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RMarkovBlanket.r
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1 | +#Efrain Gonzalez | |
2 | +#7/25/2017 | |
3 | +#Code for Markov Blanket | |
4 | + | |
5 | + | |
6 | +#The required libraries | |
7 | +library(pryr) | |
8 | +library(MASS) | |
9 | +library(dplyr) | |
10 | +library(tidyr) | |
11 | +library(readr) | |
12 | +library(stringr) | |
13 | + | |
14 | + | |
15 | +#Have the user choose an original Dot file that they want to use | |
16 | +DotFile <- file.choose() | |
17 | +TheDotP1 <- read_delim(DotFile,delim = "\t",col_names = FALSE) %>% | |
18 | + dplyr::filter(!grepl("->|[{}]",X1)) %>% | |
19 | + dplyr::filter(!grepl("Banjo",X1)) %>% | |
20 | + dplyr::filter(!grepl("labeljust",X1)) | |
21 | +counterP1 <- 1 | |
22 | +sizeDotP1 <- dim(TheDotP1)[1] | |
23 | +NewDotP1 <- matrix("0",ncol = 2, nrow = sizeDotP1) | |
24 | +for(counterP1 in 1:sizeDotP1){ | |
25 | + coldataP1 <- str_trim(TheDotP1[counterP1,1]) %>% | |
26 | + as.character(.,stringsAsFactors = FALSE) | |
27 | + if(grepl("Banjo|labeljust|>",coldataP1)==FALSE){ | |
28 | + NumberP1 <- strsplit(coldataP1," ") %>% | |
29 | + .[[1]]%>% | |
30 | + .[1] | |
31 | + VarNameP1 <- strsplit(coldataP1," ") %>% | |
32 | + .[[1]] %>% | |
33 | + .[2] %>% | |
34 | + strsplit(.,"\"") %>% | |
35 | + .[[1]] %>% | |
36 | + .[grep("^\\w|^\\d",.)] | |
37 | + NewDotP1[counterP1,1] <- VarNameP1 | |
38 | + NewDotP1[counterP1,2] <- NumberP1 | |
39 | + } | |
40 | + if(grepl("->",coldataP1) == TRUE){ | |
41 | + break | |
42 | + } | |
43 | +} | |
44 | + | |
45 | + | |
46 | +TheDotP2 <- read_delim(DotFile,delim = "\t",col_names = FALSE) %>% | |
47 | + dplyr::filter(grepl("->",X1)) | |
48 | +counterP2 <- 1 | |
49 | +sizeDotP2 <- dim(TheDotP2)[1] | |
50 | +NewDotP2 <- matrix("0",ncol = 2, nrow = sizeDotP2) | |
51 | +for(counterP2 in 1:sizeDotP2){ | |
52 | + coldataP2 <- str_trim(TheDotP2[counterP2,1]) %>% | |
53 | + as.character(.,stringsAsFactors = FALSE) | |
54 | + ParentNumP2 <- strsplit(coldataP2,"->") %>% | |
55 | + .[[1]]%>% | |
56 | + .[1] | |
57 | + ChildNumP2 <- strsplit(coldataP2,"->") %>% | |
58 | + .[[1]] %>% | |
59 | + .[2] %>% | |
60 | + strsplit(.,";") %>% | |
61 | + .[[1]] %>% | |
62 | + .[1] | |
63 | + NewDotP2[counterP2,1] <- ParentNumP2 | |
64 | + NewDotP2[counterP2,2] <- ChildNumP2 | |
65 | +} | |
66 | + | |
67 | +colnames(NewDotP2) <- c("Parents","Children") | |
68 | + | |
69 | +#Matching numbers to variable names | |
70 | +NewDotP2_2 <- NewDotP2 | |
71 | +for(i in 1:sizeDotP1){ | |
72 | + #Where is the variable located within NewDotP2 (column one only)? | |
73 | + chngreq <- grep(paste0("^",NewDotP1[i,2],"$"),NewDotP2_2[,1]) | |
74 | + if(is.na(sum(chngreq)) == FALSE){ | |
75 | + if(sum(chngreq) > 0){ | |
76 | + NewDotP2_2[chngreq,1] <- gsub(paste0("^",NewDotP1[i,2],"$"),NewDotP1[i,1],NewDotP2_2[chngreq,1]) | |
77 | + } | |
78 | + } | |
