Commit 6629da35df7d8263eb33c7af8d80fd510c683aed
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Summary of the orders
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Summary.R
| File was created | 1 | #source("/home/zgong001/Documents/Alarm/D50C9v/RCode/CombineOrders.R") | |
| 2 | getRelation = | ||
| 3 | function(st = "[6][8][5][7|6:8:5][1|7][3|7:1][4|1][2|4][0|2]"){ | ||
| 4 | re = c() | ||
| 5 | temstr = substr(st, 2, nchar(st)-1) | ||
| 6 | stlist = strsplit(chartr(old = "][", new = "##", temstr), "##") | ||
| 7 | for(i in 1:length(stlist[[1]])){ | ||
| 8 | temc = chartr(old = "|", new = "g", stlist[[1]][i]) | ||
| 9 | |||
| 10 | if (grepl("g", temc)){ | ||
| 11 | temc2 = strsplit(temc, "g") | ||
| 12 | |||
| 13 | X = temc2[[1]][1] | ||
| 14 | TY = strsplit(temc2[[1]][2], ":") | ||
| 15 | for(j in 1:length(TY[[1]])){ | ||
| 16 | Y = TY[[1]][j] | ||
| 17 | |||
| 18 | cc= paste(Y,"->", X, sep = "") | ||
| 19 | re = append(re, cc) | ||
| 20 | } | ||
| 21 | } | ||
| 22 | } | ||
| 23 | return(re) | ||
| 24 | } | ||
| 25 | |||
| 26 | creatDataframe = | ||
| 27 | function(v = c("0", "1","2","3","4","5","6","7","8"), r = 246){ | ||
| 28 | cn = c() | ||
| 29 | co= combn(v,2) | ||
| 30 | for(i in 1:ncol(co)){ | ||
| 31 | X = co[1,i] | ||
| 32 | Y = co[2,i] | ||
| 33 | c1 = paste(X, "->", Y, sep = "") | ||
| 34 | cn = append(cn,c1) | ||
| 35 | c2 = paste(Y, "->", X, sep = "") | ||
| 36 | cn = append(cn,c2) | ||
| 37 | c3 = paste(X, " NA ", Y, sep = "") | ||
| 38 | cn = append(cn,c3) | ||
| 39 | } | ||
| 40 | |||
| 41 | b= ncol(co) | ||
| 42 | |||
| 43 | re = data.frame(matrix(0, nrow=r, ncol=b*3)) | ||
| 44 | colnames(re) = cn | ||
| 45 | |||
| 46 | return(re) | ||
| 47 | } | ||
| 48 | |||
| 49 | |||
| 50 | sumTable = | ||
| 51 | function (pathname = "/home/zgong001/Documents/Alarm/D1KC9v/D1KC9v BestOrders/Strus_D1KC9v.txt", | ||
| 52 | v = c("0", "1","2","3","4","5","6","7","8"), | ||
| 53 | exfilename = "/home/zgong001/Documents/Alarm/D1KC9v/D1KC9v BestOrders/Strus_D1KC9v.xlsx", | ||
| 54 | xlsxfile = "/home/zgong001/Documents/Alarm/D50S9v2/D50S9vRS.xlsx"){ | ||
| 55 | library(bnlearn) | ||
| 56 | library(xlsx) | ||
| 57 | library(dplyr) | ||
| 58 | suminput = read.table(pathname, header = FALSE) | ||
| 59 | sumResu = data.frame() | ||
| 60 | sumAnce = data.frame() | ||
| 61 | suminput$ord = paste(suminput$V1,suminput$V2,suminput$V3,suminput$V4,suminput$V5,suminput$V6,suminput$V7,suminput$V8,suminput$V9, sep = " ") | ||
| 62 | suminput = suminput[-c(1,2,3,4,5,6,7,8,9,13)] | ||
| 63 | colnames(suminput)[1] <- "OrderScores" | ||
| 64 | colnames(suminput)[2] <- "Structures" | ||
| 65 | colnames(suminput)[3] <- "StructScores" | ||
| 66 | |||
| 67 | orders= aggregate( OrderScores ~ord, data=suminput, FUN = mean) | ||
| 68 | orders = orders[order(-orders[,2]), ] | ||
| 69 | for(i in 1:nrow(orders)){ | ||
| 70 | orders$Opercentage[i] = exp(-log(sum(exp(orders$OrderScores-orders$OrderScores[i])))) | ||
| 71 | } | ||
| 72 | |||
