0.5342288  0.3830094
EthnicityWhite                                                                                     -0.6542260  0.3416690
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:relevel(Fasting, ref = "Not Fasted")Fasted -0.5583261  0.2579416
                                                                                                   t value Pr(>|t|)    
(Intercept)                                                                                          3.534  0.00135 ** 
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake                                             -1.497  0.14496    
relevel(Fasting, ref = "Not Fasted")Fasted                                                           2.215  0.03446 *  
WBC                                                                                                  4.879 3.28e-05 ***
Choline                                                                                              2.586  0.01480 *  
Folate                                                                                              -1.310  0.20001    
BMI                                                                                                 -0.594  0.55681    
GenderMale                                                                                           0.814  0.42198    
EthnicityBlack                                                                                      -0.468  0.64303    
EthnicityMexican American                                                                           -0.542  0.59205    
EthnicityOther Hispanic                                                                             -0.929  0.36039    
EthnicityOther Race                                                                                 -1.395  0.17331    
EthnicityWhite                                                                                      -1.915  0.06510 .  
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:relevel(Fasting, ref = "Not Fasted")Fasted  -2.165  0.03851 *  
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

(Dispersion parameter for gaussian family taken to be 39.82489)

Number of Fisher Scoring iterations: 16

> confint(model1am,df=degf(d2))
                                                                                                           2.5 %
(Intercept)                                                                                         0.6009293763
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake                                            -1.1289685280
relevel(Fasting, ref = "Not Fasted")Fasted                                                          0.0265499674
WBC                                                                                                 0.0031201739
Choline                                                                                             0.0003421254
Folate                                                                                             -0.0013551679
BMI                                                                                                -0.0683664162
GenderMale                                                                                         -0.2227066655
EthnicityBlack                                                                                     -1.1428835677
EthnicityMexican American                                                                          -1.2040329091
EthnicityOther Hispanic                                                                            -1.1230615991
EthnicityOther Race                                                                                -1.3423079862
EthnicityWhite                                                                                     -1.3750846576
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:relevel(Fasting, ref = "Not Fasted")Fasted -1.1025352034
                                                                                                          97.5 %
(Intercept)                                                                                         2.3809689939
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake                                             0.1919899143
relevel(Fasting, ref = "Not Fasted")Fasted                                                          1.0866271094
WBC                                                                                                 0.0078740957
Choline                                                                                             0.0033723536
Folate                                                                                              0.0003167611
BMI                                                                                                 0.0383182943
GenderMale                                                                                          0.5025844004
EthnicityBlack                                                                                      0.7277595394
EthnicityMexican American                                                                           0.7120950024
EthnicityOther Hispanic                                                                             0.4364855964
EthnicityOther Race                                                                                 0.2738503797
EthnicityWhite                                                                                      0.0666326545
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:relevel(Fasting, ref = "Not Fasted")Fasted -0.0141169661
> summ(model1am, exp = TRUE,confint=TRUE, n.sd=2, digits= 6)
MODEL INFO:
Observations: 1211
Dependent Variable: HSCRP
Type: Analysis of complex survey design 
 Family: gaussian 
 Link function: log 

MODEL FIT:
Pseudo-R² (Cragg-Uhler) = 0.889156
Pseudo-R² (McFadden) = 0.052360
AIC = 8580.470316 

-----------------------------------------------------------------------------------------
                                  exp(Est.)       2.5%       97.5%      t val.          p
------------------------------- ----------- ---------- ----------- ----------- ----------
(Intercept)                        4.441309   1.942826   10.152851    3.534335   0.002547
relevel(Zinc, ref =                0.625947   0.338898    1.156131   -1.496529   0.152851
"Inadequate Intake")Adequate                                                             
Intake                                                                                   
relevel(Fasting, ref = "Not        1.744710   1.066302    2.854740    2.215498   0.040664
Fasted")Fasted                                                                           
WBC                                1.005512   1.003294    1.007735    4.879315   0.000141
Choline                            1.001859   1.000450    1.003270    2.586230   0.019219
Folate                             0.999481   0.998705    1.000257   -1.310371   0.207500
BMI                                0.985088   0.937463    1.035133   -0.594237   0.560179
GenderMale                         1.150203   0.821232    1.610955    0.814143   0.426821
EthnicityBlack                     0.812563   0.340803    1.937362   -0.468200   0.645588
EthnicityMexican American          0.781947   0.321106    1.904173   -0.541664   0.595078
EthnicityOther Hispanic            0.709434   0.343806    1.463896   -0.928826   0.365981
EthnicityOther Race                0.586121   0.276675    1.241668   -1.394819   0.181030
EthnicityWhite                     0.519844   0.266099    1.015553   -1.914795   0.072501
relevel(Zinc, ref =                0.572166   0.345113    0.948598   -2.164545   0.044945
"Inadequate Intake")Adequate                                                             
Intake:relevel(Fasting, ref =                                                            
"Not Fasted")Fasted                                                                      
-----------------------------------------------------------------------------------------

Estimated dispersion parameter = 39.82489 
> a1amz <-  tbl_regression(model1am,intercept= FALSE,add_estimate_to_reference_rows = TRUE
+                         , exponentiate = TRUE)%>%  bold_p(t= 0.05) %>%
+   modify_caption("**Table 2: Analysis of the Coefficients for Participants 19- 35 Years Old**")
> a1amz

> ###Wald Test
> 
> regTermTest(model1am, test.terms= ~relevel(Zinc, ref = "Inadequate Intake")* relevel(Fasting, ref="Not Fasted") + Ethnicity+
+               WBC + Choline +Folate +BMI+ Gender, method="Wald", df=degf(d2))
Wald test for relevel(Zinc, ref = "Inadequate Intake") relevel(Fasting, ref = "Not Fasted") Ethnicity WBC Choline Folate BMI Gender relevel(Zinc, ref = "Inadequate Intake"):relevel(Fasting, ref = "Not Fasted")
 in svyglm(formula = HSCRP ~ relevel(Zinc, ref = "Inadequate Intake") * 
    relevel(Fasting, ref = "Not Fasted") + WBC + Choline + 
    Folate + BMI + Gender + Ethnicity, design = d2, family = gaussian(link = "log"))
F =  53.94428  on  13  and  30  df: p= < 2.22e-16 
> 
> 
> ###Investigate terms (LRT) not significant
> regTermTest(model1am,~ relevel(Zinc, ref = "Inadequate Intake"): relevel(Fasting, ref="Not Fasted"), method = "LRT")
Working (Rao-Scott+F) LRT for relevel(Zinc, ref = "Inadequate Intake"):relevel(Fasting, ref = "Not Fasted")
 in svyglm(formula = HSCRP ~ relevel(Zinc, ref = "Inadequate Intake") * 
    relevel(Fasting, ref = "Not Fasted") + WBC + Choline + 
    Folate + BMI + Gender + Ethnicity, design = d2, family = gaussian(link = "log"))
Working 2logLR =  4.615262 p= 0.048264 
df=1;  denominator df= 17
> regTermTest(model1am, ~relevel(Zinc, ref = "Inadequate Intake")* relevel(Fasting, ref="Not Fasted"), method = "LRT")
Working (Rao-Scott+F) LRT for relevel(Zinc, ref = "Inadequate Intake") relevel(Fasting, ref = "Not Fasted") relevel(Zinc, ref = "Inadequate Intake"):relevel(Fasting, ref = "Not Fasted")
 in svyglm(formula = HSCRP ~ relevel(Zinc, ref = "Inadequate Intake") * 
    relevel(Fasting, ref = "Not Fasted") + WBC + Choline + 
    Folate + BMI + Gender + Ethnicity, design = d2, family = gaussian(link = "log"))
Working 2logLR =  9.118494 p= 0.074223 
(scale factors:  2.1 0.61 0.29 );  denominator df= 17 

> ###Checking for Overfitting
> # the caret library is loaded
> set.seed(123)
> 
> subset13am <- subset(nhanes1, Age_R < 36 )
> subset13ams4 <- na.omit(subset13am)
> 
> 
> # Fit Generalized linear regression model using caret
> modely <- train(HSCRP ~ relevel(Zinc, ref = "Inadequate Intake")* relevel(Fasting, ref="Not Fasted") +  Ethnicity+
+                  WBC + Choline +Folate +BMI,
+                subset13ams4,
+                method = "glm",
+                trControl = trainControl(
+                  method = "cv",
+                  number = 10,
+                  verboseIter = T
+                ))
+ Fold01: parameter=none 
- Fold01: parameter=none 
+ Fold02: parameter=none 
- Fold02: parameter=none 
+ Fold03: parameter=none 
- Fold03: parameter=none 
+ Fold04: parameter=none 
- Fold04: parameter=none 
+ Fold05: parameter=none 
- Fold05: parameter=none 
+ Fold06: parameter=none 
- Fold06: parameter=none 
+ Fold07: parameter=none 
- Fold07: parameter=none 
+ Fold08: parameter=none 
- Fold08: parameter=none 
+ Fold09: parameter=none 
- Fold09: parameter=none 
+ Fold10: parameter=none 
- Fold10: parameter=none 
Aggregating results
Fitting final model on full training set
> modely
Generalized Linear Model 

1211 samples
   7 predictor

No pre-processing
Resampling: Cross-Validated (10 fold) 
Summary of sample sizes: 1090, 1089, 1090, 1090, 1090, 1090, ... 
Resampling results:

  RMSE      Rsquared    MAE    
  8.041641  0.01264534  3.45972

> 
> # Function for Root Mean Squared Error
> RMSE <- function(error) { sqrt(mean(error^2)) }
> RMSE(model1am$residuals) 
[1] 2.575223
> ## Remove Ethnicity
> 
> 
> model1am <- svyglm(HSCRP ~ relevel(Zinc, ref = "Inadequate Intake")* relevel(Fasting, ref="Not Fasted") +
+                      BMI + WBC + Choline +Folate+Gender, design = d2, family = gaussian(link='log'))
> 
> 
> ###Summs
> summary(model1am,df= degf(d2))

Call:
svyglm(formula = HSCRP ~ relevel(Zinc, ref = "Inadequate Intake") * 
    relevel(Fasting, ref = "Not Fasted") + BMI + WBC + Choline + 
    Folate + Gender, design = d2, family = gaussian(link = "log"))

Survey design:
subset(nhc2, Age_R < 36)

Coefficients:
                                                                                                     Estimate Std. Error
(Intercept)                                                                                         1.3808948  0.3803844
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake                                            -0.3329300  0.2918275
relevel(Fasting, ref = "Not Fasted")Fasted                                                          0.5659947  0.2167716
BMI                                                                                                -0.0237480  0.0140981
WBC                                                                                                 0.0054761  0.0006948
Choline                                                                                             0.0019468  0.0007385
Folate                                                                                             -0.0006024  0.0003859
GenderMale                                                                                          0.1117447  0.1711926
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:relevel(Fasting, ref = "Not Fasted")Fasted -0.5734269  0.2591164
                                                                                                   t value Pr(>|t|)    
(Intercept)                                                                                          3.630  0.00104 ** 
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake                                             -1.141  0.26296    
relevel(Fasting, ref = "Not Fasted")Fasted                                                           2.611  0.01396 *  
BMI                                                                                                 -1.684  0.10247    
WBC                                                                                                  7.882 8.52e-09 ***
Choline                                                                                              2.636  0.01314 *  
Folate                                                                                              -1.561  0.12900    
GenderMale                                                                                           0.653  0.51889    
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:relevel(Fasting, ref = "Not Fasted")Fasted  -2.213  0.03465 *  
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

(Dispersion parameter for gaussian family taken to be 40.29924)

Number of Fisher Scoring iterations: 13

> confint(model1am,df=degf(d2))
                                                                                                          2.5 %
(Intercept)                                                                                         0.592025840
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake                                            -0.938143266
relevel(Fasting, ref = "Not Fasted")Fasted                                                          0.116438024
BMI                                                                                                -0.052985575
WBC                                                                                                 0.004035184
Choline                                                                                             0.000415353
Folate                                                                                             -0.001402652
GenderMale                                                                                         -0.243287015
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:relevel(Fasting, ref = "Not Fasted")Fasted -1.110801490
                                                                                                          97.5 %
(Intercept)                                                                                         2.1697637863
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake                                             0.2722833254
relevel(Fasting, ref = "Not Fasted")Fasted                                                          1.0155513924
BMI                                                                                                 0.0054896012
WBC                                                                                                 0.0069170171
Choline                                                                                             0.0034782976
Folate                                                                                              0.0001978863
GenderMale                                                                                          0.4667764645
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:relevel(Fasting, ref = "Not Fasted")Fasted -0.0360522478
> summ(model1am, exp = TRUE,confint=TRUE, n.sd=2, digits= 6)
MODEL INFO:
Observations: 1211
Dependent Variable: HSCRP
Type: Analysis of complex survey design 
 Family: gaussian 
 Link function: log 

MODEL FIT:
Pseudo-R² (Cragg-Uhler) = 0.823980
Pseudo-R² (McFadden) = 0.041351
AIC = 8584.457470 

----------------------------------------------------------------------------------------
                                  exp(Est.)       2.5%      97.5%      t val.          p
------------------------------- ----------- ---------- ---------- ----------- ----------
(Intercept)                        3.978460   1.887692   8.384917    3.630261   0.001479
relevel(Zinc, ref =                0.716820   0.404582   1.270031   -1.140845   0.266202
"Inadequate Intake")Adequate                                                            
Intake                                                                                  
relevel(Fasting, ref = "Not        1.761199   1.151575   2.693548    2.611019   0.015951
Fasted")Fasted                                                                          
BMI                                0.976532   0.949918   1.003891   -1.684486   0.106224
WBC                                1.005491   1.004123   1.006861    7.881605   0.000000
Choline                            1.001949   1.000500   1.003400    2.636331   0.015079
Folate                             0.999398   0.998642   1.000154   -1.561057   0.132781
GenderMale                         1.118227   0.799486   1.564046    0.652743   0.520685
relevel(Zinc, ref =                0.563591   0.339159   0.936535   -2.213008   0.037577
"Inadequate Intake")Adequate                                                            
Intake:relevel(Fasting, ref =                                                           
"Not Fasted")Fasted                                                                     
----------------------------------------------------------------------------------------

Estimated dispersion parameter = 40.29924 
> a1am <-  tbl_regression(model1am,intercept= FALSE,add_estimate_to_reference_rows = TRUE
+                         , exponentiate = TRUE)%>%  bold_p(t= 0.05) %>%
+   modify_caption("**Table 2: Analysis of the Coefficients for Participants 19- 35 Years Old**")
> a1am
>
> ### Make table nice looking
> a1am <-  tbl_regression(model1am,intercept= FALSE,add_estimate_to_reference_rows = TRUE
+                         , exponentiate = TRUE)%>%  
+   modify_caption("**Table 2: Analysis of the Coefficients for Participants 19- 35 Years Old**") %>%
+   modify_header(label = "**Variable**")
>   a1am
>   
>   remove_row_type(a1am,
+                   variables = everything(),
+                   type = c("header") )
>
> 
> ###Investigate terms LRT is signficant
> regTermTest(model1am,~ relevel(Zinc, ref = "Inadequate Intake"): relevel(Fasting, ref="Not Fasted"), method = "LRT")
Working (Rao-Scott+F) LRT for relevel(Zinc, ref = "Inadequate Intake"):relevel(Fasting, ref = "Not Fasted")
 in svyglm(formula = HSCRP ~ relevel(Zinc, ref = "Inadequate Intake") * 
    relevel(Fasting, ref = "Not Fasted") + BMI + WBC + 
    Choline + Folate + Gender, design = d2, family = gaussian(link = "log"))
Working 2logLR =  5.027683 p= 0.036861 
df=1;  denominator df= 22
> regTermTest(model1am,~ relevel(Zinc, ref = "Inadequate Intake")* relevel(Fasting, ref="Not Fasted"), method = "LRT")
Working (Rao-Scott+F) LRT for relevel(Zinc, ref = "Inadequate Intake") relevel(Fasting, ref = "Not Fasted") relevel(Zinc, ref = "Inadequate Intake"):relevel(Fasting, ref = "Not Fasted")
 in svyglm(formula = HSCRP ~ relevel(Zinc, ref = "Inadequate Intake") * 
    relevel(Fasting, ref = "Not Fasted") + BMI + WBC + 
    Choline + Folate + Gender, design = d2, family = gaussian(link = "log"))
Working 2logLR =  11.04525 p= 0.041547 
(scale factors:  2 0.59 0.41 );  denominator df= 22
> regTermTest(model1am,~ Choline, method = "LRT")
Working (Rao-Scott+F) LRT for Choline
 in svyglm(formula = HSCRP ~ relevel(Zinc, ref = "Inadequate Intake") * 
    relevel(Fasting, ref = "Not Fasted") + BMI + WBC + 
    Choline + Folate + Gender, design = d2, family = gaussian(link = "log"))
Working 2logLR =  4.101901 p= 0.057162 
df=1;  denominator df= 22
> regTermTest(model1am,~ BMI, method = "LRT")
Working (Rao-Scott+F) LRT for BMI
 in svyglm(formula = HSCRP ~ relevel(Zinc, ref = "Inadequate Intake") * 
    relevel(Fasting, ref = "Not Fasted") + BMI + WBC + 
    Choline + Folate + Gender, design = d2, family = gaussian(link = "log"))
Working 2logLR =  3.03031 p= 0.098416 
df=1;  denominator df= 22
> regTermTest(model1am,~ Gender, method = "LRT")
Working (Rao-Scott+F) LRT for Gender
 in svyglm(formula = HSCRP ~ relevel(Zinc, ref = "Inadequate Intake") * 
    relevel(Fasting, ref = "Not Fasted") + BMI + WBC + 
    Choline + Folate + Gender, design = d2, family = gaussian(link = "log"))
Working 2logLR =  0.3987406 p= 0.5318 
df=1;  denominator df= 22
> regTermTest(model1am,~ WBC, method = "LRT")
Working (Rao-Scott+F) LRT for WBC
 in svyglm(formula = HSCRP ~ relevel(Zinc, ref = "Inadequate Intake") * 
    relevel(Fasting, ref = "Not Fasted") + BMI + WBC + 
    Choline + Folate + Gender, design = d2, family = gaussian(link = "log"))
Working 2logLR =  21.02401 p= 0.00015686 
df=1;  denominator df= 22
> regTermTest(model1am,~ Folate, method = "LRT")
Working (Rao-Scott+F) LRT for Folate
 in svyglm(formula = HSCRP ~ relevel(Zinc, ref = "Inadequate Intake") * 
    relevel(Fasting, ref = "Not Fasted") + BMI + WBC + 
    Choline + Folate + Gender, design = d2, family = gaussian(link = "log"))
Working 2logLR =  2.421287 p= 0.13702 
df=1;  denominator df= 22
> ### To test Fasting
> modeladq1z <- svyglm(HSCRP ~ relevel(Fasting, ref="Not Fasted"), design = d2, family = gaussian(link = "log"))
> anova(model1am,modeladq1z,force=TRUE)
Working (Rao-Scott+F) LRT for relevel(Zinc, ref = "Inadequate Intake") BMI WBC Choline Folate Gender relevel(Zinc, ref = "Inadequate Intake"):relevel(Fasting, ref = "Not Fasted") -
 in svyglm(formula = HSCRP ~ relevel(Zinc, ref = "Inadequate Intake") * 
    relevel(Fasting, ref = "Not Fasted") + BMI + WBC + 
    Choline + Folate + Gender, design = d2, family = gaussian(link = "log"))
Working 2logLR =  20.93854 p= 0.04786 
(scale factors:  3 2.2 0.74 0.5 0.3 0.21 0.021 );  denominator df= 22

> ###Checking for Overfitting
> # the caret library is loaded
> set.seed(123)
> 
> subset13am <- subset(nhanes1, Age_R < 36 )
> subset13ams4 <- na.omit(subset13am)
> 
> 
> # Fit Generalized linear regression model using caret
> modelx <- train(HSCRP ~ relevel(Zinc, ref = "Inadequate Intake")* relevel(Fasting, ref="Not Fasted") + Gender+
+                  WBC + Choline +Folate +BMI,
+                subset13ams4,
+                method = "glm",
+                trControl = trainControl(
+                  method = "cv",
+                  number = 10,
+                  verboseIter = T
+                ))
+ Fold01: parameter=none 
- Fold01: parameter=none 
+ Fold02: parameter=none 
- Fold02: parameter=none 
+ Fold03: parameter=none 
- Fold03: parameter=none 
+ Fold04: parameter=none 
- Fold04: parameter=none 
+ Fold05: parameter=none 
- Fold05: parameter=none 
+ Fold06: parameter=none 
- Fold06: parameter=none 
+ Fold07: parameter=none 
- Fold07: parameter=none 
+ Fold08: parameter=none 
- Fold08: parameter=none 
+ Fold09: parameter=none 
- Fold09: parameter=none 
+ Fold10: parameter=none 
- Fold10: parameter=none 
Aggregating results
Fitting final model on full training set
> modelx
Generalized Linear Model 

1211 samples
   7 predictor

No pre-processing
Resampling: Cross-Validated (10 fold) 
Summary of sample sizes: 1090, 1089, 1090, 1090, 1090, 1090, ... 
Resampling results:

  RMSE      Rsquared     MAE     
  8.069963  0.008414136  3.453628

> 
> # Function for Root Mean Squared Error
> RMSE <- function(error) { sqrt(mean(error^2)) }
> RMSE(model1am$residuals) 
[1] 2.591557


 
> ###Plot Model for relevance 
> 
> model1am7 <- svyglm(HSCRP ~ Zinc* Fasting +BMI +
+                      WBC + Choline +Folate+Gender,design = d2, family = gaussian(link='log'))
> 
> cat_plot(model1am7, pred =Fasting, modx = Zinc, main.title = "Figure 1:Two-Way Interaction Effect Between Fasting & Dietary Zinc (Young Adult)",
+          x.label =  "Fasting", interval = TRUE)
> 
> ############################################################################################################################################
> ##################################################################################################################################
> #### Kcal
> 
> ###Not signficant w/ or w/out ethnicity
> model1aa <- svyglm(HSCRP ~ relevel(Zinc, ref = "Inadequate Intake")*  relevel(Kcal, ref = "Moderate Calorie Diet")+
+                      WBC + Choline +Folate +Ethnicity+BMI+Gender, design = d2, family = gaussian(link='log'))
> 
> summary(model1aa,df= degf(d61))

Call:
svyglm(formula = HSCRP ~ relevel(Zinc, ref = "Inadequate Intake") * 
    relevel(Kcal, ref = "Moderate Calorie Diet") + WBC + Choline + 
    Folate + Ethnicity + BMI + Gender, design = d2, family = gaussian(link = "log"))

Survey design:
subset(nhc2, Age_R < 36)

Coefficients:
                                                                                                                        Estimate
(Intercept)                                                                                                            1.4339175
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake                                                               -0.6540772
relevel(Kcal, ref = "Moderate Calorie Diet")High Calorie Diet                                                          0.0004581
relevel(Kcal, ref = "Moderate Calorie Diet")Low Calorie Diet                                                           0.0464301
WBC                                                                                                                    0.0036702
Choline                                                                                                                0.0023682
Folate                                                                                                                -0.0002727
EthnicityBlack                                                                                                        -0.2941692
EthnicityMexican American                                                                                             -0.0586508
EthnicityOther Hispanic                                                                                               -0.7231646
EthnicityOther Race                                                                                                   -0.5111299
EthnicityWhite                                                                                                        -0.6875824
BMI                                                                                                                   -0.0142421
GenderMale                                                                                                             0.3426184
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:relevel(Kcal, ref = "Moderate Calorie Diet")High Calorie Diet -0.6083612
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:relevel(Kcal, ref = "Moderate Calorie Diet")Low Calorie Diet   0.5608360
                                                                                                                      Std. Error
(Intercept)                                                                                                            0.5367763
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake                                                                0.3871875
relevel(Kcal, ref = "Moderate Calorie Diet")High Calorie Diet                                                          0.2616508
relevel(Kcal, ref = "Moderate Calorie Diet")Low Calorie Diet                                                           0.4490464
WBC                                                                                                                    0.0016132
Choline                                                                                                                0.0006489
Folate                                                                                                                 0.0004104
EthnicityBlack                                                                                                         0.4026831
EthnicityMexican American                                                                                              0.3680522
EthnicityOther Hispanic                                                                                                0.3763824
EthnicityOther Race                                                                                                    0.3033901
EthnicityWhite                                                                                                         0.3470776
BMI                                                                                                                    0.0202823
GenderMale                                                                                                             0.1845281
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:relevel(Kcal, ref = "Moderate Calorie Diet")High Calorie Diet  0.3319834
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:relevel(Kcal, ref = "Moderate Calorie Diet")Low Calorie Diet   0.5697650
                                                                                                                      t value
(Intercept)                                                                                                             2.671
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake                                                                -1.689
relevel(Kcal, ref = "Moderate Calorie Diet")High Calorie Diet                                                           0.002
relevel(Kcal, ref = "Moderate Calorie Diet")Low Calorie Diet                                                            0.103
WBC                                                                                                                     2.275
Choline                                                                                                                 3.650
Folate                                                                                                                 -0.664
EthnicityBlack                                                                                                         -0.731
EthnicityMexican American                                                                                              -0.159
EthnicityOther Hispanic                                                                                                -1.921
EthnicityOther Race                                                                                                    -1.685
EthnicityWhite                                                                                                         -1.981
BMI                                                                                                                    -0.702
GenderMale                                                                                                              1.857
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:relevel(Kcal, ref = "Moderate Calorie Diet")High Calorie Diet  -1.833
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:relevel(Kcal, ref = "Moderate Calorie Diet")Low Calorie Diet    0.984
                                                                                                                      Pr(>|t|)
(Intercept)                                                                                                            0.01209
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake                                                                0.10153
relevel(Kcal, ref = "Moderate Calorie Diet")High Calorie Diet                                                          0.99861
relevel(Kcal, ref = "Moderate Calorie Diet")Low Calorie Diet                                                           0.91834
WBC                                                                                                                    0.03021
Choline                                                                                                                0.00099
Folate                                                                                                                 0.51154
EthnicityBlack                                                                                                         0.47074
EthnicityMexican American                                                                                              0.87446
EthnicityOther Hispanic                                                                                                0.06423
EthnicityOther Race                                                                                                    0.10242
EthnicityWhite                                                                                                         0.05682
BMI                                                                                                                    0.48797
GenderMale                                                                                                             0.07319
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:relevel(Kcal, ref = "Moderate Calorie Diet")High Calorie Diet  0.07682
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:relevel(Kcal, ref = "Moderate Calorie Diet")Low Calorie Diet   0.33283
                                                                                                                         
(Intercept)                                                                                                           *  
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake                                                                  
relevel(Kcal, ref = "Moderate Calorie Diet")High Calorie Diet                                                            
relevel(Kcal, ref = "Moderate Calorie Diet")Low Calorie Diet                                                             
WBC                                                                                                                   *  
Choline                                                                                                               ***
Folate                                                                                                                   
EthnicityBlack                                                                                                           
EthnicityMexican American                                                                                                
EthnicityOther Hispanic                                                                                               .  
EthnicityOther Race                                                                                                      
EthnicityWhite                                                                                                        .  
BMI                                                                                                                      
GenderMale                                                                                                            .  
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:relevel(Kcal, ref = "Moderate Calorie Diet")High Calorie Diet .  
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:relevel(Kcal, ref = "Moderate Calorie Diet")Low Calorie Diet     
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