79 | + i <- i + 1 | |
80 | +} | |
81 | +NewDotP2_2 | |
82 | +for(j in 1:sizeDotP1){ | |
83 | + #Where is the variable located within NewDotP2 (column two only)? | |
84 | + chngreq <- grep(paste0("^",NewDotP1[j,2],"$"),NewDotP2_2[,2]) | |
85 | + if(is.na(sum(chngreq)) == FALSE){ | |
86 | + if(sum(chngreq) > 0){ | |
87 | + NewDotP2_2[chngreq,2] <- gsub(paste0("^",NewDotP1[j,2],"$"),NewDotP1[j,1],NewDotP2_2[chngreq,2]) | |
88 | + } | |
89 | + } | |
90 | + j <- j + 1 | |
91 | +} | |
92 | + | |
93 | +lrgMarkov <- dim(NewDotP2_2)[1] | |
94 | +MBlanky <- function(MarkovDegree = lrgMarkov, VariableStartName = "Alzheimer", VariableEndName = "Age"){ | |
95 | + #Finding the Parents and Children | |
96 | + d <- 1 | |
97 | + AllNamList1 <- vector("list",length = 3) | |
98 | + #AllNamList <- vector("list", length = 3) | |
99 | + ##Finding the Parents of the Parents | |
100 | + ##A list of lists | |
101 | + ##outer set by the degree of the Markov blanket | |
102 | + AllVarList <- vector("list",length = 3) | |
103 | + for(d in 1:MarkovDegree){ | |
104 | + colnames(NewDotP2_2) <- NULL | |
105 | + ##Which variable are you looking for? | |
106 | + ##This is the VariableEndName | |
107 | + if(d == 1){ | |
108 | + ##Finding the Parents for the variable | |
109 | + LocPofVar <- grep(VariableStartName,NewDotP2_2[,2]) | |
110 | + PofVar <- NewDotP2_2[LocPofVar,1] | |
111 | + AllNamList1[[1]] <- PofVar | |
112 | + | |
113 | + ##Finding the Children for the variable | |
114 | + LocCofVar <- grep(VariableStartName,NewDotP2_2[,1]) | |
115 | + CofVar <- NewDotP2_2[LocCofVar,2] | |
116 | + AllNamList1[[2]] <- CofVar | |
117 | + | |
118 | + ##Finding the Co-Parents of the Children for the variable | |
119 | + NumofChild <- length(CofVar) | |
120 | + if(NumofChild > 0){ | |
121 | + ##Creating a list of the Co-Parents for each of the children | |
122 | + ##list size is based on the amount of Children | |
123 | + COPlist <- vector("character", length = 0) | |
124 | + nc <- 1 | |
125 | + for(nc in 1:NumofChild){ | |
126 | + LocCOPofVar <- grep(CofVar[nc],NewDotP2_2[,2]) | |
127 | + COPofVar <- NewDotP2_2[LocCOPofVar,1] | |
128 | + if(grepl(COPofVar,VariableStartName)){ | |
129 | + next | |
130 | + } else{ | |
131 | + #COPlist[[nc]] <- COPofVar[COPofVar!=VariableStartName] | |
132 | + COPlist <- append(COPlist,COPofVar) | |
133 | + } | |
134 | + nc <- nc + 1 | |
135 | + } | |
136 | + } else { | |
137 | + ##Making COPlist empty | |
138 | + COPlist <- vector("character",length = 0) | |
139 | + } | |
140 | + AllNamList1[[3]] <- COPlist | |
141 | + AllVarList[[1]] <- AllNamList1 | |
142 | + } else if(d > 1){ | |
143 | + ##inner set by the length of the previous AllVarlist we are working on | |
144 | + lPreVList <- length(AllVarList[[d-1]]) | |
145 | + ef <- 1 | |
146 | + ##PCCP will eventually equal the total size that we expect for the iteration (#d) | |
147 | + ## which is just lPreVList * 3 | |