| 73 | orders$Ocumper = cumsum(orders$Opercentage) | ||
| 74 | |||
| 75 | for(i in 1:nrow(orders)){ | ||
| 76 | tem = suminput[which(suminput$ord== orders[i,1]), ] | ||
| 77 | |||
| 78 | tem$Opercentage = orders[i,3] | ||
| 79 | tem$Ocumper = orders[i,4] | ||
| 80 | |||
| 81 | for(j in 1:nrow(tem)){ | ||
| 82 | tem$Spercentage[j] = exp(-log(sum(exp(tem$StructScores-tem$StructScores[j])))) | ||
| 83 | } | ||
| 84 | tem$Scumper = cumsum(tem$Spercentage) | ||
| 85 | tem = tem[c("ord", "OrderScores", "Opercentage","Ocumper", "Structures", "StructScores","Spercentage","Scumper")] | ||
| 86 | sumResu = rbind(sumResu, tem) | ||
| 87 | } | ||
| 88 | |||
| 89 | rs = nrow(sumResu) | ||
| 90 | |||
| 91 | rl = creatDataframe(v,rs) | ||
| 92 | sumResu= cbind(sumResu, rl) | ||
| 93 | |||
| 94 | sumAnce = sumResu | ||
| 95 | |||
| 96 | co= combn(v,2) | ||
| 97 | |||
| 98 | for(i in 1:nrow(sumResu)){ | ||
| 99 | s = as.character(sumResu [i,5]) | ||
| 100 | rel = getRelation(st = s) | ||
| 101 | |||
| 102 | for(j in 1:ncol(co)){ | ||
| 103 | X = co[1,j] | ||
| 104 | Y = co[2,j] | ||
| 105 | c1 = paste(X, "->", Y, sep = "") | ||
| 106 | c2 = paste(Y, "->", X, sep = "") | ||
| 107 | c3 = paste(X, " NA ", Y, sep = "") | ||
| 108 | |||
| 109 | if (c1 %in% rel){ | ||
| 110 | sumResu[i,c1] = sumResu$Opercentage[i]*sumResu$Spercentage[i] | ||
| 111 | } | ||
| 112 | else if(c2 %in% rel){ | ||
| 113 | sumResu[i,c2] = sumResu$Opercentage[i]*sumResu$Spercentage[i] | ||
| 114 | } | ||
| 115 | else{ | ||
| 116 | sumResu[i,c3] = sumResu$Opercentage[i]*sumResu$Spercentage[i] | ||
| 117 | } | ||
| 118 | |||
| 119 | } | ||
| 120 | |||
| 121 | } | ||
| 122 | |||
| 123 | for(i in 1:nrow(sumAnce)){ | ||
| 124 | s = as.character(sumAnce [i,5]) | ||
| 125 | dags = model2network(s) | ||
| 126 | |||
| 127 | for(j in 1:ncol(co)){ | ||
| 128 | X = co[1,j] | ||
| 129 | Y = co[2,j] | ||
| 130 | c1 = paste(X, "->", Y, sep = "") | ||
| 131 | c2 = paste(Y, "->", X, sep = "") | ||
| 132 | c3 = paste(X, " NA ", Y, sep = "") | ||
| 133 | |||
| 134 | pXY = path(dags, from = X, to = Y) | ||
| 135 | pYX = path(dags, from = Y, to = X) | ||
| 136 | |||
| 137 | if (pXY){ | ||
| 138 | sumAnce[i,c1] = sumAnce$Opercentage[i]*sumAnce$Spercentage[i] | ||
| 139 | } | ||
| 140 | else if(pYX){ | ||
| 141 | sumAnce[i,c2] = sumAnce$Opercentage[i]*sumAnce$Spercentage[i] | ||
| 142 | } | ||
| 143 | else{ | ||
| 144 | sumAnce[i,c3] = sumAnce$Opercentage[i]*sumAnce$Spercentage[i] | ||
| 145 | } | ||
| 146 | |||
| 147 | } | ||
| 148 | |||
| 149 | } | ||
| 150 | |||
| 151 | |||
| 152 | |||
| 153 | sumP = colSums(sumResu[, -c(1:8)]) | ||
| 154 | sumA = colSums(sumAnce[, -c(1:8)]) | ||
| 155 | |||
| 156 | reP = read.xlsx(xlsxfile, sheetName = "Sheet1", colIndex = 1:3) | ||
| 157 | reA = read.xlsx(xlsxfile, sheetName = "Sheet2", colIndex = 1:3) | ||
| 158 | |||
| 159 | sP = cbind(reP, sumP, diffT = abs(sumP-reP[,2]), diffB = abs(sumP-reP[,3])) | ||
| 160 | sA = cbind(reA, sumA, diffT = abs(sumA-reA[,2]), diffB = abs(sumA-reA[,3])) | ||