(Dispersion parameter for gaussian family taken to be 39.55671)

Number of Fisher Scoring iterations: 14

> confint(model1aa,df=degf(d61))
                                                                                                                              2.5 %
(Intercept)                                                                                                            0.2898059142
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake                                                               -1.4793477770
relevel(Kcal, ref = "Moderate Calorie Diet")High Calorie Diet                                                         -0.5572373183
relevel(Kcal, ref = "Moderate Calorie Diet")Low Calorie Diet                                                          -0.9106896604
WBC                                                                                                                    0.0002317297
Choline                                                                                                                0.0009852147
Folate                                                                                                                -0.0011474916
EthnicityBlack                                                                                                        -1.1524678473
EthnicityMexican American                                                                                             -0.8431355171
EthnicityOther Hispanic                                                                                               -1.5254047549
EthnicityOther Race                                                                                                   -1.1577905037
EthnicityWhite                                                                                                        -1.4273608163
BMI                                                                                                                   -0.0574728872
GenderMale                                                                                                            -0.0506938457
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:relevel(Kcal, ref = "Moderate Calorie Diet")High Calorie Diet -1.3159670048
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:relevel(Kcal, ref = "Moderate Calorie Diet")Low Calorie Diet  -0.6535893189
                                                                                                                            97.5 %
(Intercept)                                                                                                           2.5780290665
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake                                                               0.1711934164
relevel(Kcal, ref = "Moderate Calorie Diet")High Calorie Diet                                                         0.5581535524
relevel(Kcal, ref = "Moderate Calorie Diet")Low Calorie Diet                                                          1.0035498333
WBC                                                                                                                   0.0071087107
Choline                                                                                                               0.0037512098
Folate                                                                                                                0.0006021495
EthnicityBlack                                                                                                        0.5641293961
EthnicityMexican American                                                                                             0.7258339701
EthnicityOther Hispanic                                                                                               0.0790755013
EthnicityOther Race                                                                                                   0.1355307786
EthnicityWhite                                                                                                        0.0521959402
BMI                                                                                                                   0.0289885933
GenderMale                                                                                                            0.7359306466
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:relevel(Kcal, ref = "Moderate Calorie Diet")High Calorie Diet 0.0992445424
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:relevel(Kcal, ref = "Moderate Calorie Diet")Low Calorie Diet  1.7752612405
> summ(model1aa, exp = TRUE,confint=TRUE, n.sd=2, digits= 6)
MODEL INFO:
Observations: 1211
Dependent Variable: HSCRP
Type: Analysis of complex survey design 
 Family: gaussian 
 Link function: log 

MODEL FIT:
Pseudo-R² (Cragg-Uhler) = 0.913522
Pseudo-R² (McFadden) = 0.058268
AIC = 8576.895823 

-----------------------------------------------------------------------------------------
                                  exp(Est.)       2.5%       97.5%      t val.          p
------------------------------- ----------- ---------- ----------- ----------- ----------
(Intercept)                        4.195101   1.465000   12.012883    2.671350   0.017431
relevel(Zinc, ref =                0.519922   0.243424    1.110484   -1.689304   0.111833
"Inadequate Intake")Adequate                                                             
Intake                                                                                   
relevel(Kcal, ref =                1.000458   0.599075    1.670769    0.001751   0.998626
"Moderate Calorie Diet")High                                                             
Calorie Diet                                                                             
relevel(Kcal, ref =                1.047525   0.434446    2.525767    0.103397   0.919018
"Moderate Calorie Diet")Low                                                              
Calorie Diet                                                                             
WBC                                1.003677   1.000509    1.006855    2.275094   0.038008
Choline                            1.002371   1.001097    1.003647    3.649844   0.002371
Folate                             0.999727   0.998923    1.000532   -0.664347   0.516551
EthnicityBlack                     0.745150   0.338438    1.640621   -0.730523   0.476327
EthnicityMexican American          0.943036   0.458397    1.940059   -0.159354   0.875515
EthnicityOther Hispanic            0.485214   0.232036    1.014637   -1.921356   0.073897
EthnicityOther Race                0.599817   0.330958    1.087089   -1.684728   0.112728
EthnicityWhite                     0.502790   0.254656    0.992704   -1.981063   0.066224
BMI                                0.985859   0.947437    1.025839   -0.702195   0.493311
GenderMale                         1.408631   0.981130    2.022404    1.856728   0.083098
relevel(Zinc, ref =                0.544242   0.283927    1.043222   -1.832505   0.086802
"Inadequate Intake")Adequate                                                             
Intake:relevel(Kcal, ref =                                                               
"Moderate Calorie Diet")High                                                             
Calorie Diet                                                                             
relevel(Zinc, ref =                1.752137   0.573566    5.352452    0.984329   0.340566
"Inadequate Intake")Adequate                                                             
Intake:relevel(Kcal, ref =                                                               
"Moderate Calorie Diet")Low                                                              
Calorie Diet                                                                             
-----------------------------------------------------------------------------------------
> a1amd1pqr32 <-  tbl_regression(model1aa,intercept= FALSE,add_estimate_to_reference_rows = TRUE
+                             , exponentiate = TRUE)%>%  bold_p(t= 0.05) %>%
+   modify_caption("**Table 3: Analysis of the Coefficients of the Participants' Energy Intake 19-35** ")
> a1amd1pqr32

> ###Investigate terms (LRT)
> regTermTest(model1aa,~ relevel(Zinc, ref = "Inadequate Intake"): relevel(Kcal, ref = "Moderate Calorie Diet"), method = "LRT")
Working (Rao-Scott+F) LRT for relevel(Zinc, ref = "Inadequate Intake"):relevel(Kcal, ref = "Moderate Calorie Diet")
 in svyglm(formula = HSCRP ~ relevel(Zinc, ref = "Inadequate Intake") * 
    relevel(Kcal, ref = "Moderate Calorie Diet") + WBC + 
    Choline + Folate + Ethnicity + BMI + Gender, design = d2, 
    family = gaussian(link = "log"))
Working 2logLR =  3.449249 p= 0.2026 
(scale factors:  1.6 0.4 );  denominator df= 15
> regTermTest(model1aa,~ relevel(Zinc, ref = "Inadequate Intake")* relevel(Kcal, ref = "Moderate Calorie Diet"), method = "LRT")
Working (Rao-Scott+F) LRT for relevel(Zinc, ref = "Inadequate Intake") relevel(Kcal, ref = "Moderate Calorie Diet") relevel(Zinc, ref = "Inadequate Intake"):relevel(Kcal, ref = "Moderate Calorie Diet")
 in svyglm(formula = HSCRP ~ relevel(Zinc, ref = "Inadequate Intake") * 
    relevel(Kcal, ref = "Moderate Calorie Diet") + WBC + 
    Choline + Folate + Ethnicity + BMI + Gender, design = d2, 
    family = gaussian(link = "log"))
Working 2logLR =  9.033076 p= 0.17936 
(scale factors:  2.1 1.6 0.87 0.29 0.17 );  denominator df= 15
> 

> ###Checking for Overfitting
> # the caret library is loaded
> set.seed(123)
> 
> subset13am <- subset(nhanes1, Age_R < 36 )
> subset13ams4 <- na.omit(subset13am)
> 
> 
> # Fit Generalized linear regression model using caret
> modelk <- train(HSCRP ~ relevel(Zinc, ref = "Inadequate Intake")*Kcal+ Ethnicity+ Gender+
+                  WBC + Choline +Folate +BMI,
+                subset13ams4,
+                method = "glm",
+                trControl = trainControl(
+                  method = "cv",
+                  number = 10,
+                  verboseIter = T
+                ))
+ Fold01: parameter=none 
- Fold01: parameter=none 
+ Fold02: parameter=none 
- Fold02: parameter=none 
+ Fold03: parameter=none 
- Fold03: parameter=none 
+ Fold04: parameter=none 
- Fold04: parameter=none 
+ Fold05: parameter=none 
- Fold05: parameter=none 
+ Fold06: parameter=none 
- Fold06: parameter=none 
+ Fold07: parameter=none 
- Fold07: parameter=none 
+ Fold08: parameter=none 
- Fold08: parameter=none 
+ Fold09: parameter=none 
- Fold09: parameter=none 
+ Fold10: parameter=none 
- Fold10: parameter=none 
Aggregating results
Fitting final model on full training set
> modelk
Generalized Linear Model 

1211 samples
   8 predictor

No pre-processing
Resampling: Cross-Validated (10 fold) 
Summary of sample sizes: 1090, 1089, 1090, 1090, 1090, 1090, ... 
Resampling results:

  RMSE      Rsquared    MAE     
  7.910883  0.02572476  3.489933

> 
> # Function for Root Mean Squared Error
> RMSE <- function(error) { sqrt(mean(error^2)) }
> RMSE(model1aa$residuals) 
[1] 2.648834
> ## Remove Ethnicity
> model1aa <- svyglm(HSCRP ~ relevel(Zinc, ref = "Inadequate Intake")* relevel(Kcal, ref = "High Calorie Diet") +
+                      WBC + Choline +Folate +BMI+Gender, design = d2, family = gaussian(link='log'))
> 
> 
> summary(model1aa,df= degf(d61))

Call:
svyglm(formula = HSCRP ~ relevel(Zinc, ref = "Inadequate Intake") * 
    relevel(Kcal, ref = "High Calorie Diet") + WBC + Choline + 
    Folate + BMI + Gender, design = d2, family = gaussian(link = "log"))

Survey design:
subset(nhc2, Age_R < 36)

Coefficients:
                                                                                                                        Estimate Std. Error t value Pr(>|t|)   
(Intercept)                                                                                                            1.5739744  0.5906221   2.665  0.01228 * 
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake                                                               -0.9290583  0.3293488  -2.821  0.00841 **
relevel(Kcal, ref = "High Calorie Diet")Low Calorie Diet                                                              -0.0126587  0.4354057  -0.029  0.97700   
relevel(Kcal, ref = "High Calorie Diet")Moderate Calorie Diet                                                          0.0973039  0.3006236   0.324  0.74843   
WBC                                                                                                                    0.0038174  0.0011912   3.205  0.00320 **
Choline                                                                                                                0.0021568  0.0006277   3.436  0.00175 **
Folate                                                                                                                -0.0004362  0.0003982  -1.095  0.28206   
BMI                                                                                                                   -0.0266347  0.0133328  -1.998  0.05489 . 
GenderMale                                                                                                             0.2316003  0.1597064   1.450  0.15739   
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:relevel(Kcal, ref = "High Calorie Diet")Low Calorie Diet       0.8844206  0.6187132   1.429  0.16321   
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:relevel(Kcal, ref = "High Calorie Diet")Moderate Calorie Diet  0.2792160  0.3342824   0.835  0.41017   
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

(Dispersion parameter for gaussian family taken to be 40.32713)

Number of Fisher Scoring iterations: 13

> confint(model1aa,df=degf(d61))
                                                                                                                              2.5 %        97.5 %
(Intercept)                                                                                                            0.3419582578  2.8059904549
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake                                                               -1.6160677601 -0.2420488514
relevel(Kcal, ref = "High Calorie Diet")Low Calorie Diet                                                              -0.9208990606  0.8955817289
relevel(Kcal, ref = "High Calorie Diet")Moderate Calorie Diet                                                         -0.5297860071  0.7243937326
WBC                                                                                                                    0.0013326909  0.0063021752
Choline                                                                                                                0.0008474613  0.0034660844
Folate                                                                                                                -0.0012669111  0.0003944781
BMI                                                                                                                   -0.0544464221  0.0011769601
GenderMale                                                                                                            -0.1015414254  0.5647420083
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:relevel(Kcal, ref = "High Calorie Diet")Low Calorie Diet      -0.4061924958  2.1750337449
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:relevel(Kcal, ref = "High Calorie Diet")Moderate Calorie Diet -0.4180847884  0.9765168634
> summ(model1aa, exp = TRUE,confint=TRUE, n.sd=2, digits= 6)
MODEL INFO:
Observations: 1211
Dependent Variable: HSCRP
Type: Analysis of complex survey design 
 Family: gaussian 
 Link function: log 

MODEL FIT:
Pseudo-R² (Cragg-Uhler) = 0.818998
Pseudo-R² (McFadden) = 0.040687
AIC = 8589.296339 

------------------------------------------------------------------------------------------
                                   exp(Est.)       2.5%       97.5%      t val.          p
-------------------------------- ----------- ---------- ----------- ----------- ----------
(Intercept)                         4.825790   1.516456   15.357015    2.664943   0.014874
relevel(Zinc, ref =                 0.394925   0.207097    0.753108   -2.820895   0.010557
"Inadequate Intake")Adequate                                                              
Intake                                                                                    
relevel(Kcal, ref = "High           0.987421   0.420615    2.318037   -0.029073   0.977094
Calorie Diet")Low Calorie                                                                 
Diet                                                                                      
relevel(Kcal, ref = "High           1.102195   0.611459    1.986780    0.323673   0.749546
Calorie Diet")Moderate Calorie                                                            
Diet                                                                                      
WBC                                 1.003825   1.001484    1.006171    3.204769   0.004448
Choline                             1.002159   1.000927    1.003393    3.436118   0.002614
Folate                              0.999564   0.998784    1.000344   -1.095387   0.286363
BMI                                 0.973717   0.948601    0.999497   -1.997688   0.059535
GenderMale                          1.260616   0.921808    1.723952    1.450163   0.162516
relevel(Zinc, ref =                 2.421581   0.720194    8.142329    1.429452   0.168310
"Inadequate Intake")Adequate                                                              
Intake:relevel(Kcal, ref =                                                                
"High Calorie Diet")Low                                                                   
Calorie Diet                                                                              
relevel(Zinc, ref =                 1.322093   0.686626    2.545679    0.835270   0.413433
"Inadequate Intake")Adequate                                                              
Intake:relevel(Kcal, ref =                                                                
"High Calorie Diet")Moderate                                                              
Calorie Diet                                                                              
------------------------------------------------------------------------------------------

Estimated dispersion parameter = 40.32713 
> 
> a1amd1pqr <-  tbl_regression(model1aa,intercept= FALSE,add_estimate_to_reference_rows = TRUE
+                              , exponentiate = TRUE)%>%  bold_p(t= 0.05) %>%
+   modify_caption("**Table S.3: Analysis of the Coefficients of the Participants' Energy Intake 19-35** ")
> a1amd1pqr
> 
> ###Investigate terms
> regTermTest(model1aa,~ relevel(Zinc, ref = "Inadequate Intake"): relevel(Kcal, ref = "High Calorie Diet"), method = "LRT")
Working (Rao-Scott+F) LRT for relevel(Zinc, ref = "Inadequate Intake"):relevel(Kcal, ref = "High Calorie Diet")
 in svyglm(formula = HSCRP ~ relevel(Zinc, ref = "Inadequate Intake") * 
    relevel(Kcal, ref = "High Calorie Diet") + WBC + Choline + 
    Folate + BMI + Gender, design = d2, family = gaussian(link = "log"))
Working 2logLR =  2.084899 p= 0.33522 
(scale factors:  1.6 0.4 );  denominator df= 20
> regTermTest(model1aa,~ relevel(Zinc, ref = "Inadequate Intake")* relevel(Kcal, ref = "High Calorie Diet"), method = "LRT")
Working (Rao-Scott+F) LRT for relevel(Zinc, ref = "Inadequate Intake") relevel(Kcal, ref = "High Calorie Diet") relevel(Zinc, ref = "Inadequate Intake"):relevel(Kcal, ref = "High Calorie Diet")
 in svyglm(formula = HSCRP ~ relevel(Zinc, ref = "Inadequate Intake") * 
    relevel(Kcal, ref = "High Calorie Diet") + WBC + Choline + 
    Folate + BMI + Gender, design = d2, family = gaussian(link = "log"))
Working 2logLR =  8.117526 p= 0.20496 
(scale factors:  1.7 1.6 1.1 0.36 0.22 );  denominator df= 20
 ###Checking for Overfitting
> # the caret library is loaded
> set.seed(123)
> 
> subset13am <- subset(nhanes1, Age_R < 36 )
> subset13ams4 <- na.omit(subset13am)
> 
> 
> # Fit Generalized linear regression model using caret
> modelk <- train(HSCRP ~ relevel(Zinc, ref = "Inadequate Intake")*Kcal+ Gender+
+                   WBC + Choline +Folate +BMI,
+                 subset13ams4,
+                 method = "glm",
+                 trControl = trainControl(
+                   method = "cv",
+                   number = 10,
+                   verboseIter = T
+                 ))
+ Fold01: parameter=none 
- Fold01: parameter=none 
+ Fold02: parameter=none 
- Fold02: parameter=none 
+ Fold03: parameter=none 
- Fold03: parameter=none 
+ Fold04: parameter=none 
- Fold04: parameter=none 
+ Fold05: parameter=none 
- Fold05: parameter=none 
+ Fold06: parameter=none 
- Fold06: parameter=none 
+ Fold07: parameter=none 
- Fold07: parameter=none 
+ Fold08: parameter=none 
- Fold08: parameter=none 
+ Fold09: parameter=none 
- Fold09: parameter=none 
+ Fold10: parameter=none 
- Fold10: parameter=none 
Aggregating results
Fitting final model on full training set
> modelk
Generalized Linear Model 

1211 samples
   7 predictor

No pre-processing
Resampling: Cross-Validated (10 fold) 
Summary of sample sizes: 1090, 1089, 1090, 1090, 1090, 1090, ... 
Resampling results:

  RMSE      Rsquared    MAE     
  7.913504  0.02369755  3.472705

> 
> # Function for Root Mean Squared Error
> RMSE <- function(error) { sqrt(mean(error^2)) }
> RMSE(model1aa$residuals) 
[1] 2.187264

> #####################################################################################################################
> #### CHO
> ### Overfitted
> 
> model1aaa <- svyglm(HSCRP ~ relevel(Zinc, ref = "Inadequate Intake")* relevel(Carbohydrate, ref = "Low Intake") +  
+                      WBC + Choline +Folate +BMI+Gender+Ethnicity , design = d2, family = gaussian(link='log'))
Warning message:
glm.fit: algorithm did not converge 
> 
> summary(model1aaa,df= degf(d61))

Call:
svyglm(formula = HSCRP ~ relevel(Zinc, ref = "Inadequate Intake") * 
    relevel(Carbohydrate, ref = "Low Intake") + WBC + Choline + 
    Folate + BMI + Gender + Ethnicity, design = d2, family = gaussian(link = "log"))

Survey design:
subset(nhc2, Age_R < 36)

Coefficients:
                                                                                                                   Estimate Std. Error t value Pr(>|t|)    
(Intercept)                                                                                                       1.2155577  0.6208782   1.958 0.059611 .  
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake                                                           0.2825996  0.4962260   0.569 0.573258    
relevel(Carbohydrate, ref = "Low Intake")High Intake                                                              0.5741759  0.2399783   2.393 0.023193 *  
relevel(Carbohydrate, ref = "Low Intake")Moderate Intake                                                          1.2020320  0.6267964   1.918 0.064708 .  
WBC                                                                                                               0.0046889  0.0013580   3.453 0.001673 ** 
Choline                                                                                                           0.0030391  0.0007849   3.872 0.000543 ***
Folate                                                                                                           -0.0024962  0.0009068  -2.753 0.009929 ** 
BMI                                                                                                               0.0019429  0.0217175   0.089 0.929309    
GenderMale                                                                                                        0.6170093  0.2757280   2.238 0.032815 *  
EthnicityBlack                                                                                                   -1.0482287  0.6349640  -1.651 0.109202    
EthnicityMexican American                                                                                        -0.9043328  0.6322019  -1.430 0.162922    
EthnicityOther Hispanic                                                                                          -1.1186228  0.3912717  -2.859 0.007660 ** 
EthnicityOther Race                                                                                              -0.9533319  0.4760324  -2.003 0.054323 .  
EthnicityWhite                                                                                                   -1.5241523  0.4766924  -3.197 0.003261 ** 
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:relevel(Carbohydrate, ref = "Low Intake")High Intake     -1.6997373  0.5623586  -3.023 0.005093 ** 
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:relevel(Carbohydrate, ref = "Low Intake")Moderate Intake -2.0040817  0.8349969  -2.400 0.022801 *  
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

(Dispersion parameter for gaussian family taken to be 38.04174)

Number of Fisher Scoring iterations: 25

> confint(model1aaa,df=degf(d61))
                                                                                                                        2.5 %        97.5 %
(Intercept)                                                                                                      -0.107812768  2.5389281982
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake                                                          -0.775081095  1.3402803141
relevel(Carbohydrate, ref = "Low Intake")High Intake                                                              0.062674266  1.0856775037
relevel(Carbohydrate, ref = "Low Intake")Moderate Intake                                                         -0.133952875  2.5380168624
WBC                                                                                                               0.001794480  0.0075833759
Choline                                                                                                           0.001366034  0.0047121819
Folate                                                                                                           -0.004428948 -0.0005635201
BMI                                                                                                              -0.044346882  0.0482326644
GenderMale                                                                                                        0.029308917  1.2047096642
EthnicityBlack                                                                                                   -2.401622460  0.3051649941
EthnicityMexican American                                                                                        -2.251839289  0.4431737706
EthnicityOther Hispanic                                                                                          -1.952598552 -0.2846469751
EthnicityOther Race                                                                                              -1.967971058  0.0613071701
EthnicityWhite                                                                                                   -2.540198165 -0.5081065238
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:relevel(Carbohydrate, ref = "Low Intake")High Intake     -2.898376231 -0.5010984209
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:relevel(Carbohydrate, ref = "Low Intake")Moderate Intake -3.783835609 -0.2243278740
> summ(model1aa, exp = TRUE,confint=TRUE, n.sd=2, digits= 6)
MODEL INFO:
Observations: 1211
Dependent Variable: HSCRP
Type: Analysis of complex survey design 
 Family: gaussian 
 Link function: log 

MODEL FIT:
Pseudo-R² (Cragg-Uhler) = 0.818998
Pseudo-R² (McFadden) = 0.040687
AIC = 8589.296339 

------------------------------------------------------------------------------------------
                                   exp(Est.)       2.5%       97.5%      t val.          p
-------------------------------- ----------- ---------- ----------- ----------- ----------
(Intercept)                         4.825790   1.516456   15.357015    2.664943   0.014874
relevel(Zinc, ref =                 0.394925   0.207097    0.753108   -2.820895   0.010557
"Inadequate Intake")Adequate                                                              
Intake                                                                                    
relevel(Kcal, ref = "High           0.987421   0.420615    2.318037   -0.029073   0.977094
Calorie Diet")Low Calorie                                                                 
Diet                                                                                      
relevel(Kcal, ref = "High           1.102195   0.611459    1.986780    0.323673   0.749546
Calorie Diet")Moderate Calorie                                                            
Diet                                                                                      
WBC                                 1.003825   1.001484    1.006171    3.204769   0.004448
Choline                             1.002159   1.000927    1.003393    3.436118   0.002614
Folate                              0.999564   0.998784    1.000344   -1.095387   0.286363
BMI                                 0.973717   0.948601    0.999497   -1.997688   0.059535
GenderMale                          1.260616   0.921808    1.723952    1.450163   0.162516
relevel(Zinc, ref =                 2.421581   0.720194    8.142329    1.429452   0.168310
"Inadequate Intake")Adequate                                                              
Intake:relevel(Kcal, ref =                                                                
"High Calorie Diet")Low                                                                   
Calorie Diet                                                                              
relevel(Zinc, ref =                 1.322093   0.686626    2.545679    0.835270   0.413433
"Inadequate Intake")Adequate                                                              
Intake:relevel(Kcal, ref =                                                                
"High Calorie Diet")Moderate                                                              
Calorie Diet                                                                              
------------------------------------------------------------------------------------------

Estimated dispersion parameter = 40.32713 
> ###Checking for Overfitting
> # the caret library is loaded
> set.seed(123)
> 
> subset13am <- subset(nhanes1, Age_R <36 )
> subset13ams <- na.omit(subset13am)
> 
> 
> # Fit Generalized linear regression model using caret
> modelp <- train( HSCRP ~ relevel(Zinc, ref = "Inadequate Intake")* Carbohydrate + Ethnicity+
+                   WBC + Choline +Folate +BMI+ Gender,
+                 subset13ams,
+                 method = "glm",
+                 trControl = trainControl(
+                   method = "cv",
+                   number = 10,
+                   verboseIter = T
+                 ))
+ Fold01: parameter=none 
- Fold01: parameter=none 
+ Fold02: parameter=none 
- Fold02: parameter=none 
+ Fold03: parameter=none 
- Fold03: parameter=none 
+ Fold04: parameter=none 
- Fold04: parameter=none 
+ Fold05: parameter=none 
- Fold05: parameter=none 
+ Fold06: parameter=none 
- Fold06: parameter=none 
+ Fold07: parameter=none 
- Fold07: parameter=none 
+ Fold08: parameter=none 
- Fold08: parameter=none 
+ Fold09: parameter=none 
- Fold09: parameter=none 
+ Fold10: parameter=none 
- Fold10: parameter=none 
Aggregating results
Fitting final model on full training set
> modelp
Generalized Linear Model 

1211 samples
   8 predictor

No pre-processing
Resampling: Cross-Validated (10 fold) 
Summary of sample sizes: 1090, 1089, 1090, 1090, 1090, 1090, ... 
Resampling results:

  RMSE      Rsquared    MAE     
  7.898697  0.02448083  3.472453

> 
> # Function for Root Mean Squared Error
> RMSE <- function(error) { sqrt(mean(error^2)) }
> RMSE(model1aaa$residuals)
[1] 70.27824

> ### Remove Ethnicity
> model1aaa <- svyglm(HSCRP ~ relevel(Zinc, ref = "Inadequate Intake")* relevel(Carbohydrate, ref = "Low Intake") +  
+                       WBC + Choline +BMI+Gender , design = d2, family = gaussian(link='log'))
> 
> summary(model1aaa,df= degf(d61))

Call:
svyglm(formula = HSCRP ~ relevel(Zinc, ref = "Inadequate Intake") * 
    relevel(Carbohydrate, ref = "Low Intake") + WBC + Choline + 
    BMI + Gender, design = d2, family = gaussian(link = "log"))

Survey design:
subset(nhc2, Age_R < 36)

Coefficients:
                                                                                                                   Estimate Std. Error t value Pr(>|t|)    
(Intercept)                                                                                                       1.1688149  0.3280101   3.563 0.001248 ** 
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake                                                           0.1196115  0.3490529   0.343 0.734233    
relevel(Carbohydrate, ref = "Low Intake")High Intake                                                              0.1594333  0.1748970   0.912 0.369255    
relevel(Carbohydrate, ref = "Low Intake")Moderate Intake                                                          0.4087280  0.4083406   1.001 0.324857    
WBC                                                                                                               0.0039447  0.0009361   4.214 0.000211 ***
Choline                                                                                                           0.0016000  0.0004028   3.972 0.000412 ***
BMI                                                                                                              -0.0203612  0.0103929  -1.959 0.059447 .  
GenderMale                                                                                                        0.3188620  0.1659511   1.921 0.064224 .  
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:relevel(Carbohydrate, ref = "Low Intake")High Intake     -0.9343058  0.3330196  -2.806 0.008734 ** 
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:relevel(Carbohydrate, ref = "Low Intake")Moderate Intake -0.9444827  0.5083167  -1.858 0.072999 .  
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