148 | + PCCP <- 1 | |
149 | + newsize <- (lPreVList * 3) | |
150 | + if(d > 3){ | |
151 | + AllVarList[[d]] <- vector("list") | |
152 | + } | |
153 | + for(ef in 1:lPreVList){ | |
154 | + ##Finding the Parents | |
155 | + NumofVars <- length(AllVarList[[d-1]][[ef]]) | |
156 | + if(NumofVars > 0){ | |
157 | + ##Creating a list of the Parents for each of the Variables | |
158 | + ##list size is based on the amount of Previous Variables | |
159 | + PofVlist <- vector("character", length = 0) | |
160 | + np <- 1 | |
161 | + for(np in 1:NumofVars){ | |
162 | + LocPofVar <- grep(AllVarList[[d-1]][[ef]][np],NewDotP2_2[,2]) | |
163 | + PofVar <- NewDotP2_2[LocPofVar,1] | |
164 | + PofVlist <- append(PofVlist,PofVar) | |
165 | + np <- np + 1 | |
166 | + } | |
167 | + } else { | |
168 | + ##Making COPlist empty | |
169 | + PofVlist <- vector("character",length = 0) | |
170 | + } | |
171 | + AllVarList[[d]][[PCCP]] <- PofVlist | |
172 | + PCCP <- PCCP + 1 | |
173 | + | |
174 | + ##Finding the Children | |
175 | + if(NumofVars > 0){ | |
176 | + ##Creating a list of the Children for each of the Previous Parents | |
177 | + ##list size is based on the amount of Previous Parents | |
178 | + CofVlist <- vector("character", length = 0) | |
179 | + np <- 1 | |
180 | + for(np in 1:NumofVars){ | |
181 | + LocCofVar <- grep(AllVarList[[d-1]][[ef]][np],NewDotP2_2[,1]) | |
182 | + CofVar <- NewDotP2_2[LocCofVar,2] | |
183 | + #if(grepl(VariableStartName,CofVar)){ | |
184 | + # next | |
185 | + #} else{ | |
186 | + CofVlist <- append(CofVlist,CofVar) | |
187 | + #} | |
188 | + np <- np + 1 | |
189 | + } | |
190 | + } else { | |
191 | + ##Making CofPlist empty | |
192 | + CofVlist <- vector("character",length = 0) | |
193 | + } | |
194 | + AllVarList[[d]][[PCCP]] <- CofVlist | |
195 | + PCCP <- PCCP + 1 | |
196 | + | |
197 | + ##Finding the Co-Parents | |
198 | + NumofCVars <- length(CofVlist) | |
199 | + if(NumofCVars > 0){ | |
200 | + ncp <- 1 | |
201 | + CPofClist <- vector("character",length = 0) | |
202 | + for(ncp in 1:NumofCVars){ | |
203 | + LocCPofCVar <- grep(CofVlist[ncp],NewDotP2_2[,2]) | |
204 | + CPofCVar <- NewDotP2_2[LocCPofCVar,1] | |
205 | + CPofClist <- append(CPofClist,CPofCVar) | |
206 | + ncp <- ncp + 1 | |
207 | + } | |
208 | + | |
209 | + } else { | |
210 | + ##Making COPlist empty | |
211 | + CPofClist <- vector("character",length = 0) | |
212 | + } | |
213 | + AllVarList[[d]][[PCCP]] <- CPofClist | |
214 | + PCCP <- PCCP + 1 | |
215 | + ef <- ef + 1 | |
216 | + } | |
217 | + } | |
218 | + ##Stop if you have found the VariableEndName value | |
219 | + if(sum(grepl(VariableEndName,AllVarList)) > 0){ | |
220 | + break | |
221 | + } | |
222 | + d <- d + 1 | |
223 | + } | |
224 | + ##The Markov Degree is that found below | |
225 | + d | |
226 | +} | |
227 | +#Now use the command MBlanky() with the appropriate settings | |
0 | 228 | \ No newline at end of file |