| 161 | |||
| 162 | distanceP = colSums(sP[,c(5,6)]) | ||
| 163 | distanceA = colSums(sA[,c(5,6)]) | ||
| 164 | |||
| 165 | |||
| 166 | |||
| 167 | write.xlsx(sumResu, exfilename, sheetName = "Parents Detail", col.names = TRUE, row.names = FALSE, append = FALSE) | ||
| 168 | write.xlsx(sP, exfilename, sheetName = "Parents Summary", col.names = TRUE, row.names = TRUE, append = TRUE) | ||
| 169 | write.xlsx(distanceP, exfilename, sheetName = "Parents Distance", col.names = TRUE, row.names = TRUE, append = TRUE) | ||
| 170 | write.xlsx(sumAnce, exfilename, sheetName = "Ancestor Detail", col.names = TRUE, row.names = FALSE, append = TRUE) | ||
| 171 | write.xlsx(sA, exfilename, sheetName = "Ancestor Summary", col.names = TRUE, row.names = TRUE, append = TRUE) | ||
| 172 | write.xlsx(distanceA, exfilename, sheetName = "Ancestor Distance", col.names = TRUE, row.names = TRUE, append = TRUE) | ||
| 173 | |||
| 174 | |||
| 175 | # return(sP) | ||
| 176 | |||
| 177 | } | ||
| 178 | |||
| 179 | #--------------------------------------------------------------------------------- | ||
| 180 | sortStru = function(st = "[5][6][8][7|5:8][1|5:7][3|7:8][2|6:1][4|1][0|2]"){ | ||
| 181 | library(dplyr) | ||
| 182 | re = "" | ||
| 183 | temstr = substr(st, 2, nchar(st)-1) | ||
| 184 | stlist = strsplit(chartr(old = "][", new = "##", temstr), "##") | ||
| 185 | stlist = sort(stlist[[1]]) | ||
| 186 | for(i in 1:length(stlist)){ | ||
| 187 | if(nchar(stlist[i])>3){ | ||
| 188 | |||
| 189 | temc = chartr(old = "|", new = "g", stlist[i]) | ||
| 190 | |||
| 191 | temc2 = strsplit(temc, "g") | ||
| 192 | X = temc2[[1]][1] | ||
| 193 | TY = strsplit(temc2[[1]][2], ":") | ||
| 194 | TY = sort(TY[[1]]) | ||
| 195 | |||
| 196 | TY2 = paste(TY, collapse = ":") | ||
| 197 | |||
| 198 | stlist[i] = paste(X,"|", TY2, sep = "") | ||
| 199 | |||
| 200 | stlist[i] <- TY %>% | ||
| 201 | paste(., collapse=":") %>% | ||
| 202 | paste(X, "|", ., sep = "") | ||
| 203 | |||
| 204 | } | ||
| 205 | |||
| 206 | } | ||
| 207 | |||
| 208 | re <- stlist %>% | ||
| 209 | paste(., collapse="][") %>% | ||
| 210 | paste("[", ., "]", sep = "") | ||
| 211 | |||
| 212 | return(re) | ||
| 213 | } | ||
| 214 | |||
| 215 | MB = | ||
| 216 | function (struc ="[6][8][5][7|6:8:5][3|7][1|7:3][4|1][2|4][0|2]", v ="1"){ | ||
| 217 | |||
| 218 | library(xlsx) | ||
| 219 | library(bnlearn) | ||
| 220 | library(dplyr) | ||
| 221 | |||
| 222 | |||
| 223 | mbs = "" | ||
| 224 | |||
| 225 | strutem <- struc %>% | ||
| 226 | as.character(.) %>% | ||
| 227 | substr(., 2, nchar(.)-1) | ||
| 228 | |||
| 229 | stru = strsplit(chartr(old = "][", new = "##", strutem), "##") | ||
| 230 | |||
| 231 | for(j in 1:length(stru[[1]])){ | ||
| 232 | if(grepl(v,stru[[1]][j])){ | ||
| 233 | mbs = paste(mbs, "[", stru[[1]][j], "]", sep = "") | ||
| 234 | } | ||
| 235 | } | ||
| 236 | return(mbs) | ||
| 237 | } | ||
| 238 | |||
| 239 | sumBlanket2 = | ||
| 240 | function (xlsxfile = "/home/zgong001/Documents/Alarm/D50S9v2/D50S9v2-newswap-0.5NONE-2-1h/Strus_D50S9v2_E30r3_o.xlsx", | ||