(Dispersion parameter for gaussian family taken to be 40.30923)

Number of Fisher Scoring iterations: 10

> confint(model1aaa,df=degf(d61))
                                                                                                                         2.5 %       97.5 %
(Intercept)                                                                                                       0.4866805716  1.850949271
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake                                                          -0.6062836828  0.845506658
relevel(Carbohydrate, ref = "Low Intake")High Intake                                                             -0.2042848199  0.523151420
relevel(Carbohydrate, ref = "Low Intake")Moderate Intake                                                         -0.4404628159  1.257918742
WBC                                                                                                               0.0019979436  0.005891409
Choline                                                                                                           0.0007623481  0.002437715
BMI                                                                                                              -0.0419743816  0.001252012
GenderMale                                                                                                       -0.0262522094  0.663976308
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:relevel(Carbohydrate, ref = "Low Intake")High Intake     -1.6268580269 -0.241753501
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:relevel(Carbohydrate, ref = "Low Intake")Moderate Intake -2.0015851717  0.112619747
> summ(model1aa, exp = TRUE,confint=TRUE, n.sd=2, digits= 6)
MODEL INFO:
Observations: 1211
Dependent Variable: HSCRP
Type: Analysis of complex survey design 
 Family: gaussian 
 Link function: log 

MODEL FIT:
Pseudo-R² (Cragg-Uhler) = 0.818998
Pseudo-R² (McFadden) = 0.040687
AIC = 8589.296339 

------------------------------------------------------------------------------------------
                                   exp(Est.)       2.5%       97.5%      t val.          p
-------------------------------- ----------- ---------- ----------- ----------- ----------
(Intercept)                         4.825790   1.516456   15.357015    2.664943   0.014874
relevel(Zinc, ref =                 0.394925   0.207097    0.753108   -2.820895   0.010557
"Inadequate Intake")Adequate                                                              
Intake                                                                                    
relevel(Kcal, ref = "High           0.987421   0.420615    2.318037   -0.029073   0.977094
Calorie Diet")Low Calorie                                                                 
Diet                                                                                      
relevel(Kcal, ref = "High           1.102195   0.611459    1.986780    0.323673   0.749546
Calorie Diet")Moderate Calorie                                                            
Diet                                                                                      
WBC                                 1.003825   1.001484    1.006171    3.204769   0.004448
Choline                             1.002159   1.000927    1.003393    3.436118   0.002614
Folate                              0.999564   0.998784    1.000344   -1.095387   0.286363
BMI                                 0.973717   0.948601    0.999497   -1.997688   0.059535
GenderMale                          1.260616   0.921808    1.723952    1.450163   0.162516
relevel(Zinc, ref =                 2.421581   0.720194    8.142329    1.429452   0.168310
"Inadequate Intake")Adequate                                                              
Intake:relevel(Kcal, ref =                                                                
"High Calorie Diet")Low                                                                   
Calorie Diet                                                                              
relevel(Zinc, ref =                 1.322093   0.686626    2.545679    0.835270   0.413433
"Inadequate Intake")Adequate                                                              
Intake:relevel(Kcal, ref =                                                                
"High Calorie Diet")Moderate                                                              
Calorie Diet                                                                              
------------------------------------------------------------------------------------------

Estimated dispersion parameter = 40.32713 
> 
> a1amd1pq <-  tbl_regression(model1aaa,intercept= FALSE,add_estimate_to_reference_rows = TRUE
+                             , exponentiate = TRUE)%>%  bold_p(t= 0.05) %>%
+   modify_caption("**Table 4: Analysis of the Coefficients of Participants Carbohydrate Intake (19-35)** ")
> a1amd1pq
> ###Investigate terms ( LRT not significant)
> regTermTest(model1aaa,~ relevel(Zinc, ref = "Inadequate Intake"): relevel(Carbohydrate, ref = "Low Intake"), method = "LRT")
Working (Rao-Scott+F) LRT for relevel(Zinc, ref = "Inadequate Intake"):relevel(Carbohydrate, ref = "Low Intake")
 in svyglm(formula = HSCRP ~ relevel(Zinc, ref = "Inadequate Intake") * 
    relevel(Carbohydrate, ref = "Low Intake") + WBC + Choline + 
    BMI + Gender, design = d2, family = gaussian(link = "log"))
Working 2logLR =  6.745205 p= 0.054141 
(scale factors:  1.2 0.79 );  denominator df= 21
> regTermTest(model1aaa,~ relevel(Zinc, ref = "Inadequate Intake")* relevel(Carbohydrate, ref = "Low Intake"), method = "LRT")
Working (Rao-Scott+F) LRT for relevel(Zinc, ref = "Inadequate Intake") relevel(Carbohydrate, ref = "Low Intake") relevel(Zinc, ref = "Inadequate Intake"):relevel(Carbohydrate, ref = "Low Intake")
 in svyglm(formula = HSCRP ~ relevel(Zinc, ref = "Inadequate Intake") * 
    relevel(Carbohydrate, ref = "Low Intake") + WBC + Choline + 
    BMI + Gender, design = d2, family = gaussian(link = "log"))
Working 2logLR =  12.11546 p= 0.089525 
(scale factors:  2.5 1.4 0.79 0.22 0.15 );  denominator df= 21
> regTermTest(mod
+ ###Checking for Overfitting
+ # the caret library is loaded
+ set.seed(123)
> 
> subset13am <- subset(nhanes1, Age_R <36 )
> subset13ams <- na.omit(subset13am)
> 
> 
> # Fit Generalized linear regression model using caret
> modelpk <- train( HSCRP ~ relevel(Zinc, ref = "Inadequate Intake")* Carbohydrate + 
+                    WBC + Choline +Folate +BMI+ Gender,
+                  subset13ams,
+                  method = "glm",
+                  trControl = trainControl(
+                    method = "cv",
+                    number = 10,
+                    verboseIter = T
+                  ))
+ Fold01: parameter=none 
- Fold01: parameter=none 
+ Fold02: parameter=none 
- Fold02: parameter=none 
+ Fold03: parameter=none 
- Fold03: parameter=none 
+ Fold04: parameter=none 
- Fold04: parameter=none 
+ Fold05: parameter=none 
- Fold05: parameter=none 
+ Fold06: parameter=none 
- Fold06: parameter=none 
+ Fold07: parameter=none 
- Fold07: parameter=none 
+ Fold08: parameter=none 
- Fold08: parameter=none 
+ Fold09: parameter=none 
- Fold09: parameter=none 
+ Fold10: parameter=none 
- Fold10: parameter=none 
Aggregating results
Fitting final model on full training set
> modelpk
Generalized Linear Model 

1211 samples
   7 predictor

No pre-processing
Resampling: Cross-Validated (10 fold) 
Summary of sample sizes: 1089, 1091, 1090, 1090, 1089, 1090, ... 
Resampling results:

  RMSE      Rsquared    MAE     
  8.007567  0.03906183  3.431521

> ## plots ## No difference, not biologically relevant
> 
> 
> model1aaa <- svyglm(HSCRP ~  Carbohydrate *relevel(Zinc, ref = "Inadequate Intake") +
+                      WBC + Choline +Folate +BMI+ Gender , design = d61, family = gaussian(link='log'))
> 
> 
> cat_plot(model1aaa, pred = Carbohydrate, modx = Zinc, main.title = "Figure 2:Two-Way Interaction Effect Between CHO & Dietary Zinc (Young Adult)",
+          x.label =  "Carbohydrate", interval = TRUE)
> > ###########################################################################################################################
> ###### Adult
> ############################################################################################################################
> ### Fasting
> ####Fasting , 36-50
> ### Not significant; algorithm wont converged for model
> d512 <- subset(nhc2, Age_R > 35 & Age_R < 51)
> d612 <- na.omit(d512)
> 
> model1amd1p2 <- svyglm(HSCRP ~ relevel(Zinc, ref = "Inadequate Intake")* relevel(Fasting, ref="Not Fasted") + Ethnicity+Gender+
+                          WBC + Choline +Folate +BMI , design = d612, family = gaussian(link='log'))
Warning message:
glm.fit: algorithm did not converge 
> 
> summary(model1amd1,df= degf(d612))

Call:
svyglm(formula = HSCRP ~ Kcal * relevel(Zinc, ref = "Inadequate Intake") + 
    Ethnicity + Gender + WBC + Choline + Folate + BMI, design = d62, 
    family = gaussian(link = "log"))

Survey design:
subset(nhc2, Age_R > 50 & Age_R < 66)

Coefficients:
                                                                                    Estimate Std. Error t value Pr(>|t|)   
(Intercept)                                                                        0.7390857  0.6879291   1.074  0.29123   
KcalLow Calorie Diet                                                              -0.1266891  0.3512892  -0.361  0.72090   
KcalModerate Calorie Diet                                                          0.4494290  0.5207284   0.863  0.39494   
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake                            0.1326667  0.3487234   0.380  0.70630   
EthnicityBlack                                                                    -0.3579195  0.3927238  -0.911  0.36936   
EthnicityMexican American                                                         -0.5727805  0.2670603  -2.145  0.04019 * 
EthnicityOther Hispanic                                                           -0.2747293  0.2723118  -1.009  0.32110   
EthnicityOther Race                                                               -0.8284611  0.2435299  -3.402  0.00191 **
EthnicityWhite                                                                    -0.7301954  0.2816109  -2.593  0.01457 * 
GenderMale                                                                        -0.0324885  0.1660145  -0.196  0.84617   
WBC                                                                                0.0586708  0.0174597   3.360  0.00213 **
Choline                                                                            0.0005851  0.0006039   0.969  0.34040   
Folate                                                                            -0.0002149  0.0002858  -0.752  0.45791   
BMI                                                                                0.0088435  0.0168740   0.524  0.60407   
KcalLow Calorie Diet:relevel(Zinc, ref = "Inadequate Intake")Adequate Intake       0.5676169  0.4800938   1.182  0.24637   
KcalModerate Calorie Diet:relevel(Zinc, ref = "Inadequate Intake")Adequate Intake -0.2077218  0.5780845  -0.359  0.72187   
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

(Dispersion parameter for gaussian family taken to be 59.45438)

Number of Fisher Scoring iterations: 12

> confint(model1amd1,df=degf(d612))
                                                                                          2.5 %        97.5 %
(Intercept)                                                                       -0.7272006160  2.2053719219
KcalLow Calorie Diet                                                              -0.8754443003  0.6220661206
KcalModerate Calorie Diet                                                         -0.6604772368  1.5593351755
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake                           -0.6106194877  0.8759529655
EthnicityBlack                                                                    -1.1949904832  0.4791514233
EthnicityMexican American                                                         -1.1420060880 -0.0035549341
EthnicityOther Hispanic                                                           -0.8551481364  0.3056895181
EthnicityOther Race                                                               -1.3475329284 -0.3093893703
EthnicityWhite                                                                    -1.3304348500 -0.1299558974
GenderMale                                                                        -0.3863400756  0.3213630821
WBC                                                                                0.0214564216  0.0958851554
Choline                                                                           -0.0007021543  0.0018722637
Folate                                                                            -0.0008242005  0.0003943017
BMI                                                                               -0.0271224923  0.0448094913
KcalLow Calorie Diet:relevel(Zinc, ref = "Inadequate Intake")Adequate Intake      -0.4556788027  1.5909127010
KcalModerate Calorie Diet:relevel(Zinc, ref = "Inadequate Intake")Adequate Intake -1.4398797382  1.0244361151
> summ(model1amd1p2, exp = TRUE,confint=TRUE, n.sd=2, digits= 6)
MODEL INFO:
Observations: 1032
Dependent Variable: HSCRP
Type: Analysis of complex survey design 
 Family: gaussian 
 Link function: log 

MODEL FIT:
Pseudo-R² (Cragg-Uhler) = 0.933675
Pseudo-R² (McFadden) = 0.074923
AIC = 7102.813897 

----------------------------------------------------------------------------------------
                                  exp(Est.)       2.5%      97.5%      t val.          p
------------------------------- ----------- ---------- ---------- ----------- ----------
(Intercept)                        1.839009   0.590882   5.723575    1.051698   0.307659
relevel(Zinc, ref =                1.483963   0.811194   2.714698    1.280920   0.217421
"Inadequate Intake")Adequate                                                            
Intake                                                                                  
relevel(Fasting, ref = "Not        2.047086   1.169033   3.584637    2.506340   0.022652
Fasted")Fasted                                                                          
EthnicityBlack                     0.946655   0.466546   1.920830   -0.151851   0.881092
EthnicityMexican American          0.424788   0.219469   0.822189   -2.541043   0.021095
EthnicityOther Hispanic            0.678804   0.298758   1.542303   -0.925228   0.367796
EthnicityOther Race                0.550031   0.262339   1.153221   -1.582556   0.131948
EthnicityWhite                     0.777093   0.385942   1.564676   -0.706260   0.489594
GenderMale                         1.423633   0.979638   2.068859    1.852091   0.081459
WBC                                1.022628   0.994850   1.051182    1.592516   0.129691
Choline                            0.999298   0.997668   1.000930   -0.843230   0.410808
Folate                             0.998196   0.997329   0.999063   -4.075210   0.000788
BMI                                1.033053   0.989844   1.078148    1.491689   0.154104
relevel(Zinc, ref =                0.800490   0.346219   1.850805   -0.520375   0.609513
"Inadequate Intake")Adequate                                                            
Intake:relevel(Fasting, ref =                                                           
"Not Fasted")Fasted                                                                     
----------------------------------------------------------------------------------------

Estimated dispersion parameter = 33.51064 
> 
> a1amd1p2 <-  tbl_regression(model1amd1p2,intercept= FALSE,add_estimate_to_reference_rows = TRUE
+                             , exponentiate = TRUE)%>%  bold_p(t= 0.05) %>%
+   modify_caption("**Table S.8: Analysis of the Coefficients for Participants 36- 50 Years Old, (Fasting)** ")
> a1amd1p2
> ###Investigate terms
> regTermTest(model1amd1p2 ,~ relevel(Zinc, ref = "Inadequate Intake"): relevel(Fasting, ref="Not Fasted"), method = "LRT")
Working (Rao-Scott+F) LRT for relevel(Zinc, ref = "Inadequate Intake"):relevel(Fasting, ref = "Not Fasted")
 in svyglm(formula = HSCRP ~ relevel(Zinc, ref = "Inadequate Intake") * 
    relevel(Fasting, ref = "Not Fasted") + Ethnicity + 
    Gender + WBC + Choline + Folate + BMI, design = d612, family = gaussian(link = "log"))
Working 2logLR =  0.2417385 p= 0.62477 
df=1;  denominator df= 17
Warning message:
glm.fit: algorithm did not converge 
> regTermTest(model1amd1p2 ,~ relevel(Zinc, ref = "Inadequate Intake")* relevel(Fasting, ref="Not Fasted"), method = "LRT")
Working (Rao-Scott+F) LRT for relevel(Zinc, ref = "Inadequate Intake") relevel(Fasting, ref = "Not Fasted") relevel(Zinc, ref = "Inadequate Intake"):relevel(Fasting, ref = "Not Fasted")
 in svyglm(formula = HSCRP ~ relevel(Zinc, ref = "Inadequate Intake") * 
    relevel(Fasting, ref = "Not Fasted") + Ethnicity + 
    Gender + WBC + Choline + Folate + BMI, design = d612, family = gaussian(link = "log"))
Working 2logLR =  9.861151 p= 0.057343 
(scale factors:  1.9 0.7 0.4 );  denominator df= 17
Warning message:
glm.fit: algorithm did not converge 
> ###Checking for Overfitting
> # the caret library is loaded
> set.seed(123)
> 
> subset13am <- subset(nhanes1, Age_R >35 & Age_R <51 )
> subset13ams <- na.omit(subset13am)
> 
> 
> # Fit Generalized linear regression model using caret
> modelpw <- train( HSCRP ~ relevel(Zinc, ref = "Inadequate Intake")* relevel(Fasting, ref="Not Fasted") + Ethnicity+
+                    WBC + Choline +Folate +BMI+ Gender,
+                  subset13ams,
+                  method = "glm",
+                  trControl = trainControl(
+                    method = "cv",
+                    number = 10,
+                    verboseIter = T
+                  ))
+ Fold01: parameter=none 
- Fold01: parameter=none 
+ Fold02: parameter=none 
- Fold02: parameter=none 
+ Fold03: parameter=none 
- Fold03: parameter=none 
+ Fold04: parameter=none 
- Fold04: parameter=none 
+ Fold05: parameter=none 
- Fold05: parameter=none 
+ Fold06: parameter=none 
- Fold06: parameter=none 
+ Fold07: parameter=none 
- Fold07: parameter=none 
+ Fold08: parameter=none 
- Fold08: parameter=none 
+ Fold09: parameter=none 
- Fold09: parameter=none 
+ Fold10: parameter=none 
- Fold10: parameter=none 
Aggregating results
Fitting final model on full training set
> modelpw
Generalized Linear Model 

1032 samples
   8 predictor

No pre-processing
Resampling: Cross-Validated (10 fold) 
Summary of sample sizes: 929, 928, 928, 930, 930, 929, ... 
Resampling results:

  RMSE      Rsquared    MAE     
  6.107037  0.03115171  3.265228

> 
> # Function for Root Mean Squared Error
> RMSE <- function(error) { sqrt(mean(error^2)) }
> RMSE(model1amd1p2$residuals)
[1] 2.792074

> ### Remove Ethnicity
> model1amd1p2 <- svyglm(HSCRP ~ relevel(Zinc, ref = "Inadequate Intake")* relevel(Fasting, ref="Not Fasted") + Gender+
+                          WBC + Choline +Folate +BMI , design = d612, family = gaussian(link='log'))
Warning message:
glm.fit: algorithm did not converge 
> 
> summary(model1amd1,df= degf(d612))

Call:
svyglm(formula = HSCRP ~ Kcal * relevel(Zinc, ref = "Inadequate Intake") + 
    Ethnicity + Gender + WBC + Choline + Folate + BMI, design = d62, 
    family = gaussian(link = "log"))

Survey design:
subset(nhc2, Age_R > 50 & Age_R < 66)

Coefficients:
                                                                                    Estimate Std. Error t value Pr(>|t|)   
(Intercept)                                                                        0.7390857  0.6879291   1.074  0.29123   
KcalLow Calorie Diet                                                              -0.1266891  0.3512892  -0.361  0.72090   
KcalModerate Calorie Diet                                                          0.4494290  0.5207284   0.863  0.39494   
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake                            0.1326667  0.3487234   0.380  0.70630   
EthnicityBlack                                                                    -0.3579195  0.3927238  -0.911  0.36936   
EthnicityMexican American                                                         -0.5727805  0.2670603  -2.145  0.04019 * 
EthnicityOther Hispanic                                                           -0.2747293  0.2723118  -1.009  0.32110   
EthnicityOther Race                                                               -0.8284611  0.2435299  -3.402  0.00191 **
EthnicityWhite                                                                    -0.7301954  0.2816109  -2.593  0.01457 * 
GenderMale                                                                        -0.0324885  0.1660145  -0.196  0.84617   
WBC                                                                                0.0586708  0.0174597   3.360  0.00213 **
Choline                                                                            0.0005851  0.0006039   0.969  0.34040   
Folate                                                                            -0.0002149  0.0002858  -0.752  0.45791   
BMI                                                                                0.0088435  0.0168740   0.524  0.60407   
KcalLow Calorie Diet:relevel(Zinc, ref = "Inadequate Intake")Adequate Intake       0.5676169  0.4800938   1.182  0.24637   
KcalModerate Calorie Diet:relevel(Zinc, ref = "Inadequate Intake")Adequate Intake -0.2077218  0.5780845  -0.359  0.72187   
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

(Dispersion parameter for gaussian family taken to be 59.45438)

Number of Fisher Scoring iterations: 12

> confint(model1amd1,df=degf(d612))
                                                                                          2.5 %        97.5 %
(Intercept)                                                                       -0.7272006160  2.2053719219
KcalLow Calorie Diet                                                              -0.8754443003  0.6220661206
KcalModerate Calorie Diet                                                         -0.6604772368  1.5593351755
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake                           -0.6106194877  0.8759529655
EthnicityBlack                                                                    -1.1949904832  0.4791514233
EthnicityMexican American                                                         -1.1420060880 -0.0035549341
EthnicityOther Hispanic                                                           -0.8551481364  0.3056895181
EthnicityOther Race                                                               -1.3475329284 -0.3093893703
EthnicityWhite                                                                    -1.3304348500 -0.1299558974
GenderMale                                                                        -0.3863400756  0.3213630821
WBC                                                                                0.0214564216  0.0958851554
Choline                                                                           -0.0007021543  0.0018722637
Folate                                                                            -0.0008242005  0.0003943017
BMI                                                                               -0.0271224923  0.0448094913
KcalLow Calorie Diet:relevel(Zinc, ref = "Inadequate Intake")Adequate Intake      -0.4556788027  1.5909127010
KcalModerate Calorie Diet:relevel(Zinc, ref = "Inadequate Intake")Adequate Intake -1.4398797382  1.0244361151
> summ(model1amd1p2, exp = TRUE,confint=TRUE, n.sd=2, digits= 6)
MODEL INFO:
Observations: 1032
Dependent Variable: HSCRP
Type: Analysis of complex survey design 
 Family: gaussian 
 Link function: log 

MODEL FIT:
Pseudo-R² (Cragg-Uhler) = 0.861941
Pseudo-R² (McFadden) = 0.054679
AIC = 7115.154945 

----------------------------------------------------------------------------------------
                                  exp(Est.)       2.5%      97.5%      t val.          p
------------------------------- ----------- ---------- ---------- ----------- ----------
(Intercept)                        1.549476   0.567567   4.230120    0.854614   0.401976
relevel(Zinc, ref =                1.491324   0.885542   2.511509    1.502875   0.147091
"Inadequate Intake")Adequate                                                            
Intake                                                                                  
relevel(Fasting, ref = "Not        2.000620   1.174610   3.407497    2.552298   0.018161
Fasted")Fasted                                                                          
GenderMale                         1.257171   0.879151   1.797734    1.254155   0.222948
WBC                                1.025297   0.997559   1.053806    1.785299   0.088008
Choline                            0.999324   0.997615   1.001037   -0.773850   0.447256
Folate                             0.998321   0.997351   0.999292   -3.387902   0.002647
BMI                                1.029418   0.987959   1.072617    1.382386   0.180728
relevel(Zinc, ref =                0.866718   0.388575   1.933219   -0.349472   0.730058
"Inadequate Intake")Adequate                                                            
Intake:relevel(Fasting, ref =                                                           
"Not Fasted")Fasted                                                                     
----------------------------------------------------------------------------------------

Estimated dispersion parameter = 34.25824 
> 
> a1amd1p2 <-  tbl_regression(model1amd1p2,intercept= FALSE,add_estimate_to_reference_rows = TRUE
+                             , exponentiate = TRUE)%>%  bold_p(t= 0.05) %>%
+   modify_caption("**Table S.9: Analysis of the Coefficients for Participants 36- 50 Years Old, (Fasting)** ")
> a1amd1p2
> ###Investigate terms
> regTermTest(model1amd1p2 ,~ relevel(Zinc, ref = "Inadequate Intake"): relevel(Fasting, ref="Not Fasted"), method = "LRT")
Working (Rao-Scott+F) LRT for relevel(Zinc, ref = "Inadequate Intake"):relevel(Fasting, ref = "Not Fasted")
 in svyglm(formula = HSCRP ~ relevel(Zinc, ref = "Inadequate Intake") * 
    relevel(Fasting, ref = "Not Fasted") + Gender + WBC + 
    Choline + Folate + BMI, design = d612, family = gaussian(link = "log"))
Working 2logLR =  0.1138927 p= 0.73266 
df=1;  denominator df= 22
Warning message:
glm.fit: algorithm did not converge 
> regTermTest(model1amd1p2 ,~ relevel(Zinc, ref = "Inadequate Intake")* relevel(Fasting, ref="Not Fasted"), method = "LRT")
Working (Rao-Scott+F) LRT for relevel(Zinc, ref = "Inadequate Intake") relevel(Fasting, ref = "Not Fasted") relevel(Zinc, ref = "Inadequate Intake"):relevel(Fasting, ref = "Not Fasted")
 in svyglm(formula = HSCRP ~ relevel(Zinc, ref = "Inadequate Intake") * 
    relevel(Fasting, ref = "Not Fasted") + Gender + WBC + 
    Choline + Folate + BMI, design = d612, family = gaussian(link = "log"))
Working 2logLR =  7.361784 p= 0.11528 
(scale factors:  2.4 0.36 0.22 );  denominator df= 22

 ###Checking for Overfitting
> # the caret library is loaded
> set.seed(123)
> 
> subset13am <- subset(nhanes1, Age_R >35 & Age_R <51 )
> subset13ams <- na.omit(subset13am)
> 
> 
> # Fit Generalized linear regression model using caret
> modelpw <- train( HSCRP ~ relevel(Zinc, ref = "Inadequate Intake")* relevel(Fasting, ref="Not Fasted") + 
+                     WBC + Choline +Folate +BMI+ Gender,
+                   subset13ams,
+                   method = "glm",
+                   trControl = trainControl(
+                     method = "cv",
+                     number = 10,
+                     verboseIter = T
+                   ))
+ Fold01: parameter=none 
- Fold01: parameter=none 
+ Fold02: parameter=none 
- Fold02: parameter=none 
+ Fold03: parameter=none 
- Fold03: parameter=none 
+ Fold04: parameter=none 
- Fold04: parameter=none 
+ Fold05: parameter=none 
- Fold05: parameter=none 
+ Fold06: parameter=none 
- Fold06: parameter=none 
+ Fold07: parameter=none 
- Fold07: parameter=none 
+ Fold08: parameter=none 
- Fold08: parameter=none 
+ Fold09: parameter=none 
- Fold09: parameter=none 
+ Fold10: parameter=none 
- Fold10: parameter=none 
Aggregating results
Fitting final model on full training set
> modelpw
Generalized Linear Model 

1032 samples
   7 predictor

No pre-processing
Resampling: Cross-Validated (10 fold) 
Summary of sample sizes: 929, 928, 928, 930, 930, 929, ... 
Resampling results:

  RMSE      Rsquared    MAE     
  6.088213  0.03707613  3.249174

> 
> # Function for Root Mean Squared Error
> RMSE <- function(error) { sqrt(mean(error^2)) }
> RMSE(model1amd1p2$residuals)
[1] 2.400418

> #### Kcal
> ###Not significant
> model1q1 <- svyglm(HSCRP ~ relevel(Zinc, ref = "Inadequate Intake")* Kcal + Ethnicity +Gender+
+                          WBC + Choline +Folate +BMI+ , design = d612, family = gaussian(link='log'))
Error: unexpected ',' in:
"model1q1 <- svyglm(HSCRP ~ relevel(Zinc, ref = "Inadequate Intake")* Kcal + Ethnicity +Gender+
                         WBC + Choline +Folate +BMI+ ,"
> 
> 
> 
> summary(model1q1,df= degf(d612))

