new build profile

diff --git a/Rscripts/chdfunct.R b/Rscripts/chdfunct.R
index 914278c..d93db99 100644 (file)
--- a/Rscripts/chdfunct.R
+++ b/Rscripts/chdfunct.R
@@ -98,12 +98,13 @@ AddCorrelationOk<-function(afc) {
        rowcoord<-afc$rowcoord
        colcoord<-afc$colcoord
        factor <- ncol(rowcoord)
+       
        hypo<-function(rowcoord,ligne) {
                somme<-0
                for (i in 1:factor) {
                        somme<-somme+(rowcoord[ligne,i])^2
                }
-       sqrt(somme)
+               sqrt(somme)
        }
        cor<-function(d,hypo) {
                d/hypo
@@ -117,8 +118,17 @@ AddCorrelationOk<-function(afc) {
                }
        out
        }
-       afc$rowcrl<-CompCrl(rowcoord)
-       afc$colcrl<-CompCrl(colcoord)
+
+       get.corr <- function(rowcol) {
+               sqrowcol <- rowcol^2
+               sqrowcol <- sqrt(rowSums(sqrowcol))
+               corr <- rowcol / sqrowcol
+               corr
+       }
+       #afc$rowcrl<-CompCrl(rowcoord)
+       afc$rowcrl <- get.corr(rowcoord)
+       #afc$colcrl<-CompCrl(colcoord)
+       afc$colcrl<-get.corr(colcoord)
        afc
 }
 
@@ -347,7 +357,79 @@ build.prof.tgen <- function(x) {
     res <- list(chi2 = chi2, pchi2 = pchi2)
 }
 
+
+new.build.prof <- function(x,dataclasse,clusternb,lim=2) {
+       cl <- dataclasse[,ncol(dataclasse)]
+       nst <- length(which(cl != 0))
+       rs <- rowSums(x)
+       mod.names<-rownames(x)
+       lnbligne <- list()
+       lchi <- list()
+       prof <- list()
+       aprof <- list()
+       for (classe in 1:clusternb) {
+               lnbligne[[classe]]<-length(which(cl==classe))
+               tmpprof <- data.frame()
+               tmpanti <- data.frame()
+               obs1 <- x[,classe] #1,1
+               obs2 <- rs - obs1 #1,2
+           obs3 <- lnbligne[[classe]] - obs1   #2,1
+               obs4 <- nst - (obs1 + obs2 + obs3) #2,2
+               exp1 <- ((obs1 + obs3) * (obs1 + obs2)) / nst
+               exp2 <- ((obs2 + obs1) * (obs2 + obs4)) / nst
+               exp3 <- ((obs3 + obs4) * (obs3 + obs1)) / nst
+               exp4 <- ((obs4 + obs3) * (obs4 + obs2)) / nst
+               chi1 <- ((obs1 - exp1)^2) / exp1
+               chi2 <- ((obs2 - exp2)^2) / exp2
+               chi3 <- ((obs3 - exp3)^2) / exp3
+               chi4 <- ((obs4 - exp4)^2) / exp4
+               chi <- chi1 + chi2 + chi3 + chi4        
+               chi[which(is.na(chi)==T)] <- 0
+               tochange <- ifelse(obs1 > exp1, 1, -1)
+               lchi[[classe]] <- chi * tochange
+               tokeep <- which(lchi[[classe]] > lim)
+               if (length(tokeep)) {
+                       tmpprof[1:length(tokeep),1] <- obs1[tokeep]
+                       tmpprof[,2] <- rs[tokeep]
+                       tmpprof[,3] <- round((obs1/rs)*100, digits=2)[tokeep]
+                       tmpprof[,4] <- round(lchi[[classe]], digits=3)[tokeep]
+                       tmpprof[,5] <- mod.names[tokeep] 
+                       tmpprof[,6] <- pchisq(lchi[[classe]] ,1, lower.tail=F)[tokeep]
+               }
+               prof[[classe]] <- tmpprof
+               toanti <- which(lchi[[classe]] < -lim)
+               if (length(toanti)) {
+                       tmpanti[1:length(toanti),1] <- obs1[toanti]
+                       tmpanti[,2] <- rs[toanti]
+                       tmpanti[,3] <- round((obs1/rs)*100, digits=2)[toanti]
+                       tmpanti[,4] <- round(lchi[[classe]], digits=3)[toanti]
+                       tmpanti[,5] <- mod.names[toanti] 
+                       tmpanti[,6] <- pchisq(-lchi[[classe]] ,1, lower.tail=F)[toanti]
+               }
+               aprof[[classe]] <- tmpanti
+               if (length(prof[[classe]])!=0) {
+                       prof[[classe]]<-prof[[classe]][order(prof[[classe]][,4],decreasing=TRUE),]
+               }
+               if (length(aprof[[classe]])!=0) {
+                       aprof[[classe]]<-aprof[[classe]][order(aprof[[classe]][,4]),]   
+               }
+       }
+    tablechi <- do.call(cbind, lchi)
+       tablep <- pchisq(tablechi,1, lower.tail=F)
+       tablep <- round(tablep, digits=3)
+       tablechi <- round(tablechi, digits=3)
+       out <- list()
+       out[[1]] <- tablep
+       out[[2]] <- tablechi
+       out[[3]] <- cbind(x, rowSums(x))
+    out[[4]] <- prof   
+       out[[5]] <- aprof
+       out
+}
+
+
 BuildProf<- function(x,dataclasse,clusternb,lim=2) {
+       print('build prof')
        ####
        #r.names<-rownames(x)
        #x<-as.matrix(x)
@@ -453,6 +535,7 @@ BuildProf<- function(x,dataclasse,clusternb,lim=2) {
                        aprof[[classe]]<-aprof[[classe]][order(aprof[[classe]][,4]),]   
                }
        }
+       print('fini build prof')
        output<-list()
        output[[1]]<-tablep
        output[[2]]<-tablesqr