| 241 | xlsxfile2 = "/home/zgong001/Documents/Alarm/D50S9v2/D50S9vRS.xlsx"){ | ||
| 242 | |||
| 243 | library(xlsx) | ||
| 244 | library(bnlearn) | ||
| 245 | library(dplyr) | ||
| 246 | |||
| 247 | re = read.xlsx(xlsxfile, sheetName = "Parents Detail", colIndex = 1:8) | ||
| 248 | re = na.omit(re) | ||
| 249 | |||
| 250 | colnames(re) = c("Order", "OrderScore", "OP", "OPC", "Structures", "StructureScore", "SP", "SPC") | ||
| 251 | |||
| 252 | truDis = vector() | ||
| 253 | besDis = vector() | ||
| 254 | |||
| 255 | for(l in 1:9){ | ||
| 256 | a = l*4-3 | ||
| 257 | b = l*4-1 | ||
| 258 | n = as.character(l-1) | ||
| 259 | |||
| 260 | rebm = read.xlsx(xlsxfile2, sheetName = "Sheet3", colIndex = a:b) | ||
| 261 | rebm = na.omit(rebm) | ||
| 262 | colnames(rebm) = c("LableM", "TrueB", "BestB") | ||
| 263 | |||
| 264 | MBS = vector(mode="character", length=0) | ||
| 265 | for(i in 1:nrow(re)){ | ||
| 266 | |||
| 267 | mbt = MB(struc = re[i,5], v = n) | ||
| 268 | st = sortStru(as.character(mbt)) | ||
| 269 | MBS = append(MBS,st) | ||
| 270 | |||
| 271 | } | ||
| 272 | |||
| 273 | blankScore = re$OP*re$SP | ||
| 274 | REE = cbind(re, MBS, blankScore) | ||
| 275 | |||
| 276 | ag = aggregate(blankScore ~ MBS, data = REE, sum ) | ||
| 277 | |||
| 278 | |||
| 279 | truedist = 0 | ||
| 280 | |||
| 281 | |||
| 282 | if(rebm[1,1] %in% ag[,1]){ | ||
| 283 | tem = ag | ||
| 284 | tem[which(tem$MBS == as.character(rebm[1,1])),2] = abs(1-tem[which(tem$MBS == as.character(rebm[1,1])),2]) | ||
| 285 | truedist = sum(tem[,2]) | ||
| 286 | } | ||
| 287 | else{ | ||
| 288 | truedist = 2 | ||
| 289 | } | ||
| 290 | |||
| 291 | truDis = append(truDis, truedist) | ||
| 292 | |||
| 293 | |||
| 294 | |||
| 295 | bestdist = 0 | ||
| 296 | |||
| 297 | tem2 = rebm[-1,1] | ||
| 298 | tem3 = ag[,1] | ||
| 299 | tt = vector() | ||
| 300 | |||
| 301 | di1 = setdiff(tem2, tem3) | ||
| 302 | di2 = setdiff(tem3, tem2) | ||
| 303 | |||
| 304 | if(length(di1) == 0 & length(di2) == 0){ | ||
| 305 | temm = ag[order(ag[,1]),] | ||
| 306 | temm1 =rebm[-1,c(1,3)] | ||
| 307 | |||
| 308 | temmm11= temm1[order(temm1[,1]),] | ||
| 309 | |||
| 310 | temm[,2] = abs(temmm11[,2] - temm[,2]) | ||
| 311 | |||
| 312 | bestdist = sum(temm[,2]) | ||
| 313 | |||
| 314 | } | ||
| 315 | else if(length(di1) == 0){ | ||
| 316 | |||
| 317 | temm = ag[which(ag[,1] %in% di2),] | ||
| 318 | temm2 =rebm[-1,c(1,3)] | ||
| 319 | temm1 = ag[which(! ag[,1] %in% di2),] | ||
| 320 | |||
| 321 | temmm21= temm1[order(temm1[,1]),] | ||
| 322 | temmm22= temm2[order(temm2[,1]),] | ||
| 323 | temmm21[,2] = abs(temmm21[,2] - temmm22[,2]) | ||
| 324 | temm=rbind(temm,temmm21) | ||
| 325 | |||
| 326 | |||
| 327 | bestdist = sum(temm[,2]) | ||
| 328 | |||
| 329 | }else if(length(di2) == 0){ | ||
| 330 | |||
| 331 | temm2 =rebm[-1,c(1,3)] | ||
| 332 | |||
| 333 | temm = temm2[which(temm2[,1] %in% di1),] | ||
| 334 | |||
| 335 | temm1 = temm2[which(! temm2[,1] %in% di1),] | ||