Call:
svyglm(formula = HSCRP ~ relevel(Zinc, ref = "Inadequate Intake") * 
    Kcal + Copper + Gender + WBC + Choline + Folate + BMI + Sugar, 
    design = d612, family = gaussian(link = "log"))

Survey design:
subset(nhc2, Age_R > 35 & Age_R < 51)

Coefficients:
                                                                                    Estimate Std. Error t value Pr(>|t|)  
(Intercept)                                                                        0.0134886  1.0481036   0.013   0.9898  
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake                           -0.4871139  0.6103490  -0.798   0.4311  
KcalLow Calorie Diet                                                              -0.0840545  0.5530660  -0.152   0.8802  
KcalModerate Calorie Diet                                                          0.1809944  0.5924924   0.305   0.7621  
Copper                                                                            -0.1450940  0.2506911  -0.579   0.5671  
GenderMale                                                                         0.3314582  0.2106520   1.573   0.1261  
WBC                                                                                0.0241330  0.0160995   1.499   0.1443  
Choline                                                                            0.0007634  0.0014522   0.526   0.6029  
Folate                                                                            -0.0016339  0.0006881  -2.374   0.0242 *
BMI                                                                                0.0376726  0.0206095   1.828   0.0775 .
Sugar                                                                              0.0035535  0.0019087   1.862   0.0725 .
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:KcalLow Calorie Diet       0.4104253  0.5743807   0.715   0.4804  
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:KcalModerate Calorie Diet  0.8750599  0.6344832   1.379   0.1780  
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

(Dispersion parameter for gaussian family taken to be 33.72455)

Number of Fisher Scoring iterations: 25

> summ(model1q1, exp = TRUE,confint=TRUE, n.sd=2, digits= 6)
MODEL INFO:
Observations: 1032
Dependent Variable: HSCRP
Type: Analysis of complex survey design 
 Family: gaussian 
 Link function: log 

MODEL FIT:
Pseudo-R² (Cragg-Uhler) = 0.917402
Pseudo-R² (McFadden) = 0.068864
AIC = 7107.551467 

----------------------------------------------------------------------------------------
                                  exp(Est.)       2.5%      97.5%      t val.          p
------------------------------- ----------- ---------- ---------- ----------- ----------
(Intercept)                        1.013580   0.129930   7.906885    0.012869   0.989873
relevel(Zinc, ref =                0.614397   0.185746   2.032259   -0.798091   0.435221
"Inadequate Intake")Adequate                                                            
Intake                                                                                  
KcalLow Calorie Diet               0.919381   0.310975   2.718105   -0.151979   0.880894
KcalModerate Calorie Diet          1.198409   0.375210   3.827677    0.305480   0.763505
Copper                             0.864941   0.529173   1.413758   -0.578776   0.569912
GenderMale                         1.392998   0.921814   2.105028    1.573487   0.133018
WBC                                1.024427   0.992606   1.057267    1.498990   0.151210
Choline                            1.000764   0.997919   1.003616    0.525725   0.605496
Folate                             0.998367   0.997022   0.999715   -2.374423   0.028903
BMI                                1.038391   0.997282   1.081195    1.827926   0.084185
Sugar                              1.003560   0.999812   1.007321    1.861712   0.079054
relevel(Zinc, ref =                1.507459   0.489026   4.646856    0.714553   0.484050
"Inadequate Intake")Adequate                                                            
Intake:KcalLow Calorie Diet                                                             
relevel(Zinc, ref =                2.399019   0.691768   8.319683    1.379169   0.184739
"Inadequate Intake")Adequate                                                            
Intake:KcalModerate Calorie                                                             
Diet                                                                                    
----------------------------------------------------------------------------------------

Estimated dispersion parameter = 33.72456 
> 
> a1amd1p2q <-  tbl_regression(model1q1,intercept= FALSE,add_estimate_to_reference_rows = TRUE
+                             , exponentiate = TRUE)%>%  bold_p(t= 0.05) %>%
+   modify_caption("**Table S.10: Analysis of the Coefficients for the Participants' Energy Intake 36- 50 Years Old** ")
> a1amd1p2q


> ###Investigate terms
> regTermTest(model1q1 ,~ relevel(Zinc, ref = "Inadequate Intake"): Kcal, method = "LRT")
Working (Rao-Scott+F) LRT for relevel(Zinc, ref = "Inadequate Intake"):Kcal
 in svyglm(formula = HSCRP ~ relevel(Zinc, ref = "Inadequate Intake") * 
    Kcal + Copper + Gender + WBC + Choline + Folate + BMI + Sugar, 
    design = d612, family = gaussian(link = "log"))
Working 2logLR =  2.730388 p= 0.25819 
(scale factors:  1.8 0.22 );  denominator df= 18
Warning message:
glm.fit: algorithm did not converge 
> regTermTest(model1q1 ,~ relevel(Zinc, ref = "Inadequate Intake")* Kcal, method = "LRT")
Working (Rao-Scott+F) LRT for relevel(Zinc, ref = "Inadequate Intake") Kcal relevel(Zinc, ref = "Inadequate Intake"):Kcal
 in svyglm(formula = HSCRP ~ relevel(Zinc, ref = "Inadequate Intake") * 
    Kcal + Copper + Gender + WBC + Choline + Folate + BMI + Sugar, 
    design = d612, family = gaussian(link = "log"))
Working 2logLR =  12.96892 p= 0.076927 
(scale factors:  2.1 1.5 0.8 0.47 0.081 );  denominator df= 18
Warning message:
glm.fit: algorithm did not converge 
> 
> # the caret library is loaded
> set.seed(123)
> 
> subset13am <- subset(nhanes1, Age_R >35 & Age_R <51 )
> subset13ams <- na.omit(subset13am)
> 
> 
> # Fit Generalized linear regression model using caret
> modelpwa <- train( HSCRP ~ relevel(Zinc, ref = "Inadequate Intake")* Kcal + Ethnicity+
+                     WBC + Choline +Folate +BMI+ Gender,
+                   subset13ams,
+                   method = "glm",
+                   trControl = trainControl(
+                     method = "cv",
+                     number = 10,
+                     verboseIter = T
+                   ))
+ Fold01: parameter=none 
- Fold01: parameter=none 
+ Fold02: parameter=none 
- Fold02: parameter=none 
+ Fold03: parameter=none 
- Fold03: parameter=none 
+ Fold04: parameter=none 
- Fold04: parameter=none 
+ Fold05: parameter=none 
- Fold05: parameter=none 
+ Fold06: parameter=none 
- Fold06: parameter=none 
+ Fold07: parameter=none 
- Fold07: parameter=none 
+ Fold08: parameter=none 
- Fold08: parameter=none 
+ Fold09: parameter=none 
- Fold09: parameter=none 
+ Fold10: parameter=none 
- Fold10: parameter=none 
Aggregating results
Fitting final model on full training set
> modelpwa
Generalized Linear Model 

1032 samples
   8 predictor

No pre-processing
Resampling: Cross-Validated (10 fold) 
Summary of sample sizes: 929, 928, 928, 930, 930, 929, ... 
Resampling results:

  RMSE      Rsquared    MAE     
  6.109996  0.02013654  3.324058

> 
> # Function for Root Mean Squared Error
> RMSE <- function(error) { sqrt(mean(error^2)) }
> RMSE(model1q1$residuals)
[1] 2.835303
>
> ### Remove Ethnicity
> 
> model1q1 <- svyglm(HSCRP ~ relevel(Zinc, ref = "Inadequate Intake")* Kcal + Gender+
+                      WBC + Choline +Folate + BMI , design = d612, family = gaussian(link='log'))
Warning message:
glm.fit: algorithm did not converge 
> 
> 
> 
> summary(model1q1,df= degf(d612))

Call:
svyglm(formula = HSCRP ~ relevel(Zinc, ref = "Inadequate Intake") * 
    Kcal + Gender + WBC + Choline + Folate + BMI, design = d612, 
    family = gaussian(link = "log"))

Survey design:
subset(nhc2, Age_R > 35 & Age_R < 51)

Coefficients:
                                                                                    Estimate Std. Error t value Pr(>|t|)  
(Intercept)                                                                        0.9642574  0.9069489   1.063   0.2962  
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake                           -0.6286397  0.5821216  -1.080   0.2888  
KcalLow Calorie Diet                                                              -0.4890488  0.5591059  -0.875   0.3887  
KcalModerate Calorie Diet                                                         -0.1277072  0.5539111  -0.231   0.8192  
GenderMale                                                                         0.2866297  0.1995182   1.437   0.1612  
WBC                                                                                0.0221609  0.0157268   1.409   0.1691  
Choline                                                                            0.0005622  0.0013201   0.426   0.6732  
Folate                                                                            -0.0016581  0.0006799  -2.439   0.0209 *
BMI                                                                                0.0261547  0.0209130   1.251   0.2207  
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:KcalLow Calorie Diet       0.5000040  0.5589621   0.895   0.3782  
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:KcalModerate Calorie Diet  0.9413186  0.6184597   1.522   0.1385  
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

(Dispersion parameter for gaussian family taken to be 34.03624)

Number of Fisher Scoring iterations: 25

> summ(model1q1, exp = TRUE,confint=TRUE, n.sd=2, digits= 6)
MODEL INFO:
Observations: 1032
Dependent Variable: HSCRP
Type: Analysis of complex survey design 
 Family: gaussian 
 Link function: log 

MODEL FIT:
Pseudo-R² (Cragg-Uhler) = 0.888999
Pseudo-R² (McFadden) = 0.060703
AIC = 7112.557556 

-----------------------------------------------------------------------------------------
                                  exp(Est.)       2.5%       97.5%      t val.          p
------------------------------- ----------- ---------- ----------- ----------- ----------
(Intercept)                        2.622839   0.443379   15.515578    1.063188   0.300366
relevel(Zinc, ref =                0.533317   0.170405    1.669122   -1.079911   0.293033
"Inadequate Intake")Adequate                                                             
Intake                                                                                   
KcalLow Calorie Diet               0.613209   0.204973    1.834512   -0.874698   0.392121
KcalModerate Calorie Diet          0.880111   0.297199    2.606318   -0.230556   0.820002
GenderMale                         1.331931   0.900848    1.969300    1.436609   0.166289
WBC                                1.022408   0.991374    1.054414    1.409120   0.174159
Choline                            1.000562   0.997977    1.003154    0.425868   0.674752
Folate                             0.998343   0.997014    0.999675   -2.438743   0.024187
BMI                                1.026500   0.985276    1.069449    1.250648   0.225497
relevel(Zinc, ref =                1.648728   0.551264    4.931039    0.894522   0.381682
"Inadequate Intake")Adequate                                                             
Intake:KcalLow Calorie Diet                                                              
relevel(Zinc, ref =                2.563359   0.762738    8.614763    1.522037   0.143654
"Inadequate Intake")Adequate                                                             
Intake:KcalModerate Calorie                                                              
Diet                                                                                     
-----------------------------------------------------------------------------------------

Estimated dispersion parameter = 34.03624 
> 
> a1amd1p2q <-  tbl_regression(model1q1,intercept= FALSE,add_estimate_to_reference_rows = TRUE
+                              , exponentiate = TRUE)%>%  bold_p(t= 0.05) %>%
+   modify_caption("**Table S.11: Analysis of the Coefficients for the Participants' Energy Intake 36- 50 Years Old** ")
> a1amd1p2q
> ###Investigate terms
> regTermTest(model1q1, ~ relevel(Zinc, ref = "Inadequate Intake"):Kcal, method = "LRT")
Working (Rao-Scott+F) LRT for relevel(Zinc, ref = "Inadequate Intake"):Kcal
 in svyglm(formula = HSCRP ~ relevel(Zinc, ref = "Inadequate Intake") * 
    Kcal + Gender + WBC + Choline + Folate + BMI, design = d612, 
    family = gaussian(link = "log"))
Working 2logLR =  3.224713 p= 0.2159 
(scale factors:  1.8 0.21 );  denominator df= 20
> regTermTest(model1q1, ~ relevel(Zinc, ref = "Inadequate Intake")*Kcal, method = "LRT")
Working (Rao-Scott+F) LRT for relevel(Zinc, ref = "Inadequate Intake") Kcal relevel(Zinc, ref = "Inadequate Intake"):Kcal
 in svyglm(formula = HSCRP ~ relevel(Zinc, ref = "Inadequate Intake") * 
    Kcal + Gender + WBC + Choline + Folate + BMI, design = d612, 
    family = gaussian(link = "log"))
Working 2logLR =  10.44012 p= 0.12458 
(scale factors:  2.2 1.5 0.66 0.51 0.06 );  denominator df= 20
> # the caret library is loaded
> set.seed(123)
> 
> subset13am <- subset(nhanes1, Age_R >35 & Age_R <51 )
> subset13ams <- na.omit(subset13am)
> 
> 
> # Fit Generalized linear regression model using caret
> modelpwa <- train( HSCRP ~ relevel(Zinc, ref = "Inadequate Intake")* Kcal 
+                    WBC + Choline +Folate +BMI+ Gender,
Error: unexpected symbol in:
"modelpwa <- train( HSCRP ~ relevel(Zinc, ref = "Inadequate Intake")* Kcal 
                   WBC"
>                    subset13ams,
Error: unexpected ',' in "                   subset13ams,"
>                    method = "glm",
Error: unexpected ',' in "                   method = "glm","
>                    trControl = trainControl(
+                      method = "cv",
+                      number = 10,
+                      verboseIter = T
+                    ))
Error: unexpected ')' in:
"                     verboseIter = T
                   ))"
> modelpwa
Generalized Linear Model 

1032 samples
   8 predictor

No pre-processing
Resampling: Cross-Validated (10 fold) 
Summary of sample sizes: 929, 928, 928, 930, 930, 929, ... 
Resampling results:

  RMSE      Rsquared    MAE     
  6.109996  0.02013654  3.324058

> 
> # Function for Root Mean Squared Error
> RMSE <- function(error) { sqrt(mean(error^2)) }
> RMSE(model1q1$residuals)
[1] 2.59721
>
> ########################
> ####CHO
> 
> ###Overfitted
> model1r1 <- svyglm(HSCRP ~ relevel(Zinc, ref = "Inadequate Intake")* Carbohydrate + Gender+ Ethnicity+
+                      WBC + Choline +Folate +BMI , design = d612, family = gaussian(link='log'))
Warning message:
glm.fit: algorithm did not converge 
> 
> 
> 
> summary(model1r1,df= degf(d612))

Call:
svyglm(formula = HSCRP ~ relevel(Zinc, ref = "Inadequate Intake") * 
    Carbohydrate + Gender + Ethnicity + WBC + Choline + Folate + 
    BMI, design = d612, family = gaussian(link = "log"))

Survey design:
subset(nhc2, Age_R > 35 & Age_R < 51)

Coefficients:
                                                                                      Estimate Std. Error t value Pr(>|t|)    
(Intercept)                                                                          0.9127154  0.7359611   1.240 0.224526    
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake                             -0.7569118  0.3259323  -2.322 0.027190 *  
CarbohydrateLow Intake                                                              -1.4109675  0.4572527  -3.086 0.004339 ** 
CarbohydrateModerate Intake                                                          0.0473598  0.3962507   0.120 0.905660    
GenderMale                                                                           0.7868338  0.2660883   2.957 0.006003 ** 
EthnicityBlack                                                                      -0.6023633  0.2004344  -3.005 0.005319 ** 
EthnicityMexican American                                                           -1.4984075  0.3041049  -4.927 2.86e-05 ***
EthnicityOther Hispanic                                                             -1.9285475  0.6595553  -2.924 0.006519 ** 
EthnicityOther Race                                                                 -1.6197106  0.5420293  -2.988 0.005552 ** 
EthnicityWhite                                                                      -0.8346938  0.2157313  -3.869 0.000546 ***
WBC                                                                                  0.0257643  0.0148222   1.738 0.092426 .  
Choline                                                                              0.0029243  0.0006706   4.361 0.000141 ***
Folate                                                                              -0.0059954  0.0011434  -5.243 1.17e-05 ***
BMI                                                                                  0.0609512  0.0188983   3.225 0.003034 ** 
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:CarbohydrateLow Intake       1.1722783  0.6320680   1.855 0.073496 .  
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:CarbohydrateModerate Intake  1.1284371  0.4753251   2.374 0.024194 *  
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

(Dispersion parameter for gaussian family taken to be 30.09762)

Number of Fisher Scoring iterations: 25

> confint(modelr1,df=degf(d612))
Error in confint(modelr1, df = degf(d612)) : object 'modelr1' not found
> summ(model1r1, exp = TRUE,confint=TRUE, n.sd=2, digits= 6)
MODEL INFO:
Observations: 1032
Dependent Variable: HSCRP
Type: Analysis of complex survey design 
 Family: gaussian 
 Link function: log 

MODEL FIT:
Pseudo-R² (Cragg-Uhler) = 0.988993
Pseudo-R² (McFadden) = 0.124521
AIC = 7049.945111 

-----------------------------------------------------------------------------------------
                                  exp(Est.)       2.5%       97.5%      t val.          p
------------------------------- ----------- ---------- ----------- ----------- ----------
(Intercept)                        2.491078   0.588757   10.539949    1.240168   0.233963
relevel(Zinc, ref =                0.469113   0.247653    0.888610   -2.322298   0.034694
"Inadequate Intake")Adequate                                                             
Intake                                                                                   
CarbohydrateLow Intake             0.243907   0.099543    0.597639   -3.085750   0.007533
CarbohydrateModerate               1.048499   0.482257    2.279593    0.119520   0.906450
Intake                                                                                   
GenderMale                         2.196431   1.303835    3.700091    2.957040   0.009792
EthnicityBlack                     0.547516   0.369647    0.810974   -3.005290   0.008877
EthnicityMexican American          0.223486   0.123139    0.405606   -4.927271   0.000182
EthnicityOther Hispanic            0.145359   0.039905    0.529489   -2.924012   0.010472
EthnicityOther Race                0.197956   0.068421    0.572723   -2.988234   0.009190
EthnicityWhite                     0.434007   0.284359    0.662411   -3.869137   0.001514
WBC                                1.026099   0.996719    1.056345    1.738229   0.102649
Choline                            1.002929   1.001611    1.004248    4.360654   0.000559
Folate                             0.994023   0.991797    0.996253   -5.243498   0.000099
BMI                                1.062847   1.024199    1.102953    3.225229   0.005664
relevel(Zinc, ref =                3.229342   0.935614   11.146313    1.854671   0.083407
"Inadequate Intake")Adequate                                                             
Intake:CarbohydrateLow                                                                   
Intake                                                                                   
relevel(Zinc, ref =                3.090822   1.217521    7.846419    2.374032   0.031376
"Inadequate Intake")Adequate                                                             
Intake:CarbohydrateModerate                                                              
Intake                                                                                   
-----------------------------------------------------------------------------------------

Estimated dispersion parameter = 30.09762 
> 
> a1amd1p2qr <-  tbl_regression(model1r1,intercept= FALSE,add_estimate_to_reference_rows = TRUE
+                              , exponentiate = TRUE)%>%  bold_p(t= 0.05) %>%
+   modify_caption("**Table S.12: Analysis of the Coefficients for the Participants' CHO Intake 36- 50 Years Old** ")
> a1amd1p2qr
> confint(model1r1,df=degf(d612))
                                                                                           2.5 %       97.5 %
(Intercept)                                                                         -0.655948549  2.481379431
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake                             -1.451619977 -0.062203630
CarbohydrateLow Intake                                                              -2.385578500 -0.436356416
CarbohydrateModerate Intake                                                         -0.797228512  0.891948128
GenderMale                                                                           0.219679973  1.353987716
EthnicityBlack                                                                      -1.029578966 -0.175147552
EthnicityMexican American                                                           -2.146591883 -0.850223208
EthnicityOther Hispanic                                                             -3.334356324 -0.522738583
EthnicityOther Race                                                                 -2.775018667 -0.464402497
EthnicityWhite                                                                      -1.294514109 -0.374873546
WBC                                                                                 -0.005828374  0.057357022
Choline                                                                              0.001494949  0.004353735
Folate                                                                              -0.008432444 -0.003558286
BMI                                                                                  0.020670521  0.101231898
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:CarbohydrateLow Intake      -0.174942611  2.519499299
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:CarbohydrateModerate Intake  0.115305583  2.141568618

 
> # Fit Generalized linear regression model using caret
> modelpwa1 <- train( HSCRP ~ relevel(Zinc, ref = "Inadequate Intake")* Carbohydrate + 
+                       WBC + Choline +Folate +BMI+ Gender,
+                     subset13ams,
+                     method = "glm",
+                     trControl = trainControl(
+                       method = "cv",
+                       number = 10,
+                       verboseIter = T
+                     ))
+ Fold01: parameter=none 
- Fold01: parameter=none 
+ Fold02: parameter=none 
- Fold02: parameter=none 
+ Fold03: parameter=none 
- Fold03: parameter=none 
+ Fold04: parameter=none 
- Fold04: parameter=none 
+ Fold05: parameter=none 
- Fold05: parameter=none 
+ Fold06: parameter=none 
- Fold06: parameter=none 
+ Fold07: parameter=none 
- Fold07: parameter=none 
+ Fold08: parameter=none 
- Fold08: parameter=none 
+ Fold09: parameter=none 
- Fold09: parameter=none 
+ Fold10: parameter=none 
- Fold10: parameter=none 
Aggregating results
Fitting final model on full training set
> modelpwa1
Generalized Linear Model 

1032 samples
   7 predictor

No pre-processing
Resampling: Cross-Validated (10 fold) 
Summary of sample sizes: 929, 928, 928, 930, 930, 929, ... 
Resampling results:

  RMSE      Rsquared    MAE     
  6.110514  0.01345758  3.298093

> 
> # Function for Root Mean Squared Error
> RMSE <- function(error) { sqrt(mean(error^2)) }
> RMSE(model1r1$residuals)
[1] 6.544913
> 

> #w/Ethnicity ### Still Overfitted
> model1r1 <- svyglm(HSCRP ~ relevel(Zinc, ref = "Inadequate Intake")* Carbohydrate + Gender+ Ethnicity+
+                      WBC + Choline +Folate +BMI , design = d612, family = gaussian(link='log'))
Warning message:
glm.fit: algorithm did not converge 
> 
> summ(model1r1, exp = TRUE,confint=TRUE, n.sd=2, digits= 6)
MODEL INFO:
Observations: 1032
Dependent Variable: HSCRP
Type: Analysis of complex survey design 
 Family: gaussian 
 Link function: log 

MODEL FIT:
Pseudo-R² (Cragg-Uhler) = 0.988993
Pseudo-R² (McFadden) = 0.124521
AIC = 7049.945111 

-----------------------------------------------------------------------------------------
                                  exp(Est.)       2.5%       97.5%      t val.          p
------------------------------- ----------- ---------- ----------- ----------- ----------
(Intercept)                        2.491078   0.588757   10.539949    1.240168   0.233963
relevel(Zinc, ref =                0.469113   0.247653    0.888610   -2.322298   0.034694
"Inadequate Intake")Adequate                                                             
Intake                                                                                   
CarbohydrateLow Intake             0.243907   0.099543    0.597639   -3.085750   0.007533
CarbohydrateModerate               1.048499   0.482257    2.279593    0.119520   0.906450
Intake                                                                                   
GenderMale                         2.196431   1.303835    3.700091    2.957040   0.009792
EthnicityBlack                     0.547516   0.369647    0.810974   -3.005290   0.008877
EthnicityMexican American          0.223486   0.123139    0.405606   -4.927271   0.000182
EthnicityOther Hispanic            0.145359   0.039905    0.529489   -2.924012   0.010472
EthnicityOther Race                0.197956   0.068421    0.572723   -2.988234   0.009190
EthnicityWhite                     0.434007   0.284359    0.662411   -3.869137   0.001514
WBC                                1.026099   0.996719    1.056345    1.738229   0.102649
Choline                            1.002929   1.001611    1.004248    4.360654   0.000559
Folate                             0.994023   0.991797    0.996253   -5.243498   0.000099
BMI                                1.062847   1.024199    1.102953    3.225229   0.005664
relevel(Zinc, ref =                3.229342   0.935614   11.146313    1.854671   0.083407
"Inadequate Intake")Adequate                                                             
Intake:CarbohydrateLow                                                                   
Intake                                                                                   
relevel(Zinc, ref =                3.090822   1.217521    7.846419    2.374032   0.031376
"Inadequate Intake")Adequate                                                             
Intake:CarbohydrateModerate                                                              
Intake                                                                                   
-----------------------------------------------------------------------------------------

Estimated dispersion parameter = 30.09762 
> 
> a1amd1p2qr <-  tbl_regression(model1r1,intercept= FALSE,add_estimate_to_reference_rows = TRUE
+                               , exponentiate = TRUE)%>%  bold_p(t= 0.05) %>%
+   modify_caption("**Table S.13: Analysis of the Coefficients for the Participants' CHO Intake 36- 50 Years Old** ")
> a1amd1p2qr
> 
> 
> # Fit Generalized linear regression model using caret
> modelpwa1 <- train( HSCRP ~ relevel(Zinc, ref = "Inadequate Intake")* Carbohydrate + Ethnicity+
+                       WBC + Choline +Folate +BMI+ Gender,
+                     subset13ams,
+                     method = "glm",
+                     trControl = trainControl(
+                       method = "cv",
+                       number = 10,
+                       verboseIter = T
+                     ))
+ Fold01: parameter=none 
- Fold01: parameter=none 
+ Fold02: parameter=none 
- Fold02: parameter=none 
+ Fold03: parameter=none 
- Fold03: parameter=none 
+ Fold04: parameter=none 
- Fold04: parameter=none 
+ Fold05: parameter=none 
- Fold05: parameter=none 
+ Fold06: parameter=none 
- Fold06: parameter=none 
+ Fold07: parameter=none 
- Fold07: parameter=none 
+ Fold08: parameter=none 
- Fold08: parameter=none 
+ Fold09: parameter=none 
- Fold09: parameter=none 
+ Fold10: parameter=none 
- Fold10: parameter=none 
Aggregating results
Fitting final model on full training set
> modelpwa1
Generalized Linear Model 

1032 samples
   8 predictor

No pre-processing
Resampling: Cross-Validated (10 fold) 
Summary of sample sizes: 929, 928, 930, 928, 929, 930, ... 
Resampling results:

  RMSE      Rsquared    MAE    
  6.107894  0.01212679  3.30054

> 
> # Function for Root Mean Squared Error
> RMSE <- function(error) { sqrt(mean(error^2)) }
> RMSE(model1r1$residuals)
[1] 1592.309

> ##################################################################################################################################
> ###Middle-Aged Adult
> #############################################################################################################################
> d52 <- subset(nhc2, Age_R > 50 & Age_R < 66)
> d62 <- na.omit(d52)
> model1amd1p23 <- svyglm(HSCRP ~ relevel(Zinc, ref = "Inadequate Intake")* relevel(Fasting, ref="Not Fasted") + Ethnicity+Gender+
+                           WBC + Choline +Folate  +BMI , design = d62, family = gaussian(link='log'))
> 
> 
> 
> summary(model1amd1,df= degf(d62))

Call:
svyglm(formula = HSCRP ~ Kcal * relevel(Zinc, ref = "Inadequate Intake") + 
    Ethnicity + Gender + WBC + Choline + Folate + BMI, design = d62, 
    family = gaussian(link = "log"))

Survey design:
subset(nhc2, Age_R > 50 & Age_R < 66)

Coefficients:
                                                                                    Estimate Std. Error t value Pr(>|t|)   
(Intercept)                                                                        0.7390857  0.6879291   1.074  0.29123   
KcalLow Calorie Diet                                                              -0.1266891  0.3512892  -0.361  0.72090   
KcalModerate Calorie Diet                                                          0.4494290  0.5207284   0.863  0.39494   
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake                            0.1326667  0.3487234   0.380  0.70630   
EthnicityBlack                                                                    -0.3579195  0.3927238  -0.911  0.36936   
EthnicityMexican American                                                         -0.5727805  0.2670603  -2.145  0.04019 * 
EthnicityOther Hispanic                                                           -0.2747293  0.2723118  -1.009  0.32110   
EthnicityOther Race                                                               -0.8284611  0.2435299  -3.402  0.00191 **
EthnicityWhite                                                                    -0.7301954  0.2816109  -2.593  0.01457 * 
GenderMale                                                                        -0.0324885  0.1660145  -0.196  0.84617   
WBC                                                                                0.0586708  0.0174597   3.360  0.00213 **
Choline                                                                            0.0005851  0.0006039   0.969  0.34040   
Folate                                                                            -0.0002149  0.0002858  -0.752  0.45791   
BMI                                                                                0.0088435  0.0168740   0.524  0.60407   
KcalLow Calorie Diet:relevel(Zinc, ref = "Inadequate Intake")Adequate Intake       0.5676169  0.4800938   1.182  0.24637   
KcalModerate Calorie Diet:relevel(Zinc, ref = "Inadequate Intake")Adequate Intake -0.2077218  0.5780845  -0.359  0.72187   
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

(Dispersion parameter for gaussian family taken to be 59.45438)

Number of Fisher Scoring iterations: 12

> confint(model1amd1,df=degf(d62))
                                                                                          2.5 %        97.5 %
(Intercept)                                                                       -0.7272006160  2.2053719219
KcalLow Calorie Diet                                                              -0.8754443003  0.6220661206
KcalModerate Calorie Diet                                                         -0.6604772368  1.5593351755
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake                           -0.6106194877  0.8759529655
EthnicityBlack                                                                    -1.1949904832  0.4791514233
EthnicityMexican American                                                         -1.1420060880 -0.0035549341
EthnicityOther Hispanic                                                           -0.8551481364  0.3056895181
EthnicityOther Race                                                               -1.3475329284 -0.3093893703
EthnicityWhite                                                                    -1.3304348500 -0.1299558974
GenderMale                                                                        -0.3863400756  0.3213630821
WBC                                                                                0.0214564216  0.0958851554
Choline                                                                           -0.0007021543  0.0018722637
Folate                                                                            -0.0008242005  0.0003943017
BMI                                                                               -0.0271224923  0.0448094913
KcalLow Calorie Diet:relevel(Zinc, ref = "Inadequate Intake")Adequate Intake      -0.4556788027  1.5909127010
KcalModerate Calorie Diet:relevel(Zinc, ref = "Inadequate Intake")Adequate Intake -1.4398797382  1.0244361151
> summ(model1amd1p23, exp = TRUE,confint=TRUE, n.sd=2, digits= 6)
MODEL INFO:
Observations: 1177
Dependent Variable: HSCRP
Type: Analysis of complex survey design 
 Family: gaussian 
 Link function: log 

MODEL FIT:
Pseudo-R² (Cragg-Uhler) = 0.874750
Pseudo-R² (McFadden) = 0.033794
AIC = 8846.345455 

----------------------------------------------------------------------------------------
                                  exp(Est.)       2.5%      97.5%      t val.          p
------------------------------- ----------- ---------- ---------- ----------- ----------
(Intercept)                        2.352311   0.705363   7.844710    1.391973   0.181875
relevel(Zinc, ref =                1.970541   0.912327   4.256183    1.726426   0.102397
"Inadequate Intake")Adequate                                                            
Intake                                                                                  
relevel(Fasting, ref = "Not        1.750749   0.965996   3.173020    1.845934   0.082390
Fasted")Fasted                                                                          
EthnicityBlack                     0.709257   0.298057   1.687750   -0.776670   0.448026
EthnicityMexican American          0.531698   0.317849   0.889425   -2.406355   0.027767
EthnicityOther Hispanic            0.669220   0.389972   1.148429   -1.457686   0.163153
EthnicityOther Race                0.410146   0.236663   0.710796   -3.176739   0.005517
EthnicityWhite                     0.453371   0.258574   0.794920   -2.761061   0.013355
GenderMale                         0.865131   0.552281   1.355202   -0.632648   0.535381
WBC                                1.065551   1.027536   1.104972    3.425498   0.003225
Choline                            1.000195   0.998930   1.001462    0.301955   0.766349
Folate                             0.999609   0.998729   1.000489   -0.870985   0.395896
BMI                                1.006120   0.972558   1.040841    0.352483   0.728808
relevel(Zinc, ref =                0.393221   0.150132   1.029915   -1.899963   0.074537
"Inadequate Intake")Adequate                                                            
Intake:relevel(Fasting, ref =                                                           
"Not Fasted")Fasted                                                                     
----------------------------------------------------------------------------------------

Estimated dispersion parameter = 59.44284 
> a1amd1p23 <-  tbl_regression(model1amd1p23,intercept= FALSE,add_estimate_to_reference_rows = TRUE
+                              , exponentiate = TRUE)%>%  bold_p(t= 0.05) %>%
+   modify_caption("**Table S.14: Analysis of the Coefficients for Participants 51- 65 Years Old, (Fasting)** ")
> a1amd1p23
> ###Investigate terms
> regTermTest(model1amd1p23 ,~ relevel(Zinc, ref = "Inadequate Intake"): relevel(Fasting, ref="Not Fasted"), method = "LRT")
Working (Rao-Scott+F) LRT for relevel(Zinc, ref = "Inadequate Intake"):relevel(Fasting, ref = "Not Fasted")
 in svyglm(formula = HSCRP ~ relevel(Zinc, ref = "Inadequate Intake") * 
    relevel(Fasting, ref = "Not Fasted") + Ethnicity + 
    Gender + WBC + Choline + Folate + BMI, design = d62, family = gaussian(link = "log"))
Working 2logLR =  2.993785 p= 0.10458 
df=1;  denominator df= 17
> regTermTest(model1amd1p23 ,~ relevel(Zinc, ref = "Inadequate Intake")* relevel(Fasting, ref="Not Fasted"), method = "LRT")
Working (Rao-Scott+F) LRT for relevel(Zinc, ref = "Inadequate Intake") relevel(Fasting, ref = "Not Fasted") relevel(Zinc, ref = "Inadequate Intake"):relevel(Fasting, ref = "Not Fasted")
 in svyglm(formula = HSCRP ~ relevel(Zinc, ref = "Inadequate Intake") * 
    relevel(Fasting, ref = "Not Fasted") + Ethnicity + 
    Gender + WBC + Choline + Folate + BMI, design = d62, family = gaussian(link = "log"))
Working 2logLR =  2.769745 p= 0.3968 
(scale factors:  2 0.8 0.19 );  denominator df= 17

> ###Checking for Overfitting
> # the caret library is loaded
> set.seed(123)
> 
> subset13amp <- subset(nhanes1, Age_R >50 & Age_R <66 )
> subset13amsp <- na.omit(subset13amp)
> 
> 
> # Fit Generalized linear regression model using caret
> modelpwp <- train( HSCRP ~ relevel(Zinc, ref = "Inadequate Intake")* relevel(Fasting, ref="Not Fasted") + Ethnicity+
+                     WBC + Choline +Folate +BMI+ Gender,
+                   subset13amsp,
+                   method = "glm",
+                   trControl = trainControl(
+                     method = "cv",
+                     number = 10,
+                     verboseIter = T
+                   ))
+ Fold01: parameter=none 
- Fold01: parameter=none 
+ Fold02: parameter=none 
- Fold02: parameter=none 
+ Fold03: parameter=none 
- Fold03: parameter=none 
+ Fold04: parameter=none 
- Fold04: parameter=none 
+ Fold05: parameter=none 
- Fold05: parameter=none 
+ Fold06: parameter=none 
- Fold06: parameter=none 
+ Fold07: parameter=none 
- Fold07: parameter=none 
+ Fold08: parameter=none 
- Fold08: parameter=none 
+ Fold09: parameter=none 
- Fold09: parameter=none 
+ Fold10: parameter=none 
- Fold10: parameter=none 
Aggregating results
Fitting final model on full training set
> modelpwp
Generalized Linear Model 

1177 samples
   8 predictor

No pre-processing
Resampling: Cross-Validated (10 fold) 
Summary of sample sizes: 1057, 1058, 1061, 1060, 1060, 1059, ... 
Resampling results:

  RMSE      Rsquared    MAE     
  6.486674  0.03347759  3.403047

> 
> # Function for Root Mean Squared Error
> RMSE <- function(error) { sqrt(mean(error^2)) }
> RMSE(model1amd1p23$residuals)
[1] 2.34234
> ###Remove Ethnicity
> 
> model1amd1p23 <- svyglm(HSCRP ~ relevel(Zinc, ref = "Inadequate Intake")* relevel(Fasting, ref="Not Fasted") + Gender+
+                           WBC + Choline +Folate  +BMI , design = d62, family = gaussian(link='log'))
> 
> 
> 
> summary(model1amd1,df= degf(d62))

Call:
svyglm(formula = HSCRP ~ Kcal * relevel(Zinc, ref = "Inadequate Intake") + 
    Ethnicity + Gender + WBC + Choline + Folate + BMI, design = d62, 
    family = gaussian(link = "log"))

Survey design:
subset(nhc2, Age_R > 50 & Age_R < 66)

Coefficients:
                                                                                    Estimate Std. Error t value Pr(>|t|)   
(Intercept)                                                                        0.7390857  0.6879291   1.074  0.29123   
KcalLow Calorie Diet                                                              -0.1266891  0.3512892  -0.361  0.72090   
KcalModerate Calorie Diet                                                          0.4494290  0.5207284   0.863  0.39494   
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake                            0.1326667  0.3487234   0.380  0.70630   
EthnicityBlack                                                                    -0.3579195  0.3927238  -0.911  0.36936   
EthnicityMexican American                                                         -0.5727805  0.2670603  -2.145  0.04019 * 
EthnicityOther Hispanic                                                           -0.2747293  0.2723118  -1.009  0.32110   
EthnicityOther Race                                                               -0.8284611  0.2435299  -3.402  0.00191 **
EthnicityWhite                                                                    -0.7301954  0.2816109  -2.593  0.01457 * 
GenderMale                                                                        -0.0324885  0.1660145  -0.196  0.84617   
WBC                                                                                0.0586708  0.0174597   3.360  0.00213 **
Choline                                                                            0.0005851  0.0006039   0.969  0.34040   
Folate                                                                            -0.0002149  0.0002858  -0.752  0.45791   
BMI                                                                                0.0088435  0.0168740   0.524  0.60407   
KcalLow Calorie Diet:relevel(Zinc, ref = "Inadequate Intake")Adequate Intake       0.5676169  0.4800938   1.182  0.24637   
KcalModerate Calorie Diet:relevel(Zinc, ref = "Inadequate Intake")Adequate Intake -0.2077218  0.5780845  -0.359  0.72187   
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

(Dispersion parameter for gaussian family taken to be 59.45438)

Number of Fisher Scoring iterations: 12

> confint(model1amd1,df=degf(d62))
                                                                                          2.5 %        97.5 %
(Intercept)                                                                       -0.7272006160  2.2053719219
KcalLow Calorie Diet                                                              -0.8754443003  0.6220661206
KcalModerate Calorie Diet                                                         -0.6604772368  1.5593351755
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake                           -0.6106194877  0.8759529655
EthnicityBlack                                                                    -1.1949904832  0.4791514233
EthnicityMexican American                                                         -1.1420060880 -0.0035549341
EthnicityOther Hispanic                                                           -0.8551481364  0.3056895181
EthnicityOther Race                                                               -1.3475329284 -0.3093893703
EthnicityWhite                                                                    -1.3304348500 -0.1299558974
GenderMale                                                                        -0.3863400756  0.3213630821
WBC                                                                                0.0214564216  0.0958851554
Choline                                                                           -0.0007021543  0.0018722637
Folate                                                                            -0.0008242005  0.0003943017
BMI                                                                               -0.0271224923  0.0448094913
KcalLow Calorie Diet:relevel(Zinc, ref = "Inadequate Intake")Adequate Intake      -0.4556788027  1.5909127010
KcalModerate Calorie Diet:relevel(Zinc, ref = "Inadequate Intake")Adequate Intake -1.4398797382  1.0244361151
> summ(model1amd1p23, exp = TRUE,confint=TRUE, n.sd=2, digits= 6)
MODEL INFO:
Observations: 1177
Dependent Variable: HSCRP
Type: Analysis of complex survey design 
 Family: gaussian 
 Link function: log 

MODEL FIT:
Pseudo-R² (Cragg-Uhler) = 0.700683
Pseudo-R² (McFadden) = 0.019622
AIC = 8853.483754 

----------------------------------------------------------------------------------------
                                  exp(Est.)       2.5%      97.5%      t val.          p
------------------------------- ----------- ---------- ---------- ----------- ----------
(Intercept)                        1.680615   0.628004   4.497532    1.033693   0.312510
relevel(Zinc, ref =                1.700435   0.834068   3.466719    1.460730   0.158225
"Inadequate Intake")Adequate                                                            
Intake                                                                                  
relevel(Fasting, ref = "Not        1.533331   0.897558   2.619444    1.564408   0.131993
Fasted")Fasted                                                                          
GenderMale                         0.927993   0.609084   1.413880   -0.347853   0.731257
WBC                                1.051012   1.018351   1.084721    3.088971   0.005362
Choline                            0.999923   0.998909   1.000937   -0.149721   0.882349
Folate                             0.999713   0.998980   1.000448   -0.765244   0.452258
BMI                                1.008541   0.976845   1.041266    0.522029   0.606867
relevel(Zinc, ref =                0.569136   0.246110   1.316146   -1.317724   0.201154
"Inadequate Intake")Adequate                                                            
Intake:relevel(Fasting, ref =                                                           
"Not Fasted")Fasted                                                                     
----------------------------------------------------------------------------------------

Estimated dispersion parameter = 60.31622 
> ###Investigate terms
> regTermTest(model1amd1p23 ,~ relevel(Zinc, ref = "Inadequate Intake"): relevel(Fasting, ref="Not Fasted"), method = "LRT")
Working (Rao-Scott+F) LRT for relevel(Zinc, ref = "Inadequate Intake"):relevel(Fasting, ref = "Not Fasted")
 in svyglm(formula = HSCRP ~ relevel(Zinc, ref = "Inadequate Intake") * 
    relevel(Fasting, ref = "Not Fasted") + Gender + WBC + 
    Choline + Folate + BMI, design = d62, family = gaussian(link = "log"))
Working 2logLR =  1.647856 p= 0.21563 
df=1;  denominator df= 22
> regTermTest(model1amd1p23 ,~ relevel(Zinc, ref = "Inadequate Intake")* relevel(Fasting, ref="Not Fasted"), method = "LRT")
Working (Rao-Scott+F) LRT for relevel(Zinc, ref = "Inadequate Intake") relevel(Fasting, ref = "Not Fasted") relevel(Zinc, ref = "Inadequate Intake"):relevel(Fasting, ref = "Not Fasted")
 in svyglm(formula = HSCRP ~ relevel(Zinc, ref = "Inadequate Intake") * 
    relevel(Fasting, ref = "Not Fasted") + Gender + WBC + 
    Choline + Folate + BMI, design = d62, family = gaussian(link = "log"))
Working 2logLR =  2.328964 p= 0.46753 
(scale factors:  1.9 0.79 0.34 );  denominator df= 22

+ ###Checking for Overfitting
+ # the caret library is loaded
+ set.seed(123)
Error: unexpected symbol in:
"# the caret library is loaded
set.seed"
> 
> subset13amp <- subset(nhanes1, Age_R >50 & Age_R <66 )
> subset13amsp <- na.omit(subset13amp)
> 
> 
> # Fit Generalized linear regression model using caret
> modelpwp <- train( HSCRP ~ relevel(Zinc, ref = "Inadequate Intake")* relevel(Fasting, ref="Not Fasted") + 
+                      WBC + Choline +Folate +BMI+ Gender,
+                    subset13amsp,
+                    method = "glm",
+                    trControl = trainControl(
+                      method = "cv",
+                      number = 10,
+                      verboseIter = T
+                    ))
+ Fold01: parameter=none 
- Fold01: parameter=none 
+ Fold02: parameter=none 
- Fold02: parameter=none 
+ Fold03: parameter=none 
- Fold03: parameter=none 
+ Fold04: parameter=none 
- Fold04: parameter=none 
+ Fold05: parameter=none 
- Fold05: parameter=none 
+ Fold06: parameter=none 
- Fold06: parameter=none 
+ Fold07: parameter=none 
- Fold07: parameter=none 
+ Fold08: parameter=none 
- Fold08: parameter=none 
+ Fold09: parameter=none 
- Fold09: parameter=none 
+ Fold10: parameter=none 
- Fold10: parameter=none 
Aggregating results
Fitting final model on full training set
> modelpwp
Generalized Linear Model 

1177 samples
   7 predictor

No pre-processing
Resampling: Cross-Validated (10 fold) 
Summary of sample sizes: 1060, 1061, 1059, 1059, 1060, 1059, ... 
Resampling results:

  RMSE      Rsquared    MAE     
  6.503545  0.03639044  3.384816

> 
> # Function for Root Mean Squared Error
> RMSE <- function(error) { sqrt(mean(error^2)) }
> RMSE(model1amd1p23$residuals)
[1] 1.85546
<
> ####Kcal
> ##Not sign
> 
> model1amd1 <- svyglm(HSCRP ~ relevel(Zinc, ref = "Inadequate Intake")* Kcal + Ethnicity+Gender+
+                          WBC + Choline +Folate +BMI, design = d62, family = gaussian(link='log'))
> 
> 
> 
> summary(model1amd1,df= degf(d62))

Call:
svyglm(formula = HSCRP ~ relevel(Zinc, ref = "Inadequate Intake") * 
    Kcal + Ethnicity + Gender + WBC + Choline + Folate + BMI, 
    design = d62, family = gaussian(link = "log"))

Survey design:
subset(nhc2, Age_R > 50 & Age_R < 66)

Coefficients:
                                                                                    Estimate Std. Error t value
(Intercept)                                                                        0.7390857  0.6879291   1.074
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake                            0.1326667  0.3487234   0.380
KcalLow Calorie Diet                                                              -0.1266891  0.3512892  -0.361
KcalModerate Calorie Diet                                                          0.4494290  0.5207284   0.863
EthnicityBlack                                                                    -0.3579195  0.3927238  -0.911
EthnicityMexican American                                                         -0.5727805  0.2670603  -2.145
EthnicityOther Hispanic                                                           -0.2747293  0.2723118  -1.009
EthnicityOther Race                                                               -0.8284611  0.2435299  -3.402
EthnicityWhite                                                                    -0.7301954  0.2816109  -2.593
GenderMale                                                                        -0.0324885  0.1660145  -0.196
WBC                                                                                0.0586708  0.0174597   3.360
Choline                                                                            0.0005851  0.0006039   0.969
Folate                                                                            -0.0002149  0.0002858  -0.752
BMI                                                                                0.0088435  0.0168740   0.524
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:KcalLow Calorie Diet       0.5676169  0.4800938   1.182
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:KcalModerate Calorie Diet -0.2077218  0.5780845  -0.359
                                                                                  Pr(>|t|)   
(Intercept)                                                                        0.29123   
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake                            0.70630   
KcalLow Calorie Diet                                                               0.72090   
KcalModerate Calorie Diet                                                          0.39494   
EthnicityBlack                                                                     0.36936   
EthnicityMexican American                                                          0.04019 * 
EthnicityOther Hispanic                                                            0.32110   
EthnicityOther Race                                                                0.00191 **
EthnicityWhite                                                                     0.01457 * 
GenderMale                                                                         0.84617   
WBC                                                                                0.00213 **
Choline                                                                            0.34040   
Folate                                                                             0.45791   
BMI                                                                                0.60407   
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:KcalLow Calorie Diet       0.24637   
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:KcalModerate Calorie Diet  0.72187   
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

(Dispersion parameter for gaussian family taken to be 59.45438)

Number of Fisher Scoring iterations: 12

> confint(model1amd1,df=degf(d62))
                                                                                          2.5 %        97.5 %
(Intercept)                                                                       -0.7272006160  2.2053719219
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake                           -0.6106194877  0.8759529655
KcalLow Calorie Diet                                                              -0.8754443003  0.6220661206
KcalModerate Calorie Diet                                                         -0.6604772368  1.5593351755
EthnicityBlack                                                                    -1.1949904832  0.4791514233
EthnicityMexican American                                                         -1.1420060880 -0.0035549341
EthnicityOther Hispanic                                                           -0.8551481364  0.3056895181
EthnicityOther Race                                                               -1.3475329284 -0.3093893703
EthnicityWhite                                                                    -1.3304348500 -0.1299558974
GenderMale                                                                        -0.3863400756  0.3213630821
WBC                                                                                0.0214564216  0.0958851554
Choline                                                                           -0.0007021543  0.0018722637
Folate                                                                            -0.0008242005  0.0003943017
BMI                                                                               -0.0271224923  0.0448094913
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:KcalLow Calorie Diet      -0.4556788027  1.5909127010
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:KcalModerate Calorie Diet -1.4398797382  1.0244361151
> summ(model1amd1, exp = TRUE,confint=TRUE, n.sd=2, digits= 6)
MODEL INFO:
Observations: 1177
Dependent Variable: HSCRP
Type: Analysis of complex survey design 
 Family: gaussian 
 Link function: log 

MODEL FIT:
Pseudo-R² (Cragg-Uhler) = 0.873705
Pseudo-R² (McFadden) = 0.033659
AIC = 8850.510030 

----------------------------------------------------------------------------------------
                                  exp(Est.)       2.5%      97.5%      t val.          p
------------------------------- ----------- ---------- ---------- ----------- ----------
(Intercept)                        2.094020   0.543769   8.063938    1.074363   0.299639
relevel(Zinc, ref =                1.141869   0.576478   2.261780    0.380435   0.708955
"Inadequate Intake")Adequate                                                            
Intake                                                                                  
KcalLow Calorie Diet               0.881008   0.442549   1.753871   -0.360640   0.723397
KcalModerate Calorie Diet          1.567417   0.564859   4.349399    0.863078   0.401684
EthnicityBlack                     0.699129   0.323795   1.509540   -0.911377   0.376511
EthnicityMexican American          0.563955   0.334135   0.951846   -2.144761   0.048756
EthnicityOther Hispanic            0.759778   0.445548   1.295623   -1.008878   0.329032
EthnicityOther Race                0.436721   0.270964   0.703877   -3.401886   0.003942
EthnicityWhite                     0.481815   0.277442   0.836735   -2.592923   0.020384
GenderMale                         0.968034   0.699163   1.340301   -0.195697   0.847474
WBC                                1.060426   1.024752   1.097342    3.360364   0.004293
Choline                            1.000585   0.999402   1.001770    0.968774   0.348020
Folate                             0.999785   0.999225   1.000345   -0.751995   0.463691
BMI                                1.008883   0.976062   1.042807    0.524092   0.607873
relevel(Zinc, ref =                1.764058   0.688424   4.520323    1.182304   0.255488
"Inadequate Intake")Adequate                                                            
Intake:KcalLow Calorie Diet                                                             
relevel(Zinc, ref =                0.812433   0.261650   2.522632   -0.359328   0.724358
"Inadequate Intake")Adequate                                                            
Intake:KcalModerate Calorie                                                             
Diet                                                                                    
----------------------------------------------------------------------------------------

Estimated dispersion parameter = 59.45438 
> 
> a1amd1p2 <-  tbl_regression(model1amd1,intercept= FALSE,add_estimate_to_reference_rows = TRUE
+                             , exponentiate = TRUE)%>%  bold_p(t= 0.05) %>%
+   modify_caption("**Table S.16: Analysis of the Coefficients for the Participants' Energy Intake 51- 65 Years Old** ")
> a1amd1p2
> ###Investigate terms
> regTermTest(model1amd1 , ~relevel(Zinc, ref = "Inadequate Intake")* Kcal, method = "LRT")
Working (Rao-Scott+F) LRT for relevel(Zinc, ref = "Inadequate Intake") Kcal relevel(Zinc, ref = "Inadequate Intake"):Kcal
 in svyglm(formula = HSCRP ~ relevel(Zinc, ref = "Inadequate Intake") * 
    Kcal + Ethnicity + Gender + WBC + Choline + Folate + BMI, 
    design = d62, family = gaussian(link = "log"))
Working 2logLR =  3.648622 p= 0.53893 
(scale factors:  2.4 1.6 0.64 0.27 0.15 );  denominator df= 15
> regTermTest(model1amd1 , ~relevel(Zinc, ref = "Inadequate Intake")* Kcal, method = "LRT")
Working (Rao-Scott+F) LRT for relevel(Zinc, ref = "Inadequate Intake") Kcal relevel(Zinc, ref = "Inadequate Intake"):Kcal
 in svyglm(formula = HSCRP ~ relevel(Zinc, ref = "Inadequate Intake") * 
    Kcal + Ethnicity + Gender + WBC + Choline + Folate + BMI, 
    design = d62, family = gaussian(link = "log"))
Working 2logLR =  3.648622 p= 0.53893 
(scale factors:  2.4 1.6 0.64 0.27 0.15 );  denominator df= 15
> ### Overfitting
> subset13amp <- subset(nhanes1, Age_R >50 & Age_R <66 )
> subset13amsp <- na.omit(subset13amp)
> 
> 
> # Fit Generalized linear regression model using caret
> modelpwp4 <- train( HSCRP ~ relevel(Zinc, ref = "Inadequate Intake")* Kcal + Ethnicity+
+                      WBC + Choline +Folate +BMI+ Gender,
+                    subset13amsp,
+                    method = "glm",
+                    trControl = trainControl(
+                      method = "cv",
+                      number = 10,
+                      verboseIter = T
+                    ))
+ Fold01: parameter=none 
- Fold01: parameter=none 
+ Fold02: parameter=none 
- Fold02: parameter=none 
+ Fold03: parameter=none 
- Fold03: parameter=none 
+ Fold04: parameter=none 
- Fold04: parameter=none 
+ Fold05: parameter=none 
- Fold05: parameter=none 
+ Fold06: parameter=none 
- Fold06: parameter=none 
+ Fold07: parameter=none 
- Fold07: parameter=none 
+ Fold08: parameter=none 
- Fold08: parameter=none 
+ Fold09: parameter=none 
- Fold09: parameter=none 
+ Fold10: parameter=none 
- Fold10: parameter=none 
Aggregating results
Fitting final model on full training set
> modelpwp4
Generalized Linear Model 