| 336 | |||
| 337 | |||
| 338 | temmm21= temm1[order(temm1[,1]),] | ||
| 339 | temmm22= ag[order(ag[,1]),] | ||
| 340 | |||
| 341 | |||
| 342 | temmm21[,2] = abs(temmm21[,2] - temmm22[,2]) | ||
| 343 | temm=rbind(temm,temmm21) | ||
| 344 | |||
| 345 | |||
| 346 | bestdist = sum(temm[,2]) | ||
| 347 | |||
| 348 | |||
| 349 | }else{ | ||
| 350 | comm = intersect(tem2, tem3) | ||
| 351 | |||
| 352 | |||
| 353 | temmm1 = rebm[which(rebm$LableM %in% comm),c(1,3)] | ||
| 354 | temmm12= temmm1[order(temmm1[,1]),] | ||
| 355 | temmm2 = ag[which(ag[,1] %in% comm),] | ||
| 356 | temmm22= temmm2[order(temmm2[,1]),] | ||
| 357 | temmm12[,2] = abs(temmm12[,2] - temmm22[,2]) | ||
| 358 | temt = rbind(temmm12, rebm[which(rebm$LableM %in% di1),c(1,3)]) | ||
| 359 | |||
| 360 | temt = rbind(data.frame(MBS = temt[,1], blankScore =temt[,2] ), ag[which(ag[,1] %in% di2),]) | ||
| 361 | bestdist = sum(temt[,2]) | ||
| 362 | } | ||
| 363 | |||
| 364 | besDis = append(besDis, bestdist) | ||
| 365 | |||
| 366 | |||
| 367 | } | ||
| 368 | |||
| 369 | td = sum(truDis) | ||
| 370 | bd = sum(besDis) | ||
| 371 | |||
| 372 | write.xlsx(data.frame("True dis"= td, "Best dis" = bd), xlsxfile, sheetName = "Blanket Distance", col.names = TRUE, row.names = FALSE, append = TRUE) | ||
| 373 | |||
| 374 | return(re) | ||
| 375 | } | ||
| 376 | |||
| 377 | processFile = function(filepath = "/home/zgong001/Documents/Alarm/D50S9v2/D50S9v2-newswap-0.5NONE-1h/D50S9v2-E15-1hr1.txt") { | ||
| 378 | re = data.frame() | ||
| 379 | li = vector() | ||
| 380 | con = file(filepath, "r") | ||
| 381 | while ( TRUE ) { | ||
| 382 | line = readLines(con, n = 1) | ||
| 383 | if ( length(line) == 0 ) { | ||
| 384 | break | ||
| 385 | } | ||
| 386 | li = append(li, line) | ||
| 387 | } | ||
| 388 | close(con) | ||
| 389 | |||
| 390 | for(i in 1:length(li)){ | ||
| 391 | s = strsplit(li[i], " ") | ||
| 392 | b = strsplit(s[[1]][2], " ") | ||
| 393 | l = data.frame(st=s[[1]][1], sc= as.numeric(as.character(b[[1]][1]))) | ||
| 394 | re = rbind(re, l) | ||
| 395 | } | ||
| 396 | |||
| 397 | re = na.omit(re) | ||
| 398 | |||
| 399 | re = unique(re) | ||
| 400 | re = re[order(-re[,2]), ] | ||
| 401 | |||
| 402 | m = re[1,2] | ||
| 403 | |||
| 404 | n=0 | ||
| 405 | |||
| 406 | for(j in 2:nrow(re) ){ | ||
| 407 | s0 = re[j,2] | ||
| 408 | |||
| 409 | te = -log(exp(s0-m)+1) | ||
| 410 | |||
| 411 | m = m - te; | ||
| 412 | |||
| 413 | if(exp(te) >= 0.99){ | ||
| 414 | break | ||
| 415 | } | ||
| 416 | n = j | ||
| 417 | } | ||
| 418 | |||
| 419 | ree = re[1:n,] | ||
| 420 | |||
| 421 | # sink("/home/zgong001/Documents/Alarm/D50S9v2/D50S9v2-newswap-0.5NONE-1h/myfile.txt", append=TRUE, split=TRUE) | ||
| 422 | |||
| 423 | write.table("------", filepath, sep="\t", row.names=F, col.names=F, append=TRUE) | ||
| 424 | |||
| 425 | write.table(ree, filepath, sep="\t", row.names=F, col.names=F,append=TRUE) | ||
| 426 | |||
| 427 | return(ree) | ||
| 428 | |||
| 429 | |||
| 430 | } | ||
| 431 |