1177 samples
   8 predictor

No pre-processing
Resampling: Cross-Validated (10 fold) 
Summary of sample sizes: 1059, 1059, 1060, 1060, 1058, 1060, ... 
Resampling results:

  RMSE      Rsquared    MAE     
  6.538448  0.01762647  3.436587

> 
> # Function for Root Mean Squared Error
> RMSE <- function(error) { sqrt(mean(error^2)) }
> RMSE(model1amd1$residuals)
[1] 2.218652

> ##w/out Ethnicity
> model1amd1 <- svyglm(HSCRP ~ relevel(Zinc, ref = "Inadequate Intake")* Kcal +Gender+
+                        WBC + Choline +Folate +BMI, design = d62, family = gaussian(link='log'))
> 
> 
> 
> summary(model1amd1,df= degf(d62))

Call:
svyglm(formula = HSCRP ~ relevel(Zinc, ref = "Inadequate Intake") * 
    Kcal + Gender + WBC + Choline + Folate + BMI, design = d62, 
    family = gaussian(link = "log"))

Survey design:
subset(nhc2, Age_R > 50 & Age_R < 66)

Coefficients:
                                                                                    Estimate Std. Error t value Pr(>|t|)   
(Intercept)                                                                        0.6343429  0.5489648   1.156  0.25700   
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake                            0.1619608  0.3359513   0.482  0.63324   
KcalLow Calorie Diet                                                              -0.1469556  0.3275514  -0.449  0.65691   
KcalModerate Calorie Diet                                                          0.2687742  0.4569002   0.588  0.56076   
GenderMale                                                                        -0.0514285  0.1743660  -0.295  0.77007   
WBC                                                                                0.0476318  0.0161966   2.941  0.00625 **
Choline                                                                            0.0001185  0.0004808   0.247  0.80695   
Folate                                                                            -0.0002337  0.0003360  -0.695  0.49217   
BMI                                                                                0.0083677  0.0154515   0.542  0.59213   
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:KcalLow Calorie Diet       0.3936935  0.3948894   0.997  0.32675   
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:KcalModerate Calorie Diet -0.0891227  0.5372333  -0.166  0.86935   
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

(Dispersion parameter for gaussian family taken to be 60.28289)

Number of Fisher Scoring iterations: 11

> confint(model1amd1,df=degf(d62))
                                                                                          2.5 %       97.5 %
(Intercept)                                                                       -0.5107776034 1.7794634531
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake                           -0.5388214115 0.8627429544
KcalLow Calorie Diet                                                              -0.8302157958 0.5363046023
KcalModerate Calorie Diet                                                         -0.6843028599 1.2218513377
GenderMale                                                                        -0.4151496915 0.3122926963
WBC                                                                                0.0138462696 0.0814173084
Choline                                                                           -0.0008844030 0.0011214631
Folate                                                                            -0.0009346362 0.0004672853
BMI                                                                               -0.0238636163 0.0405990773
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:KcalLow Calorie Diet      -0.4300313606 1.2174183991
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:KcalModerate Calorie Diet -1.2097716265 1.0315262445
> summ(model1amd1, exp = TRUE,confint=TRUE, n.sd=2, digits= 6)
MODEL INFO:
Observations: 1177
Dependent Variable: HSCRP
Type: Analysis of complex survey design 
 Family: gaussian 
 Link function: log 

MODEL FIT:
Pseudo-R² (Cragg-Uhler) = 0.710448
Pseudo-R² (McFadden) = 0.020162
AIC = 8856.835782 

----------------------------------------------------------------------------------------
                                  exp(Est.)       2.5%      97.5%      t val.          p
------------------------------- ----------- ---------- ---------- ----------- ----------
(Intercept)                        1.885783   0.643001   5.530588    1.155526   0.261494
relevel(Zinc, ref =                1.175814   0.608662   2.271438    0.482096   0.634972
"Inadequate Intake")Adequate                                                            
Intake                                                                                  
KcalLow Calorie Diet               0.863332   0.454324   1.640553   -0.448649   0.658508
KcalModerate Calorie Diet          1.308360   0.534334   3.203622    0.588256   0.562945
GenderMale                         0.949872   0.674907   1.336859   -0.294946   0.771075
WBC                                1.048784   1.016014   1.082612    2.940851   0.008081
Choline                            1.000119   0.999177   1.001061    0.246526   0.807787
Folate                             0.999766   0.999108   1.000425   -0.695386   0.494814
BMI                                1.008403   0.978322   1.039409    0.541547   0.594113
relevel(Zinc, ref =                1.482446   0.683673   3.214470    0.996972   0.330688
"Inadequate Intake")Adequate                                                            
Intake:KcalLow Calorie Diet                                                             
relevel(Zinc, ref =                0.914733   0.319154   2.621732   -0.165892   0.869907
"Inadequate Intake")Adequate                                                            
Intake:KcalModerate Calorie                                                             
Diet                                                                                    
----------------------------------------------------------------------------------------

Estimated dispersion parameter = 60.28289 
> 
> a1amd1p2 <-  tbl_regression(model1amd1,intercept= FALSE,add_estimate_to_reference_rows = TRUE
+                             , exponentiate = TRUE)%>%  bold_p(t= 0.05) %>%
+   modify_caption("**Table S.16: Analysis of the Coefficients for the Participants' Energy Intake 51- 65 Years Old** ")
> a1amd1p2
> ###Investigate terms
> regTermTest(model1amd1 , ~relevel(Zinc, ref = "Inadequate Intake")* Kcal, method = "LRT")
Working (Rao-Scott+F) LRT for relevel(Zinc, ref = "Inadequate Intake") Kcal relevel(Zinc, ref = "Inadequate Intake"):Kcal
 in svyglm(formula = HSCRP ~ relevel(Zinc, ref = "Inadequate Intake") * 
    Kcal + Gender + WBC + Choline + Folate + BMI, design = d62, 
    family = gaussian(link = "log"))
Working 2logLR =  3.176345 p= 0.60412 
(scale factors:  2.3 1.5 0.63 0.43 0.17 );  denominator df= 20
> regTermTest(model1amd1 , ~relevel(Zinc, ref = "Inadequate Intake")* Kcal, method = "LRT")
Working (Rao-Scott+F) LRT for relevel(Zinc, ref = "Inadequate Intake") Kcal relevel(Zinc, ref = "Inadequate Intake"):Kcal
 in svyglm(formula = HSCRP ~ relevel(Zinc, ref = "Inadequate Intake") * 
    Kcal + Gender + WBC + Choline + Folate + BMI, design = d62, 
    family = gaussian(link = "log"))
Working 2logLR =  3.176345 p= 0.60412 
(scale factors:  2.3 1.5 0.63 0.43 0.17 );  denominator df= 20
> # Fit Generalized linear regression model using caret
> modelpwp4 <- train( HSCRP ~ relevel(Zinc, ref = "Inadequate Intake")* Kcal +
+                       WBC + Choline +Folate +BMI+ Gender,
+                     subset13amsp,
+                     method = "glm",
+                     trControl = trainControl(
+                       method = "cv",
+                       number = 10,
+                       verboseIter = T
+                     ))
+ Fold01: parameter=none 
- Fold01: parameter=none 
+ Fold02: parameter=none 
- Fold02: parameter=none 
+ Fold03: parameter=none 
- Fold03: parameter=none 
+ Fold04: parameter=none 
- Fold04: parameter=none 
+ Fold05: parameter=none 
- Fold05: parameter=none 
+ Fold06: parameter=none 
- Fold06: parameter=none 
+ Fold07: parameter=none 
- Fold07: parameter=none 
+ Fold08: parameter=none 
- Fold08: parameter=none 
+ Fold09: parameter=none 
- Fold09: parameter=none 
+ Fold10: parameter=none 
- Fold10: parameter=none 
Aggregating results
Fitting final model on full training set
> modelpwp4
Generalized Linear Model 

1177 samples
   7 predictor

No pre-processing
Resampling: Cross-Validated (10 fold) 
Summary of sample sizes: 1060, 1057, 1059, 1060, 1058, 1060, ... 
Resampling results:

  RMSE      Rsquared    MAE     
  6.499069  0.02786072  3.403986

> 
> # Function for Root Mean Squared Error
> RMSE <- function(error) { sqrt(mean(error^2)) }
> RMSE(model1amd1$residuals)
[1] 1.877942

> #############################################
> ####CHO
> 
> ### Overfitted with Ethnicity
> 
> model2p <- svyglm(HSCRP ~ relevel(Zinc, ref = "Inadequate Intake")* Carbohydrate+Gender+
+                          WBC + Choline +Folate +BMI+ Ethnicity, design = d62, family = gaussian(link='log'))
Warning message:
glm.fit: algorithm did not converge 
> 
> 
> 
> summary(model2p,df= degf(d62))

Call:
svyglm(formula = HSCRP ~ relevel(Zinc, ref = "Inadequate Intake") * 
    Carbohydrate + Gender + WBC + Choline + Folate + BMI + Ethnicity, 
    design = d62, family = gaussian(link = "log"))

Survey design:
subset(nhc2, Age_R > 50 & Age_R < 66)

Coefficients:
                                                                                      Estimate Std. Error t value Pr(>|t|)    
(Intercept)                                                                         -1.592e+01  3.026e+00  -5.260 1.12e-05 ***
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake                             -6.436e+00  8.256e-01  -7.795 1.07e-08 ***
CarbohydrateLow Intake                                                              -1.463e+00  6.150e-01  -2.379  0.02390 *  
CarbohydrateModerate Intake                                                          1.698e+00  9.767e-01   1.739  0.09236 .  
GenderMale                                                                          -5.052e-01  4.273e-01  -1.182  0.24643    
WBC                                                                                  1.191e+00  1.501e-01   7.935 7.42e-09 ***
Choline                                                                             -5.605e-04  1.283e-03  -0.437  0.66530    
Folate                                                                               5.369e-03  1.128e-03   4.758 4.61e-05 ***
BMI                                                                                 -4.197e-02  4.809e-02  -0.873  0.38976    
EthnicityBlack                                                                       9.683e-01  3.113e-01   3.111  0.00407 ** 
EthnicityMexican American                                                           -1.915e+00  3.924e-01  -4.880 3.27e-05 ***
EthnicityOther Hispanic                                                             -8.765e+00  1.685e+00  -5.201 1.32e-05 ***
EthnicityOther Race                                                                  3.062e-01  4.901e-01   0.625  0.53685    
EthnicityWhite                                                                      -3.075e+01  3.835e+00  -8.017 6.00e-09 ***
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:CarbohydrateLow Intake       1.513e+01  1.676e+00   9.028 4.68e-10 ***
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:CarbohydrateModerate Intake  8.026e+00  8.549e-01   9.388 1.95e-10 ***
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

(Dispersion parameter for gaussian family taken to be 35.33817)

Number of Fisher Scoring iterations: 25

> confint(model2p,df=degf(d62))
                                                                                            2.5 %        97.5 %
(Intercept)                                                                         -22.365466157  -9.466434783
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake                              -8.195453610  -4.675841444
CarbohydrateLow Intake                                                               -2.774096823  -0.152443923
CarbohydrateModerate Intake                                                          -0.383726243   3.780037505
GenderMale                                                                           -1.415954053   0.405647869
WBC                                                                                   0.870997457   1.510812940
Choline                                                                              -0.003294686   0.002173727
Folate                                                                                0.002964148   0.007774486
BMI                                                                                  -0.144483149   0.060539523
EthnicityBlack                                                                        0.304786486   1.631822800
EthnicityMexican American                                                            -2.751010746  -1.078458023
EthnicityOther Hispanic                                                             -12.356366682  -5.172693972
EthnicityOther Race                                                                  -0.738490869   1.350929514
EthnicityWhite                                                                      -38.921654191 -22.572398880
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:CarbohydrateLow Intake       11.560540893  18.705863541
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:CarbohydrateModerate Intake   6.203798505   9.848229302
> summ(model2p, exp = TRUE,confint=TRUE, n.sd=2, digits= 6)
MODEL INFO:
Observations: 1177
Dependent Variable: HSCRP
Type: Analysis of complex survey design 
 Family: gaussian 
 Link function: log 

MODEL FIT:
Pseudo-R² (Cragg-Uhler) = 1.000000
Pseudo-R² (McFadden) = 0.262853
AIC = 8531.860956 

---------------------------------------------------------------------------------------------------------
                                       exp(Est.)            2.5%             97.5%      t val.          p
------------------------------- ---------------- --------------- ----------------- ----------- ----------
(Intercept)                             0.000000        0.000000          0.000046   -5.259937   0.000096
relevel(Zinc, ref =                     0.001603        0.000318          0.008088   -7.794755   0.000001
"Inadequate Intake")Adequate                                                                             
Intake                                                                                                   
CarbohydrateLow Intake                  0.231478        0.069347          0.772668   -2.379329   0.031053
CarbohydrateModerate                    5.463861        0.805551         37.060062    1.738587   0.102584
Intake                                                                                                   
GenderMale                              0.603413        0.261146          1.394268   -1.182155   0.255546
WBC                                     3.290058        2.451587          4.415296    7.934645   0.000001
Choline                                 0.999440        0.996930          1.001956   -0.436922   0.668393
Folate                                  1.005384        1.003163          1.007610    4.758264   0.000254
BMI                                     0.958897        0.872637          1.053683   -0.872692   0.396586
EthnicityBlack                          2.633476        1.430708          4.847386    3.110529   0.007162
EthnicityMexican American               0.147381        0.068308          0.317988   -4.880157   0.000200
EthnicityOther Hispanic                 0.000156        0.000006          0.004246   -5.201004   0.000108
EthnicityOther Race                     1.358280        0.519734          3.549751    0.624758   0.541517
EthnicityWhite                          0.000000        0.000000          0.000000   -8.016969   0.000001
relevel(Zinc, ref =               3734790.249548   139801.523186   99774722.694260    9.028468   0.000000
"Inadequate Intake")Adequate                                                                             
Intake:CarbohydrateLow                                                                                   
Intake                                                                                                   
relevel(Zinc, ref =                  3059.521786      572.724423      16344.114527    9.388047   0.000000
"Inadequate Intake")Adequate                                                                             
Intake:CarbohydrateModerate                                                                              
Intake                                                                                                   
---------------------------------------------------------------------------------------------------------

Estimated dispersion parameter = 35.33817 
> 
> a1amd1p24 <-  tbl_regression(model2p,intercept= FALSE,add_estimate_to_reference_rows = TRUE
+                             , exponentiate = TRUE)%>%  bold_p(t= 0.05) %>%
+   modify_caption("**Table S.8: Analysis of the Coefficients for the Participants' CHO Intake 51- 65 Years Old** ")
> a1amd1p24
> 
> ### Overfitting
> subset13amp <- subset(nhanes1, Age_R >50 & Age_R <66 )
> subset13amsp <- na.omit(subset13amp)
> 
> 
> # Fit Generalized linear regression model using caret
> modelpwp41 <- train( HSCRP ~ relevel(Zinc, ref = "Inadequate Intake")* Carbohydrate +Ethnicity+
+                        WBC + Choline +Folate +BMI+ Gender,
+                      subset13amsp,
+                      method = "glm",
+                      trControl = trainControl(
+                        method = "cv",
+                        number = 10,
+                        verboseIter = T
+                      ))
+ Fold01: parameter=none 
- Fold01: parameter=none 
+ Fold02: parameter=none 
- Fold02: parameter=none 
+ Fold03: parameter=none 
- Fold03: parameter=none 
+ Fold04: parameter=none 
- Fold04: parameter=none 
+ Fold05: parameter=none 
- Fold05: parameter=none 
+ Fold06: parameter=none 
- Fold06: parameter=none 
+ Fold07: parameter=none 
- Fold07: parameter=none 
+ Fold08: parameter=none 
- Fold08: parameter=none 
+ Fold09: parameter=none 
- Fold09: parameter=none 
+ Fold10: parameter=none 
- Fold10: parameter=none 
Aggregating results
Fitting final model on full training set
> modelpwp41
Generalized Linear Model 

1177 samples
   8 predictor

No pre-processing
Resampling: Cross-Validated (10 fold) 
Summary of sample sizes: 1059, 1057, 1059, 1059, 1060, 1060, ... 
Resampling results:

  RMSE      Rsquared    MAE     
  6.631678  0.01890985  3.440605

> 
> 
> # Function for Root Mean Squared Error
> RMSE <- function(error) { sqrt(mean(error^2)) }
> RMSE(model2p$residuals)
[1] 1.463483e+16
> 
> 
> ### Remove ethnicity
> model2p <- svyglm(HSCRP ~ relevel(Zinc, ref = "Inadequate Intake")* Carbohydrate+Gender+
+                     WBC + Choline +Folate +BMI, design = d62, family = gaussian(link='log'))
> 
> 
> 
> summary(model2p,df= degf(d62))

Call:
svyglm(formula = HSCRP ~ relevel(Zinc, ref = "Inadequate Intake") * 
    Carbohydrate + Gender + WBC + Choline + Folate + BMI, design = d62, 
    family = gaussian(link = "log"))

Survey design:
subset(nhc2, Age_R > 50 & Age_R < 66)

Coefficients:
                                                                                      Estimate Std. Error t value Pr(>|t|)   
(Intercept)                                                                          6.625e-01  3.853e-01   1.719  0.09583 . 
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake                              1.222e-01  2.291e-01   0.533  0.59783   
CarbohydrateLow Intake                                                              -5.706e-01  2.441e-01  -2.338  0.02627 * 
CarbohydrateModerate Intake                                                          1.641e-01  2.797e-01   0.587  0.56176   
GenderMale                                                                          -2.045e-01  3.234e-01  -0.632  0.53197   
WBC                                                                                  5.479e-02  1.886e-02   2.905  0.00683 **
Choline                                                                             -2.122e-04  5.377e-04  -0.395  0.69588   
Folate                                                                              -9.745e-05  2.342e-04  -0.416  0.68028   
BMI                                                                                  1.111e-02  1.741e-02   0.638  0.52823   
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:CarbohydrateLow Intake       1.354e+00  8.278e-01   1.636  0.11229   
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:CarbohydrateModerate Intake -2.589e-01  3.934e-01  -0.658  0.51546   
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

(Dispersion parameter for gaussian family taken to be 59.39442)

Number of Fisher Scoring iterations: 11

> confint(model2p,df=degf(d62))
                                                                                            2.5 %        97.5 %
(Intercept)                                                                         -0.1412121699  1.4661866465
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake                             -0.3558011404  0.6001552100
CarbohydrateLow Intake                                                              -1.0798354799 -0.0614262939
CarbohydrateModerate Intake                                                         -0.4192678609  0.7474483626
GenderMale                                                                          -0.8790231659  0.4700765295
WBC                                                                                  0.0154510019  0.0941243536
Choline                                                                             -0.0013338292  0.0009094018
Folate                                                                              -0.0005859636  0.0003910587
BMI                                                                                 -0.0252074415  0.0474277742
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:CarbohydrateLow Intake      -0.3724726739  3.0809746487
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:CarbohydrateModerate Intake -1.0795036008  0.5616805785
> summ(model2p, exp = TRUE,confint=TRUE, n.sd=2, digits= 6)
MODEL INFO:
Observations: 1177
Dependent Variable: HSCRP
Type: Analysis of complex survey design 
 Family: gaussian 
 Link function: log 

MODEL FIT:
Pseudo-R² (Cragg-Uhler) = 0.881076
Pseudo-R² (McFadden) = 0.034637
AIC = 8839.317965 

----------------------------------------------------------------------------------------
                                 exp(Est.)       2.5%       97.5%      t val.          p
------------------------------ ----------- ---------- ----------- ----------- ----------
(Intercept)                       1.939611   0.911498    4.127370    1.719454   0.100971
relevel(Zinc, ref =               1.129954   0.721135    1.770538    0.533198   0.599772
"Inadequate Intake")Adequate                                                            
Intake                                                                                  
CarbohydrateLow Intake            0.565169   0.350261    0.911937   -2.337597   0.029915
CarbohydrateModerate              1.178321   0.681110    2.038494    0.586752   0.563936
Intake                                                                                  
GenderMale                        0.815076   0.432455    1.536230   -0.632309   0.534348
WBC                               1.056316   1.017987    1.096089    2.905306   0.008750
Choline                           0.999788   0.998735    1.000842   -0.394672   0.697262
Folate                            0.999903   0.999444    1.000362   -0.416126   0.681749
BMI                               1.011172   0.977249    1.046273    0.638131   0.530628
relevel(Zinc, ref =               3.873858   0.764776   19.622454    1.635999   0.117481
"Inadequate Intake")Adequate                                                            
Intake:CarbohydrateLow                                                                  
Intake                                                                                  
relevel(Zinc, ref =               0.771891   0.357029    1.668815   -0.658159   0.517941
"Inadequate Intake")Adequate                                                            
Intake:CarbohydrateModerate                                                             
Intake                                                                                  
----------------------------------------------------------------------------------------

Estimated dispersion parameter = 59.39442 
> 
> a1amd1p24 <-  tbl_regression(model2p,intercept= FALSE,add_estimate_to_reference_rows = TRUE
+                              , exponentiate = TRUE)%>%  bold_p(t= 0.05) %>%
+   modify_caption("**Table S.8: Analysis of the Coefficients for the Participants' CHO Intake 51- 65 Years Old** ")
> a1amd1p24
> ###Investigate terms
> regTermTest(model2p ,~ relevel(Zinc, ref = "Inadequate Intake"): Carbohydrate, method = "LRT")
Working (Rao-Scott+F) LRT for relevel(Zinc, ref = "Inadequate Intake"):Carbohydrate
 in svyglm(formula = HSCRP ~ relevel(Zinc, ref = "Inadequate Intake") * 
    Carbohydrate + Gender + WBC + Choline + Folate + BMI, design = d62, 
    family = gaussian(link = "log"))
Working 2logLR =  7.256113 p= 0.052728 
(scale factors:  1.5 0.51 );  denominator df= 20
> regTermTest(model2p,~ relevel(Zinc, ref = "Inadequate Intake")* Carbohydrate, method = "LRT")
Working (Rao-Scott+F) LRT for relevel(Zinc, ref = "Inadequate Intake") Carbohydrate relevel(Zinc, ref = "Inadequate Intake"):Carbohydrate
 in svyglm(formula = HSCRP ~ relevel(Zinc, ref = "Inadequate Intake") * 
    Carbohydrate + Gender + WBC + Choline + Folate + BMI, design = d62, 
    family = gaussian(link = "log"))
Working 2logLR =  4.193028 p= 0.3954 
(scale factors:  4 0.52 0.33 0.093 0.042 );  denominator df= 20
> ### Overfitting
> subset13amp <- subset(nhanes1, Age_R >50 & Age_R <66 )
> subset13amsp <- na.omit(subset13amp)
> 
> 
> # Fit Generalized linear regression model using caret
> modelpwp41 <- train( HSCRP ~ relevel(Zinc, ref = "Inadequate Intake")* Carbohydrate +
+                       WBC + Choline +Folate +BMI+ Gender,
+                     subset13amsp,
+                     method = "glm",
+                     trControl = trainControl(
+                       method = "cv",
+                       number = 10,
+                       verboseIter = T
+                     ))
+ Fold01: parameter=none 
- Fold01: parameter=none 
+ Fold02: parameter=none 
- Fold02: parameter=none 
+ Fold03: parameter=none 
- Fold03: parameter=none 
+ Fold04: parameter=none 
- Fold04: parameter=none 
+ Fold05: parameter=none 
- Fold05: parameter=none 
+ Fold06: parameter=none 
- Fold06: parameter=none 
+ Fold07: parameter=none 
- Fold07: parameter=none 
+ Fold08: parameter=none 
- Fold08: parameter=none 
+ Fold09: parameter=none 
- Fold09: parameter=none 
+ Fold10: parameter=none 
- Fold10: parameter=none 
Aggregating results
Fitting final model on full training set
> modelpwp41
Generalized Linear Model 

1177 samples
   7 predictor

No pre-processing
Resampling: Cross-Validated (10 fold) 
Summary of sample sizes: 1059, 1059, 1058, 1060, 1059, 1059, ... 
Resampling results:

  RMSE      Rsquared    MAE     
  6.680217  0.01857536  3.420685

> 
> 
> # Function for Root Mean Squared Error
> RMSE <- function(error) { sqrt(mean(error^2)) }
> RMSE(model2p$residuals)
[1] 1.887836
>
> ##########################################################################################################################################
> ### Elderly
> ###############################################################################################################################
> #### Age 66 +
> d5 <- subset(nhc2, Age_R > 65)
> d6 <- na.omit(d5)
> 
> ### W/ Ethnicity ### no difference when plotted
> 
> model1am1p <- svyglm(HSCRP ~ relevel(Zinc, ref = "Inadequate Intake")* relevel(Fasting, ref="Not Fasted") +
+                      WBC + Choline +Folate + BMI+ Gender+ Ethnicity, design = d6, family = gaussian(link='log'))
> 
> 
> summary(model1am1p,df= degf(d6))

Call:
svyglm(formula = HSCRP ~ relevel(Zinc, ref = "Inadequate Intake") * 
    relevel(Fasting, ref = "Not Fasted") + WBC + Choline + Folate + 
    BMI + Gender + Ethnicity, design = d6, family = gaussian(link = "log"))

Survey design:
subset(nhc2, Age_R > 65)

Coefficients:
                                                                                                     Estimate Std. Error t value Pr(>|t|)    
(Intercept)                                                                                         0.2582581  0.5043663   0.512  0.61237    
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake                                            -0.4193757  0.1580570  -2.653  0.01262 *  
relevel(Fasting, ref = "Not Fasted")Fasted                                                         -0.6627412  0.2366431  -2.801  0.00884 ** 
WBC                                                                                                 0.1932058  0.0289173   6.681 2.11e-07 ***
Choline                                                                                             0.0009434  0.0003407   2.769  0.00955 ** 
Folate                                                                                             -0.0002808  0.0002674  -1.050  0.30200    
BMI                                                                                                -0.0318338  0.0171766  -1.853  0.07369 .  
GenderMale                                                                                          0.2887852  0.1614177   1.789  0.08371 .  
EthnicityBlack                                                                                      0.0211975  0.3697662   0.057  0.95466    
EthnicityMexican American                                                                           0.7714282  0.3421556   2.255  0.03162 *  
EthnicityOther Hispanic                                                                            -0.1520918  0.3286854  -0.463  0.64690    
EthnicityOther Race                                                                                -0.4081973  0.4998738  -0.817  0.42059    
EthnicityWhite                                                                                      0.0988583  0.2989117   0.331  0.74315    
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:relevel(Fasting, ref = "Not Fasted")Fasted  0.6260708  0.2645406   2.367  0.02460 *  
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

(Dispersion parameter for gaussian family taken to be 26.99074)

Number of Fisher Scoring iterations: 15

> confint(model1am1p,df=degf(d6))
                                                                                                           2.5 %        97.5 %
(Intercept)                                                                                        -0.8058616648  1.3223779133
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake                                            -0.7528468503 -0.0859044956
relevel(Fasting, ref = "Not Fasted")Fasted                                                         -1.1620144112 -0.1634680161
WBC                                                                                                 0.1321956632  0.2542159276
Choline                                                                                             0.0002245375  0.0016622792
Folate                                                                                             -0.0008449629  0.0002833197
BMI                                                                                                -0.0680732550  0.0044056995
GenderMale                                                                                         -0.0517763380  0.6293466589
EthnicityBlack                                                                                     -0.7589408734  0.8013359267
EthnicityMexican American                                                                           0.0495430160  1.4933134310
EthnicityOther Hispanic                                                                            -0.8455573150  0.5413737662
EthnicityOther Race                                                                                -1.4628388090  0.6464441283
EthnicityWhite                                                                                     -0.5317901832  0.7295068811
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:relevel(Fasting, ref = "Not Fasted")Fasted  0.0679389552  1.1842025489
> summ(model1am1p, exp = TRUE,confint=TRUE, n.sd=2, digits= 6)
MODEL INFO:
Observations: 995
Dependent Variable: HSCRP
Type: Analysis of complex survey design 
 Family: gaussian 
 Link function: log 

MODEL FIT:
Pseudo-R² (Cragg-Uhler) = 0.980460
Pseudo-R² (McFadden) = 0.126614
AIC = 6661.387138 

----------------------------------------------------------------------------------------
                                  exp(Est.)       2.5%      97.5%      t val.          p
------------------------------- ----------- ---------- ---------- ----------- ----------
(Intercept)                        1.294673   0.481773   3.479184    0.512045   0.615207
relevel(Zinc, ref =                0.657457   0.482313   0.896202   -2.653319   0.016725
"Inadequate Intake")Adequate                                                            
Intake                                                                                  
relevel(Fasting, ref = "Not        0.515436   0.324149   0.819608   -2.800594   0.012290
Fasted")Fasted                                                                          
WBC                                1.213132   1.146288   1.283875    6.681326   0.000004
Choline                            1.000944   1.000276   1.001613    2.768811   0.013139
Folate                             0.999719   0.999195   1.000243   -1.050237   0.308311
BMI                                0.968668   0.936600   1.001833   -1.853321   0.081275
GenderMale                         1.334805   0.972789   1.831542    1.789056   0.091438
EthnicityBlack                     1.021424   0.494835   2.108393    0.057327   0.954953
EthnicityMexican American          2.162853   1.106073   4.229319    2.254612   0.037637
EthnicityOther Hispanic            0.858909   0.450993   1.635780   -0.462728   0.649428
EthnicityOther Race                0.664848   0.249591   1.770987   -0.816601   0.425452
EthnicityWhite                     1.103910   0.614468   1.983206    0.330728   0.744892
relevel(Zinc, ref =                1.870247   1.113581   3.141061    2.366634   0.030086
"Inadequate Intake")Adequate                                                            
Intake:relevel(Fasting, ref =                                                           
"Not Fasted")Fasted                                                                     
----------------------------------------------------------------------------------------

Estimated dispersion parameter = 26.99074 
> 
> a1amd1p <-  tbl_regression(model1am1p,intercept= FALSE,add_estimate_to_reference_rows = TRUE
+                            , exponentiate = TRUE)%>%  bold_p(t= 0.05) %>%
+   modify_caption("**Table 5: Analysis of the Coefficients of Participants 66 & Older (Fasting)** ")
> a1amd1p
> ###Investigate terms
> regTermTest(model1am1p,~ relevel(Zinc, ref = "Inadequate Intake"): relevel(Fasting, ref="Not Fasted"), method = "LRT")
Working (Rao-Scott+F) LRT for relevel(Zinc, ref = "Inadequate Intake"):relevel(Fasting, ref = "Not Fasted")
 in svyglm(formula = HSCRP ~ relevel(Zinc, ref = "Inadequate Intake") * 
    relevel(Fasting, ref = "Not Fasted") + WBC + Choline + 
    Folate + BMI + Gender + Ethnicity, design = d6, family = gaussian(link = "log"))
Working 2logLR =  6.470198 p= 0.022038 
df=1;  denominator df= 17
> regTermTest(model1am1p, ~relevel(Zinc, ref = "Inadequate Intake")* relevel(Fasting, ref="Not Fasted"), method = "LRT")
Working (Rao-Scott+F) LRT for relevel(Zinc, ref = "Inadequate Intake") relevel(Fasting, ref = "Not Fasted") relevel(Zinc, ref = "Inadequate Intake"):relevel(Fasting, ref = "Not Fasted")
 in svyglm(formula = HSCRP ~ relevel(Zinc, ref = "Inadequate Intake") * 
    relevel(Fasting, ref = "Not Fasted") + WBC + Choline + 
    Folate + BMI + Gender + Ethnicity, design = d6, family = gaussian(link = "log"))
Working 2logLR =  16.04474 p= 0.011499 
(scale factors:  1.6 0.92 0.53 );  denominator df= 17
> ###Checking for Overfitting
> # the caret library is loaded
> set.seed(123)
> 
> subset13amw <- subset(nhanes1, Age_R > 65 )
> subset13amsw <- na.omit(subset13amw)
> 
> 
> # Fit Generalized linear regression model using caret
> modelz <- train(HSCRP ~ relevel(Zinc, ref = "Inadequate Intake")* relevel(Fasting, ref="Not Fasted") + Ethnicity+
+                  WBC + Choline +Folate + Gender +BMI,
+                subset13amsw,
+                method = "glm",
+                trControl = trainControl(
+                  method = "cv",
+                  number = 10,
+                  verboseIter = T
+                ))
+ Fold01: parameter=none 
- Fold01: parameter=none 
+ Fold02: parameter=none 
- Fold02: parameter=none 
+ Fold03: parameter=none 
- Fold03: parameter=none 
+ Fold04: parameter=none 
- Fold04: parameter=none 
+ Fold05: parameter=none 
- Fold05: parameter=none 
+ Fold06: parameter=none 
- Fold06: parameter=none 
+ Fold07: parameter=none 
- Fold07: parameter=none 
+ Fold08: parameter=none 
- Fold08: parameter=none 
+ Fold09: parameter=none 
- Fold09: parameter=none 
+ Fold10: parameter=none 
- Fold10: parameter=none 
Aggregating results
Fitting final model on full training set
> modelz
Generalized Linear Model 

995 samples
  8 predictor

No pre-processing
Resampling: Cross-Validated (10 fold) 
Summary of sample sizes: 894, 894, 897, 896, 896, 896, ... 
Resampling results:

  RMSE      Rsquared    MAE     
  5.554439  0.01866653  3.246264

> 
> # Function for Root Mean Squared Error
> RMSE <- function(error) { sqrt(mean(error^2)) }
> RMSE(model1am1p$residuals)
[1] 3.031869


> ###Plots (not significant)
> 
> modelkq <- svyglm(HSCRP ~ Zinc* Fasting +BMI +
+                       WBC + Choline +Folate+Gender+Ethnicity,design = d6, family = gaussian(link='log'))
> cat_plot(modelkq, pred =Fasting, modx = Zinc, main.title = "Figure 2:Two-Way Interaction Effect Between Fasting & Dietary Zinc (Older Adult)",
+          x.label =  "Fasting", interval = TRUE)
> 
> ###Remove Ethnicity
> 
> model1am <- svyglm(HSCRP ~ relevel(Zinc, ref = "Inadequate Intake")* relevel(Fasting, ref="Not Fasted") +
+                      WBC + Choline +Folate +BMI+ Gender, design = d2, family = gaussian(link='log'))
> 
> a1amz <-  tbl_regression(model1am,intercept= FALSE,add_estimate_to_reference_rows = TRUE
+                          , exponentiate = TRUE)%>%  bold_p(t= 0.05) %>%
+   modify_caption("**Table 2: Analysis of the Coefficients for Participants**")
> a1amz
> 
> summ(model1am1p, exp = TRUE,confint=TRUE, n.sd=2, digits= 6)
MODEL INFO:
Observations: 995
Dependent Variable: HSCRP
Type: Analysis of complex survey design 
 Family: gaussian 
 Link function: log 

MODEL FIT:
Pseudo-R² (Cragg-Uhler) = 0.980460
Pseudo-R² (McFadden) = 0.126614
AIC = 6661.387138 

----------------------------------------------------------------------------------------
                                  exp(Est.)       2.5%      97.5%      t val.          p
------------------------------- ----------- ---------- ---------- ----------- ----------
(Intercept)                        1.294673   0.481773   3.479184    0.512045   0.615207
relevel(Zinc, ref =                0.657457   0.482313   0.896202   -2.653319   0.016725
"Inadequate Intake")Adequate                                                            
Intake                                                                                  
relevel(Fasting, ref = "Not        0.515436   0.324149   0.819608   -2.800594   0.012290
Fasted")Fasted                                                                          
WBC                                1.213132   1.146288   1.283875    6.681326   0.000004
Choline                            1.000944   1.000276   1.001613    2.768811   0.013139
Folate                             0.999719   0.999195   1.000243   -1.050237   0.308311
BMI                                0.968668   0.936600   1.001833   -1.853321   0.081275
GenderMale                         1.334805   0.972789   1.831542    1.789056   0.091438
EthnicityBlack                     1.021424   0.494835   2.108393    0.057327   0.954953
EthnicityMexican American          2.162853   1.106073   4.229319    2.254612   0.037637
EthnicityOther Hispanic            0.858909   0.450993   1.635780   -0.462728   0.649428
EthnicityOther Race                0.664848   0.249591   1.770987   -0.816601   0.425452
EthnicityWhite                     1.103910   0.614468   1.983206    0.330728   0.744892
relevel(Zinc, ref =                1.870247   1.113581   3.141061    2.366634   0.030086
"Inadequate Intake")Adequate                                                            
Intake:relevel(Fasting, ref =                                                           
"Not Fasted")Fasted                                                                     
----------------------------------------------------------------------------------------

Estimated dispersion parameter = 26.99074 
> 
> ###Investigate terms
> regTermTest(model1am1p,~ relevel(Zinc, ref = "Inadequate Intake"): relevel(Fasting, ref="Not Fasted"), method = "LRT")
Working (Rao-Scott+F) LRT for relevel(Zinc, ref = "Inadequate Intake"):relevel(Fasting, ref = "Not Fasted")
 in svyglm(formula = HSCRP ~ relevel(Zinc, ref = "Inadequate Intake") * 
    relevel(Fasting, ref = "Not Fasted") + WBC + Choline + 
    Folate + BMI + Gender + Ethnicity, design = d6, family = gaussian(link = "log"))
Working 2logLR =  6.470198 p= 0.022038 
df=1;  denominator df= 17
> regTermTest(model1am1p, ~relevel(Zinc, ref = "Inadequate Intake")* relevel(Fasting, ref="Not Fasted"), method = "LRT")
Working (Rao-Scott+F) LRT for relevel(Zinc, ref = "Inadequate Intake") relevel(Fasting, ref = "Not Fasted") relevel(Zinc, ref = "Inadequate Intake"):relevel(Fasting, ref = "Not Fasted")
 in svyglm(formula = HSCRP ~ relevel(Zinc, ref = "Inadequate Intake") * 
    relevel(Fasting, ref = "Not Fasted") + WBC + Choline + 
    Folate + BMI + Gender + Ethnicity, design = d6, family = gaussian(link = "log"))
Working 2logLR =  16.04474 p= 0.011499 
(scale factors:  1.6 0.92 0.53 );  denominator df= 17

> ###Plots(not significant)
> 
> modelkq <- svyglm(HSCRP ~ Zinc* Fasting +BMI +
+                     WBC + Choline +Folate+Gender,design = d6, family = gaussian(link='log'))
> 
> cat_plot(modelkq, pred =Fasting, modx = Zinc, main.title = "Figure 2:Two-Way Interaction Effect Between Fasting & Dietary Zinc (Older Adult)",
+          x.label =  "Fasting", interval = TRUE)
> 

> model1am1p <- svyglm(HSCRP ~ relevel(Zinc, ref = "Inadequate Intake")* relevel(Fasting, ref="Not Fasted") +
+                        WBC + Choline +Folate + BMI+ Gender, design = d6, family = gaussian(link='log'))
> ###Checking for Overfitting
> # the caret library is loaded
> set.seed(123)
> 
> subset13amw <- subset(nhanes1, Age_R > 65 )
> subset13amsw <- na.omit(subset13amw)
> 
> 
> # Fit Generalized linear regression model using caret
> modelz <- train(HSCRP ~ relevel(Zinc, ref = "Inadequate Intake")* relevel(Fasting, ref="Not Fasted") +
+                   WBC + Choline +Folate + Gender +BMI,
+                 subset13amsw,
+                 method = "glm",
+                 trControl = trainControl(
+                   method = "cv",
+                   number = 10,
+                   verboseIter = T
+                 ))
+ Fold01: parameter=none 
- Fold01: parameter=none 
+ Fold02: parameter=none 
- Fold02: parameter=none 
+ Fold03: parameter=none 
- Fold03: parameter=none 
+ Fold04: parameter=none 
- Fold04: parameter=none 
+ Fold05: parameter=none 
- Fold05: parameter=none 
+ Fold06: parameter=none 
- Fold06: parameter=none 
+ Fold07: parameter=none 
- Fold07: parameter=none 
+ Fold08: parameter=none 
- Fold08: parameter=none 
+ Fold09: parameter=none 
- Fold09: parameter=none 
+ Fold10: parameter=none 
- Fold10: parameter=none 
Aggregating results
Fitting final model on full training set
> modelz
Generalized Linear Model 

995 samples
  7 predictor

No pre-processing
Resampling: Cross-Validated (10 fold) 
Summary of sample sizes: 894, 894, 897, 896, 896, 896, ... 
Resampling results:

  RMSE      Rsquared    MAE     
  5.531519  0.02558835  3.232241

> 
> # Function for Root Mean Squared Error
> RMSE <- function(error) { sqrt(mean(error^2)) }
> RMSE(model1am1p$residuals)
[1] 2.298652
> 
> ################################
> ###KCAL
> ###########################################################################################################
> ### Elderly ### Plot not significant
> model1amd1pq <- svyglm(HSCRP ~ relevel(Zinc, ref = "Inadequate Intake")* relevel(Kcal, ref = "High Calorie Diet") + Ethnicity+
+                          WBC + Choline +Folate +BMI+ Gender , design = d6, family = gaussian(link='log'))
> 
> 
> 
> summary(model1amd1pq ,df= degf(d6))

Call:
svyglm(formula = HSCRP ~ relevel(Zinc, ref = "Inadequate Intake") * 
    relevel(Kcal, ref = "High Calorie Diet") + Ethnicity + WBC + 
    Choline + Folate + BMI + Gender, design = d6, family = gaussian(link = "log"))

Survey design:
subset(nhc2, Age_R > 65)

Coefficients:
                                                                                                                        Estimate Std. Error
(Intercept)                                                                                                           -0.7917188  0.5820833
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake                                                                0.6228317  0.2844509
relevel(Kcal, ref = "High Calorie Diet")Low Calorie Diet                                                               0.6351746  0.2386868
relevel(Kcal, ref = "High Calorie Diet")Moderate Calorie Diet                                                          1.1434575  0.2670486
EthnicityBlack                                                                                                         0.0384238  0.4054430
EthnicityMexican American                                                                                              0.7645011  0.3682715
EthnicityOther Hispanic                                                                                               -0.2391745  0.4548569
EthnicityOther Race                                                                                                   -0.3107011  0.5060253
EthnicityWhite                                                                                                         0.1540486  0.3346350
WBC                                                                                                                    0.1809427  0.0280241
Choline                                                                                                                0.0009036  0.0004410
Folate                                                                                                                -0.0004001  0.0003468
BMI                                                                                                                   -0.0245770  0.0159668
GenderMale                                                                                                             0.2471097  0.1525034
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:relevel(Kcal, ref = "High Calorie Diet")Low Calorie Diet      -0.2227873  0.3939556
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:relevel(Kcal, ref = "High Calorie Diet")Moderate Calorie Diet -1.2066102  0.3684514
                                                                                                                      t value Pr(>|t|)    
(Intercept)                                                                                                            -1.360 0.183917    
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake                                                                 2.190 0.036467 *  
relevel(Kcal, ref = "High Calorie Diet")Low Calorie Diet                                                                2.661 0.012388 *  
relevel(Kcal, ref = "High Calorie Diet")Moderate Calorie Diet                                                           4.282 0.000175 ***
EthnicityBlack                                                                                                          0.095 0.925128    
EthnicityMexican American                                                                                               2.076 0.046569 *  
EthnicityOther Hispanic                                                                                                -0.526 0.602876    
EthnicityOther Race                                                                                                    -0.614 0.543842    
EthnicityWhite                                                                                                          0.460 0.648586    
WBC                                                                                                                     6.457 3.92e-07 ***
Choline                                                                                                                 2.049 0.049286 *  
Folate                                                                                                                 -1.154 0.257726    
BMI                                                                                                                    -1.539 0.134224    
GenderMale                                                                                                              1.620 0.115622    
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:relevel(Kcal, ref = "High Calorie Diet")Low Calorie Diet       -0.566 0.575930    
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:relevel(Kcal, ref = "High Calorie Diet")Moderate Calorie Diet  -3.275 0.002669 ** 
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

(Dispersion parameter for gaussian family taken to be 26.825)

Number of Fisher Scoring iterations: 15

> confint(model1amd1pq ,df=degf(d6))
                                                                                                                              2.5 %
(Intercept)                                                                                                           -2.032400e+00
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake                                                                1.653892e-02
relevel(Kcal, ref = "High Calorie Diet")Low Calorie Diet                                                               1.264257e-01
relevel(Kcal, ref = "High Calorie Diet")Moderate Calorie Diet                                                          5.742570e-01
EthnicityBlack                                                                                                        -8.257576e-01
EthnicityMexican American                                                                                             -2.045087e-02
EthnicityOther Hispanic                                                                                               -1.208679e+00
EthnicityOther Race                                                                                                   -1.389268e+00
EthnicityWhite                                                                                                        -5.592091e-01
WBC                                                                                                                    1.212108e-01
Choline                                                                                                               -3.631241e-05
Folate                                                                                                                -1.139293e-03
BMI                                                                                                                   -5.860950e-02
GenderMale                                                                                                            -7.794356e-02
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:relevel(Kcal, ref = "High Calorie Diet")Low Calorie Diet      -1.062484e+00
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:relevel(Kcal, ref = "High Calorie Diet")Moderate Calorie Diet -1.991946e+00
                                                                                                                             97.5 %
(Intercept)                                                                                                            0.4489624083
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake                                                                1.2291243942
relevel(Kcal, ref = "High Calorie Diet")Low Calorie Diet                                                               1.1439234732
relevel(Kcal, ref = "High Calorie Diet")Moderate Calorie Diet                                                          1.7126580496
EthnicityBlack                                                                                                         0.9026051720
EthnicityMexican American                                                                                              1.5494531569
EthnicityOther Hispanic                                                                                                0.7303301037
EthnicityOther Race                                                                                                    0.7678662401
EthnicityWhite                                                                                                         0.8673061861
WBC                                                                                                                    0.2406747003
Choline                                                                                                                0.0018435854
Folate                                                                                                                 0.0003390782
BMI                                                                                                                    0.0094554079
GenderMale                                                                                                             0.5721628662
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:relevel(Kcal, ref = "High Calorie Diet")Low Calorie Diet       0.6169090425
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:relevel(Kcal, ref = "High Calorie Diet")Moderate Calorie Diet -0.4212744950
> summ(model1amd1pq, exp = TRUE,confint=TRUE, n.sd=2, digits= 6)
MODEL INFO:
Observations: 995
Dependent Variable: HSCRP
Type: Analysis of complex survey design 
 Family: gaussian 
 Link function: log 

MODEL FIT:
Pseudo-R² (Cragg-Uhler) = 0.984487
Pseudo-R² (McFadden) = 0.134039
AIC = 6656.891839 

-----------------------------------------------------------------------------------------
                                   exp(Est.)       2.5%      97.5%      t val.          p
-------------------------------- ----------- ---------- ---------- ----------- ----------
(Intercept)                         0.453065   0.144774   1.417853   -1.360147   0.193876
relevel(Zinc, ref =                 1.864199   1.067499   3.255498    2.189593   0.044776
"Inadequate Intake")Adequate                                                             
Intake                                                                                   
relevel(Kcal, ref = "High           1.887352   1.182176   3.013168    2.661121   0.017791
Calorie Diet")Low Calorie                                                                
Diet                                                                                     
relevel(Kcal, ref = "High           3.137598   1.859025   5.295530    4.281834   0.000655
Calorie Diet")Moderate Calorie                                                           
Diet                                                                                     
EthnicityBlack                      1.039172   0.469433   2.300387    0.094770   0.925752
EthnicityMexican American           2.147923   1.043627   4.420708    2.075917   0.055510
EthnicityOther Hispanic             0.787277   0.322814   1.920007   -0.525824   0.606698
EthnicityOther Race                 0.732933   0.271853   1.976031   -0.614003   0.548413
EthnicityWhite                      1.166548   0.605425   2.247731    0.460348   0.651869
WBC                                 1.198347   1.134301   1.266008    6.456683   0.000011
Choline                             1.000904   1.000039   1.001770    2.049107   0.058365
Folate                              0.999600   0.998921   1.000280   -1.153714   0.266670
BMI                                 0.975723   0.945661   1.006740   -1.539258   0.144568
GenderMale                          1.280319   0.949527   1.726352    1.620355   0.125984
relevel(Zinc, ref =                 0.800285   0.369751   1.732129   -0.565514   0.580086
"Inadequate Intake")Adequate                                                             
Intake:relevel(Kcal, ref =                                                               
"High Calorie Diet")Low                                                                  
Calorie Diet                                                                             
relevel(Zinc, ref =                 0.299210   0.145328   0.616031   -3.274815   0.005116
"Inadequate Intake")Adequate                                                             
Intake:relevel(Kcal, ref =                                                               
"High Calorie Diet")Moderate                                                             
Calorie Diet                                                                             
-----------------------------------------------------------------------------------------

Estimated dispersion parameter = 26.825 
> 
> a1amd1pq <-  tbl_regression(model1amd1pq,intercept= FALSE,add_estimate_to_reference_rows = TRUE
+                             , exponentiate = TRUE)%>%  bold_p(t= 0.05) %>%
+   modify_caption("**Table 3: Analysis of the Coefficients of the Participants' Energy Intake in Older Adult** ")
> a1amd1pq
> ###Investigate terms
> regTermTest(model1amd1pq, ~ relevel(Zinc, ref = "Inadequate Intake"):relevel(Kcal, ref = "High Calorie Diet"), method = "LRT")
Working (Rao-Scott+F) LRT for relevel(Zinc, ref = "Inadequate Intake"):relevel(Kcal, ref = "High Calorie Diet")
 in svyglm(formula = HSCRP ~ relevel(Zinc, ref = "Inadequate Intake") * 
    relevel(Kcal, ref = "High Calorie Diet") + Ethnicity + 
    WBC + Choline + Folate + BMI + Gender, design = d6, family = gaussian(link = "log"))
Working 2logLR =  13.09902 p= 0.019248 
(scale factors:  1.8 0.17 );  denominator df= 15
> regTermTest(model1amd1pq, ~ relevel(Zinc, ref = "Inadequate Intake") * relevel(Kcal, ref = "High Calorie Diet"), method = "LRT")
Working (Rao-Scott+F) LRT for relevel(Zinc, ref = "Inadequate Intake") relevel(Kcal, ref = "High Calorie Diet") relevel(Zinc, ref = "Inadequate Intake"):relevel(Kcal, ref = "High Calorie Diet")
 in svyglm(formula = HSCRP ~ relevel(Zinc, ref = "Inadequate Intake") * 
    relevel(Kcal, ref = "High Calorie Diet") + Ethnicity + 
    WBC + Choline + Folate + BMI + Gender, design = d6, family = gaussian(link = "log"))
Working 2logLR =  20.86754 p= 0.021977 
(scale factors:  2 1.6 0.81 0.54 0.058 );  denominator df= 15
> ###Checking for Overfitting
> # the caret library is loaded
> set.seed(123)
> 
> subset13amc <- subset(nhanes1, Age_R > 65 )
> subset13amsc <- na.omit(subset13amc)
> 
> 
> # Fit Generalized linear regression model using caret
> modelf <- train( HSCRP ~ relevel(Zinc, ref = "Inadequate Intake")* Kcal + Ethnicity+
+                   WBC + Choline +Folate + Gender +BMI,
+                 subset13amsc,
+                 method = "glm",
+                 trControl = trainControl(
+                   method = "cv",
+                   number = 10,
+                   verboseIter = T
+                 ))
+ Fold01: parameter=none 
- Fold01: parameter=none 
+ Fold02: parameter=none 
- Fold02: parameter=none 
+ Fold03: parameter=none 
- Fold03: parameter=none 
+ Fold04: parameter=none 
- Fold04: parameter=none 
+ Fold05: parameter=none 
- Fold05: parameter=none 
+ Fold06: parameter=none 
- Fold06: parameter=none 
+ Fold07: parameter=none 
- Fold07: parameter=none 
+ Fold08: parameter=none 
- Fold08: parameter=none 
+ Fold09: parameter=none 
- Fold09: parameter=none 
+ Fold10: parameter=none 
- Fold10: parameter=none 
Aggregating results
Fitting final model on full training set
> modelf
Generalized Linear Model 

995 samples
  8 predictor

No pre-processing
Resampling: Cross-Validated (10 fold) 
Summary of sample sizes: 894, 894, 897, 896, 896, 896, ... 
Resampling results:

  RMSE      Rsquared    MAE     
  5.557326  0.01688198  3.234081

> 
> # Function for Root Mean Squared Error
> RMSE <- function(error) { sqrt(mean(error^2)) }
> RMSE(model1amd1pq$residuals)
[1] 3.054936
> ###Plots (not sig)
> 
> model1amd1 <- svyglm(HSCRP ~ Kcal* relevel(Zinc, ref = "Inadequate Intake") + Ethnicity+Gender+
+                        WBC + Choline +Folate +BMI, design = d62, family = gaussian(link='log'))
> cat_plot(model1amd1, pred = Kcal, modx =Zinc, main.title = "Figure 3:Two-Way Interaction Effect Between Energy Intake & Dietary Zinc (66+)",
+          x.label =  "Energy Intake (Kcals)", interval = TRUE)

#### Remove ethnicity
> 
> model1amd1pq <- svyglm(HSCRP ~ relevel(Zinc, ref = "Inadequate Intake")* relevel(Kcal, ref = "High Calorie Diet") +
+                         WBC + Choline +Folate +BMI+ Gender , design = d6, family = gaussian(link='log'))
> 
> 
> 
> summary(model1amd1pq ,df= degf(d6))

Call:
svyglm(formula = HSCRP ~ relevel(Zinc, ref = "Inadequate Intake") * 
    relevel(Kcal, ref = "High Calorie Diet") + WBC + Choline + 
    Folate + BMI + Gender, design = d6, family = gaussian(link = "log"))

Survey design:
subset(nhc2, Age_R > 65)

Coefficients:
                                                                                                                        Estimate Std. Error
(Intercept)                                                                                                           -0.5394831  0.4610444
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake                                                                0.5600632  0.2942305
relevel(Kcal, ref = "High Calorie Diet")Low Calorie Diet                                                               0.7063316  0.2628479
relevel(Kcal, ref = "High Calorie Diet")Moderate Calorie Diet                                                          1.2331479  0.4010388
WBC                                                                                                                    0.1567430  0.0402742
Choline                                                                                                                0.0012658  0.0005444
Folate                                                                                                                -0.0003428  0.0004636
BMI                                                                                                                   -0.0235040  0.0159661
GenderMale                                                                                                             0.2588423  0.2000613
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:relevel(Kcal, ref = "High Calorie Diet")Low Calorie Diet      -0.3287954  0.3549945
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:relevel(Kcal, ref = "High Calorie Diet")Moderate Calorie Diet -1.2092400  0.4690213
                                                                                                                      t value Pr(>|t|)    
(Intercept)                                                                                                            -1.170 0.251160    
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake                                                                 1.903 0.066611 .  
relevel(Kcal, ref = "High Calorie Diet")Low Calorie Diet                                                                2.687 0.011637 *  
relevel(Kcal, ref = "High Calorie Diet")Moderate Calorie Diet                                                           3.075 0.004461 ** 
WBC                                                                                                                     3.892 0.000513 ***
Choline                                                                                                                 2.325 0.027009 *  
Folate                                                                                                                 -0.739 0.465440    
BMI                                                                                                                    -1.472 0.151403    
GenderMale                                                                                                              1.294 0.205602    
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:relevel(Kcal, ref = "High Calorie Diet")Low Calorie Diet       -0.926 0.361734    
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:relevel(Kcal, ref = "High Calorie Diet")Moderate Calorie Diet  -2.578 0.015084 *  
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

(Dispersion parameter for gaussian family taken to be 28.45821)

Number of Fisher Scoring iterations: 14

> confint(model1amd1pq ,df=degf(d6))
                                                                                                                              2.5 %
(Intercept)                                                                                                           -1.5012047843
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake                                                               -0.0536907760
relevel(Kcal, ref = "High Calorie Diet")Low Calorie Diet                                                               0.1580405274
relevel(Kcal, ref = "High Calorie Diet")Moderate Calorie Diet                                                          0.3965956858
WBC                                                                                                                    0.0727324643
Choline                                                                                                                0.0001302664
Folate                                                                                                                -0.0013097824
BMI                                                                                                                   -0.0568088440
GenderMale                                                                                                            -0.1584781774
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:relevel(Kcal, ref = "High Calorie Diet")Low Calorie Diet      -1.0693008445
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:relevel(Kcal, ref = "High Calorie Diet")Moderate Calorie Diet -2.1876013978
                                                                                                                             97.5 %
(Intercept)                                                                                                            0.4222386326
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake                                                                1.1738171776
relevel(Kcal, ref = "High Calorie Diet")Low Calorie Diet                                                               1.2546226703
relevel(Kcal, ref = "High Calorie Diet")Moderate Calorie Diet                                                          2.0697000936
WBC                                                                                                                    0.2407534709
Choline                                                                                                                0.0024012626
Folate                                                                                                                 0.0006242735
BMI                                                                                                                    0.0098007580
GenderMale                                                                                                             0.6761628109
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:relevel(Kcal, ref = "High Calorie Diet")Low Calorie Diet       0.4117101275
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:relevel(Kcal, ref = "High Calorie Diet")Moderate Calorie Diet -0.2308786547
> summ(model1amd1pq, exp = TRUE,confint=TRUE, n.sd=2, digits= 6)
MODEL INFO:
Observations: 995
Dependent Variable: HSCRP
Type: Analysis of complex survey design 
 Family: gaussian 
 Link function: log 

MODEL FIT:
Pseudo-R² (Cragg-Uhler) = 0.927696
Pseudo-R² (McFadden) = 0.084516
AIC = 6702.226333 

-----------------------------------------------------------------------------------------
                                   exp(Est.)       2.5%      97.5%      t val.          p
-------------------------------- ----------- ---------- ---------- ----------- ----------
(Intercept)                         0.583050   0.236191   1.439286   -1.170133   0.255703
relevel(Zinc, ref =                 1.750783   0.983519   3.116605    1.903485   0.071469
"Inadequate Intake")Adequate                                                             
Intake                                                                                   
relevel(Kcal, ref = "High           2.026543   1.210652   3.392286    2.687226   0.014168
Calorie Diet")Low Calorie                                                                
Diet                                                                                     
relevel(Kcal, ref = "High           3.432016   1.563812   7.532066    3.074885   0.005975
Calorie Diet")Moderate Calorie                                                           
Diet                                                                                     
WBC                                 1.169695   1.080914   1.265768    3.891896   0.000906
Choline                             1.001267   1.000199   1.002335    2.325269   0.030694
Folate                              0.999657   0.998749   1.000566   -0.739351   0.468283
BMI                                 0.976770   0.946677   1.007819   -1.472117   0.156551
GenderMale                          1.295430   0.875228   1.917371    1.293815   0.210472
relevel(Zinc, ref =                 0.719790   0.358950   1.443371   -0.926199   0.365385
"Inadequate Intake")Adequate                                                             
Intake:relevel(Kcal, ref =                                                               
"High Calorie Diet")Low                                                                  
Calorie Diet                                                                             
relevel(Zinc, ref =                 0.298424   0.119015   0.748282   -2.578220   0.017952
"Inadequate Intake")Adequate                                                             
Intake:relevel(Kcal, ref =                                                               
"High Calorie Diet")Moderate                                                             
Calorie Diet                                                                             
-----------------------------------------------------------------------------------------

Estimated dispersion parameter = 28.45821 
> 
> a1amd1pq <-  tbl_regression(model1amd1pq,intercept= FALSE,add_estimate_to_reference_rows = TRUE
+                             , exponentiate = TRUE)%>%  bold_p(t= 0.05) %>%
+   modify_caption("**Table 3: Analysis of the Coefficients of the Participants' Energy Intake in Older Adult** ")
> a1amd1pq
> ###Investigate terms
> regTermTest(model1amd1pq, ~ relevel(Zinc, ref = "Inadequate Intake"):relevel(Kcal, ref = "High Calorie Diet"), method = "LRT")
Working (Rao-Scott+F) LRT for relevel(Zinc, ref = "Inadequate Intake"):relevel(Kcal, ref = "High Calorie Diet")
 in svyglm(formula = HSCRP ~ relevel(Zinc, ref = "Inadequate Intake") * 
    relevel(Kcal, ref = "High Calorie Diet") + WBC + Choline + 
    Folate + BMI + Gender, design = d6, family = gaussian(link = "log"))
Working 2logLR =  10.40445 p= 0.030689 
(scale factors:  1.9 0.15 );  denominator df= 20
> regTermTest(model1amd1pq, ~ relevel(Zinc, ref = "Inadequate Intake") * relevel(Kcal, ref = "High Calorie Diet"), method = "LRT")
Working (Rao-Scott+F) LRT for relevel(Zinc, ref = "Inadequate Intake") relevel(Kcal, ref = "High Calorie Diet") relevel(Zinc, ref = "Inadequate Intake"):relevel(Kcal, ref = "High Calorie Diet")
 in svyglm(formula = HSCRP ~ relevel(Zinc, ref = "Inadequate Intake") * 
    relevel(Kcal, ref = "High Calorie Diet") + WBC + Choline + 
    Folate + BMI + Gender, design = d6, family = gaussian(link = "log"))
Working 2logLR =  11.19508 p= 0.12266 
(scale factors:  3.5 0.7 0.47 0.34 0.031 );  denominator df= 20
> ###Checking for Overfitting
> # the caret library is loaded
> set.seed(123)
> 
> subset13amc <- subset(nhanes1, Age_R > 65 )
> subset13amsc <- na.omit(subset13amc)
> 
> 
> # Fit Generalized linear regression model using caret
> modelf <- train( HSCRP ~ relevel(Zinc, ref = "Inadequate Intake")* Kcal +
+                    WBC + Choline +Folate + Gender +BMI,
+                  subset13amsc,
+                  method = "glm",
+                  trControl = trainControl(
+                    method = "cv",
+                    number = 10,
+                    verboseIter = T
+                  ))
+ Fold01: parameter=none 
- Fold01: parameter=none 
+ Fold02: parameter=none 
- Fold02: parameter=none 
+ Fold03: parameter=none 
- Fold03: parameter=none 
+ Fold04: parameter=none 
- Fold04: parameter=none 
+ Fold05: parameter=none 
- Fold05: parameter=none 
+ Fold06: parameter=none 
- Fold06: parameter=none 
+ Fold07: parameter=none 
- Fold07: parameter=none 
+ Fold08: parameter=none 
- Fold08: parameter=none 
+ Fold09: parameter=none 
- Fold09: parameter=none 
+ Fold10: parameter=none 
- Fold10: parameter=none 
Aggregating results
Fitting final model on full training set
> modelf
Generalized Linear Model 

995 samples
  7 predictor

No pre-processing
Resampling: Cross-Validated (10 fold) 
Summary of sample sizes: 894, 894, 897, 896, 896, 896, ... 
Resampling results:

  RMSE      Rsquared    MAE     
  5.533471  0.02326556  3.218907

> 
> # Function for Root Mean Squared Error
> RMSE <- function(error) { sqrt(mean(error^2)) }
> RMSE(model1amd1pq$residuals)
[1] 2.533435
> ###Plots (not sig)
> 
> model1amd1 <- svyglm(HSCRP ~ Kcal* relevel(Zinc, ref = "Inadequate Intake")+Gender+
+                        WBC + Choline +Folate +BMI, design = d62, family = gaussian(link='log'))
> 
> 
> 
> cat_plot(model1amd1, pred = Kcal, modx =Zinc, main.title = "Figure 3:Two-Way Interaction Effect Between Energy Intake & Dietary Zinc (66+)",
+          x.label =  "Energy Intake (Kcals)", interval = TRUE)
> 

> ###########################################################################################################################
> #### CHO
> ######################################################################################################################
> 
> ###w/ Ethnicity
> model1amd1pqz <- svyglm(HSCRP ~ relevel(Zinc, ref = "Inadequate Intake")* Carbohydrate + Ethnicity+
+                          WBC + Choline +Folate +BMI+Gender , design = d6, family = gaussian(link='log'))
> 
> 
> 
> summary(model1amd1pqz,df= degf(d6))

Call:
svyglm(formula = HSCRP ~ relevel(Zinc, ref = "Inadequate Intake") * 
    Carbohydrate + Ethnicity + WBC + Choline + Folate + BMI + 
    Gender, design = d6, family = gaussian(link = "log"))

Survey design:
subset(nhc2, Age_R > 65)

Coefficients:
                                                                                      Estimate Std. Error t value Pr(>|t|)    
(Intercept)                                                                         -0.0074344  0.5608116  -0.013   0.9895    
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake                             -0.3922651  0.1990263  -1.971   0.0580 .  
CarbohydrateLow Intake                                                              -0.4450014  0.2320344  -1.918   0.0647 .  
CarbohydrateModerate Intake                                                         -0.4706282  0.2733685  -1.722   0.0954 .  
EthnicityBlack                                                                       0.1382183  0.4153721   0.333   0.7416    
EthnicityMexican American                                                            0.8722329  0.3923051   2.223   0.0339 *  
EthnicityOther Hispanic                                                              0.0360170  0.4008627   0.090   0.9290    
EthnicityOther Race                                                                 -0.2639680  0.5269428  -0.501   0.6201    
EthnicityWhite                                                                       0.1800591  0.3491877   0.516   0.6099    
WBC                                                                                  0.1925141  0.0295420   6.517 3.32e-07 ***
Choline                                                                              0.0005113  0.0004211   1.214   0.2341    
Folate                                                                              -0.0002066  0.0003949  -0.523   0.6047    
BMI                                                                                 -0.0192756  0.0165241  -1.167   0.2526    
GenderMale                                                                           0.2577977  0.1541421   1.672   0.1048    
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:CarbohydrateLow Intake       0.9048963  0.4258000   2.125   0.0419 *  
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:CarbohydrateModerate Intake  0.1291478  0.3344953   0.386   0.7021    
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

(Dispersion parameter for gaussian family taken to be 26.94409)

Number of Fisher Scoring iterations: 16

> confint(model1amd1pqz,df=degf(d6))
                                                                                            2.5 %       97.5 %
(Intercept)                                                                         -1.2027760946 1.1879072618
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake                             -0.8164795798 0.0319493234
CarbohydrateLow Intake                                                              -0.9395710038 0.0495681483
CarbohydrateModerate Intake                                                         -1.0532994118 0.1120429720
EthnicityBlack                                                                      -0.7471264030 1.0235630963
EthnicityMexican American                                                            0.0360544300 1.7084113845
EthnicityOther Hispanic                                                             -0.8184016665 0.8904356480
EthnicityOther Race                                                                 -1.3871199127 0.8591839751
EthnicityWhite                                                                      -0.5642168545 0.9243350827
WBC                                                                                  0.1295468215 0.2554812892
Choline                                                                             -0.0003862628 0.0014088743
Folate                                                                              -0.0010483122 0.0006351386
BMI                                                                                 -0.0544958407 0.0159447307
GenderMale                                                                          -0.0707484035 0.5863438558
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:CarbohydrateLow Intake      -0.0026749219 1.8124674560
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:CarbohydrateModerate Intake -0.5838120801 0.8421077790
> summ(model1amd1pqz, exp = TRUE,confint=TRUE, n.sd=2, digits= 6)
MODEL INFO:
Observations: 995
Dependent Variable: HSCRP
Type: Analysis of complex survey design 
 Family: gaussian 
 Link function: log 

MODEL FIT:
Pseudo-R² (Cragg-Uhler) = 0.982485
Pseudo-R² (McFadden) = 0.130133
AIC = 6661.369683 

----------------------------------------------------------------------------------------
                                  exp(Est.)       2.5%      97.5%      t val.          p
------------------------------- ----------- ---------- ---------- ----------- ----------
(Intercept)                        0.992593   0.330680   2.979442   -0.013257   0.989598
relevel(Zinc, ref =                0.675525   0.457330   0.997822   -1.970921   0.067474
"Inadequate Intake")Adequate                                                            
Intake                                                                                  
CarbohydrateLow Intake             0.640823   0.406659   1.009826   -1.917825   0.074375
CarbohydrateModerate               0.624610   0.365525   1.067334   -1.721589   0.105696
Intake                                                                                  
EthnicityBlack                     1.148226   0.508700   2.591749    0.332758   0.743922
EthnicityMexican American          2.392247   1.108856   5.161033    2.223354   0.041979
EthnicityOther Hispanic            1.036673   0.472527   2.274348    0.089849   0.929596
EthnicityOther Race                0.767998   0.273417   2.157221   -0.500942   0.623682
EthnicityWhite                     1.197288   0.603906   2.373711    0.515651   0.613614
WBC                                1.212294   1.144094   1.284559    6.516627   0.000010
Choline                            1.000511   0.999686   1.001338    1.214194   0.243444
Folate                             0.999793   0.999020   1.000568   -0.523127   0.608528
BMI                                0.980909   0.949650   1.013197   -1.166512   0.261620
GenderMale                         1.294077   0.956652   1.750516    1.672468   0.115155
relevel(Zinc, ref =                2.471676   1.072877   5.694205    2.125167   0.050597
"Inadequate Intake")Adequate                                                            
Intake:CarbohydrateLow                                                                  
Intake                                                                                  
relevel(Zinc, ref =                1.137858   0.590698   2.191852    0.386098   0.704846
"Inadequate Intake")Adequate                                                            
Intake:CarbohydrateModerate                                                             
Intake                                                                                  
----------------------------------------------------------------------------------------

Estimated dispersion parameter = 26.94409 
> 
> a1amd1pqz <-  tbl_regression(model1amd1pqz,intercept= FALSE,add_estimate_to_reference_rows = TRUE
+                             , exponentiate = TRUE)%>%  bold_p(t= 0.05) %>%
+   modify_caption("**Table S.10: Analysis of the Coefficients of Participants' CHO Intake 66 and older**")
> a1amd1pqz

> ###Investigate terms
> regTermTest(model1amd1pqz, ~ relevel(Zinc, ref = "Inadequate Intake"):Carbohydrate, method = "LRT")
Working (Rao-Scott+F) LRT for relevel(Zinc, ref = "Inadequate Intake"):Carbohydrate
 in svyglm(formula = HSCRP ~ relevel(Zinc, ref = "Inadequate Intake") * 
    Carbohydrate + WBC + Choline + Folate + BMI + Gender + Ethnicity, 
    design = d6, family = gaussian(link = "log"))
Working 2logLR =  5.262241 p= 0.11192 
(scale factors:  1.6 0.39 );  denominator df= 15
> regTermTest(model1amd1pqz, ~ relevel(Zinc, ref = "Inadequate Intake") * Carbohydrate, method = "LRT")
Working (Rao-Scott+F) LRT for relevel(Zinc, ref = "Inadequate Intake") Carbohydrate relevel(Zinc, ref = "Inadequate Intake"):Carbohydrate
 in svyglm(formula = HSCRP ~ relevel(Zinc, ref = "Inadequate Intake") * 
    Carbohydrate + WBC + Choline + Folate + BMI + Gender + Ethnicity, 
    design = d6, family = gaussian(link = "log"))
Working 2logLR =  12.32516 p= 0.09059 
(scale factors:  2.3 1.2 0.73 0.46 0.27 );  denominator df= 15
> ###Checking for Overfitting
> # the caret library is loaded
> set.seed(123)
> 
> subset13amz <- subset(nhanes1, Age_R > 65 )
> subset13amsz <- na.omit(subset13amz)
> 
> 
> # Fit Generalized linear regression model using caret
> modelfz <- train( HSCRP ~ relevel(Zinc, ref = "Inadequate Intake")* Carbohydrate + Ethnicity+
+                    WBC + Choline +Folate + Gender +BMI,
+                  subset13amsz,
+                  method = "glm",
+                  trControl = trainControl(
+                    method = "cv",
+                    number = 10,
+                    verboseIter = T
+                  ))
+ Fold01: parameter=none 
- Fold01: parameter=none 
+ Fold02: parameter=none 
- Fold02: parameter=none 
+ Fold03: parameter=none 
- Fold03: parameter=none 
+ Fold04: parameter=none 
- Fold04: parameter=none 
+ Fold05: parameter=none 
- Fold05: parameter=none 
+ Fold06: parameter=none 
- Fold06: parameter=none 
+ Fold07: parameter=none 
- Fold07: parameter=none 
+ Fold08: parameter=none 
- Fold08: parameter=none 
+ Fold09: parameter=none 
- Fold09: parameter=none 
+ Fold10: parameter=none 
- Fold10: parameter=none 
Aggregating results
Fitting final model on full training set
> modelfz
Generalized Linear Model 

995 samples
  8 predictor

No pre-processing
Resampling: Cross-Validated (10 fold) 
Summary of sample sizes: 894, 894, 897, 896, 896, 896, ... 
Resampling results:

  RMSE      Rsquared    MAE     
  5.552029  0.02220069  3.242195

> 
> # Function for Root Mean Squared Error
> RMSE <- function(error) { sqrt(mean(error^2)) }
> RMSE(model1amd1pqz$residuals)
[1] 2.597208
>

> #### w/out Ethnicity

> model1amd1pqz <- svyglm(HSCRP ~ relevel(Zinc, ref = "Inadequate Intake")* Carbohydrate +
+                           WBC + Choline +Folate +BMI+Gender , design = d6, family = gaussian(link='log'))
> 
> 
> 
> summary(model1amd1pqz,df= degf(d6))

Call:
svyglm(formula = HSCRP ~ relevel(Zinc, ref = "Inadequate Intake") * 
    Carbohydrate + WBC + Choline + Folate + BMI + Gender, design = d6, 
    family = gaussian(link = "log"))

Survey design:
subset(nhc2, Age_R > 65)

Coefficients:
                                                                                      Estimate Std. Error t value Pr(>|t|)    
(Intercept)                                                                          0.3975644  0.3901794   1.019 0.316385    
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake                             -0.4992299  0.3419037  -1.460 0.154643    
CarbohydrateLow Intake                                                              -0.3410777  0.4034972  -0.845 0.404633    
CarbohydrateModerate Intake                                                         -0.6978771  0.4189623  -1.666 0.106178    
WBC                                                                                  0.1526095  0.0408523   3.736 0.000785 ***
Choline                                                                              0.0008091  0.0005217   1.551 0.131402    
Folate                                                                              -0.0001981  0.0005185  -0.382 0.705088    
BMI                                                                                 -0.0115294  0.0169672  -0.680 0.502022    
GenderMale                                                                           0.2587068  0.2023042   1.279 0.210772    
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:CarbohydrateLow Intake       0.9578628  0.4626465   2.070 0.047117 *  
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:CarbohydrateModerate Intake  0.5200354  0.3969346   1.310 0.200096    
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

(Dispersion parameter for gaussian family taken to be 28.49766)

Number of Fisher Scoring iterations: 14

> confint(model1amd1pqz,df=degf(d6))
                                                                                            2.5 %       97.5 %
(Intercept)                                                                         -0.4163355090 1.2114643117
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake                             -1.2124284827 0.2139687107
CarbohydrateLow Intake                                                              -1.1827581711 0.5006027117
CarbohydrateModerate Intake                                                         -1.5718172339 0.1760630125
WBC                                                                                  0.0673930682 0.2378259435
Choline                                                                             -0.0002791036 0.0018972598
Folate                                                                              -0.0012797175 0.0008834804
BMI                                                                                 -0.0469223100 0.0238634476
GenderMale                                                                          -0.1632924514 0.6807059587
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:CarbohydrateLow Intake      -0.0072009133 1.9229265621
relevel(Zinc, ref = "Inadequate Intake")Adequate Intake:CarbohydrateModerate Intake -0.3079556051 1.3480264897
> summ(model1amd1pqz, exp = TRUE,confint=TRUE, n.sd=2, digits= 6)
MODEL INFO:
Observations: 995
Dependent Variable: HSCRP
Type: Analysis of complex survey design 
 Family: gaussian 
 Link function: log 

MODEL FIT:
Pseudo-R² (Cragg-Uhler) = 0.926127
Pseudo-R² (McFadden) = 0.083826
AIC = 6702.976638 

---------------------------------------------------------------------------------------
                                 exp(Est.)       2.5%      97.5%      t val.          p
------------------------------ ----------- ---------- ---------- ----------- ----------
(Intercept)                       1.488196   0.692690   3.197285    1.018927   0.320406
relevel(Zinc, ref =               0.606998   0.310569   1.186359   -1.460148   0.159781
"Inadequate Intake")Adequate                                                           
Intake                                                                                 
CarbohydrateLow Intake            0.711004   0.322414   1.567939   -0.845304   0.407941
CarbohydrateModerate              0.497641   0.218925   1.131194   -1.665728   0.111355
Intake                                                                                 
WBC                               1.164870   1.075236   1.261976    3.735639   0.001304
Choline                           1.000809   0.999787   1.001833    1.550943   0.136596
Folate                            0.999802   0.998786   1.000818   -0.382090   0.706424
BMI                               0.988537   0.956204   1.021963   -0.679514   0.504601
GenderMale                        1.295254   0.871271   1.925558    1.278801   0.215607
relevel(Zinc, ref =               2.606121   1.052420   6.453569    2.070399   0.051574
"Inadequate Intake")Adequate                                                           
Intake:CarbohydrateLow                                                                 
Intake                                                                                 
relevel(Zinc, ref =               1.682087   0.772640   3.662013    1.310129   0.205001
"Inadequate Intake")Adequate                                                           
Intake:CarbohydrateModerate                                                            
Intake                                                                                 
---------------------------------------------------------------------------------------

Estimated dispersion parameter = 28.49766 
> 
> a1amd1pqz <-  tbl_regression(model1amd1pqz,intercept= FALSE,add_estimate_to_reference_rows = TRUE
+                              , exponentiate = TRUE)%>%  bold_p(t= 0.05) %>%
+   modify_caption("**Table S.10: Analysis of the Coefficients of Participants' CHO Intake 66 and older**")
> a1amd1pqz
> ###Investigate terms
> regTermTest(model1amd1pqz, ~ relevel(Zinc, ref = "Inadequate Intake"):Carbohydrate, method = "LRT")
Working (Rao-Scott+F) LRT for relevel(Zinc, ref = "Inadequate Intake"):Carbohydrate
 in svyglm(formula = HSCRP ~ relevel(Zinc, ref = "Inadequate Intake") * 
    Carbohydrate + WBC + Choline + Folate + BMI + Gender, design = d6, 
    family = gaussian(link = "log"))
Working 2logLR =  6.200519 p= 0.080731 
(scale factors:  1.7 0.34 );  denominator df= 20
> regTermTest(model1amd1pqz, ~ relevel(Zinc, ref = "Inadequate Intake") * Carbohydrate, method = "LRT")
Working (Rao-Scott+F) LRT for relevel(Zinc, ref = "Inadequate Intake") Carbohydrate relevel(Zinc, ref = "Inadequate Intake"):Carbohydrate
 in svyglm(formula = HSCRP ~ relevel(Zinc, ref = "Inadequate Intake") * 
    Carbohydrate + WBC + Choline + Folate + BMI + Gender, design = d6, 
    family = gaussian(link = "log"))
Working 2logLR =  8.080474 p= 0.20221 
(scale factors:  3 1.2 0.42 0.22 0.13 );  denominator df= 20
> ###Checking for Overfitting
> # the caret library is loaded
> set.seed(123)
> 
> subset13amz <- subset(nhanes1, Age_R > 65 )
> subset13amsz <- na.omit(subset13amz)
> 
> 
> # Fit Generalized linear regression model using caret
> modelfz <- train( HSCRP ~ relevel(Zinc, ref = "Inadequate Intake")* Carbohydrate +
+                     WBC + Choline +Folate + Gender +BMI,
+                   subset13amsz,
+                   method = "glm",
+                   trControl = trainControl(
+                     method = "cv",
+                     number = 10,
+                     verboseIter = T
+                   ))
+ Fold01: parameter=none 
- Fold01: parameter=none 
+ Fold02: parameter=none 
- Fold02: parameter=none 
+ Fold03: parameter=none 
- Fold03: parameter=none 
+ Fold04: parameter=none 
- Fold04: parameter=none 
+ Fold05: parameter=none 
- Fold05: parameter=none 
+ Fold06: parameter=none 
- Fold06: parameter=none 
+ Fold07: parameter=none 
- Fold07: parameter=none 
+ Fold08: parameter=none 
- Fold08: parameter=none 
+ Fold09: parameter=none 
- Fold09: parameter=none 
+ Fold10: parameter=none 
- Fold10: parameter=none 
Aggregating results
Fitting final model on full training set
> modelfz
Generalized Linear Model 

995 samples
  7 predictor

No pre-processing
Resampling: Cross-Validated (10 fold) 
Summary of sample sizes: 894, 894, 897, 896, 896, 896, ... 
Resampling results:

  RMSE      Rsquared   MAE     
  5.529644  0.0291514  3.227182

> 
> # Function for Root Mean Squared Error
> RMSE <- function(error) { sqrt(mean(error^2)) }
> RMSE(model1amd1pqz$residuals)
[1] 2.11096