X-Git-Url: http://iramuteq.org/git?p=iramuteq;a=blobdiff_plain;f=Rscripts%2Fchdfunct.R;h=914278c3dd7d726e4c3f13a47ea49ea0d5fa32f0;hp=2ca1eac603ae3d2af1ea109b5da4719d343f06ea;hb=83802e662acde01994fe0bd2bf6978fef90b14f8;hpb=8fa853a25a9d62b1446e1bc543e5a3a4d0e03dcf

diff --git a/Rscripts/chdfunct.R b/Rscripts/chdfunct.R
index 2ca1eac..914278c 100644
--- a/Rscripts/chdfunct.R
+++ b/Rscripts/chdfunct.R
@@ -293,95 +293,12 @@ AsLexico2<- function(mat, chip = FALSE) {
     out
 }
 
-
-#from textometrieR
-#http://txm.sourceforge.net/doc/R/textometrieR-package.html
-#Sylvain Loiseau
-specificites.probabilities <- function (lexicaltable, types = NULL, parts = NULL) 
-{
-    rowMargin <- rowSums(lexicaltable)
-    colMargin <- colSums(lexicaltable)
-    F <- sum(lexicaltable)
-    if (!is.null(types)) {
-        if (is.character(types)) {
-            if (is.null(rownames(lexicaltable))) 
-                stop("The lexical table has no row names and the \"types\" argument is a character vector.")
-            if (!all(types %in% rownames(lexicaltable))) 
-                stop(paste("Some requested types are not known in the lexical table: ", 
-                  paste(types[!(types %in% rownames(lexicaltable))], 
-                    collapse = " ")))
-        }
-        else {
-            if (any(types < 1)) 
-                stop("The row index must be greater than 0.")
-            if (max(types) > nrow(lexicaltable)) 
-                stop("Row index must be smaller than the number of rows.")
-        }
-        lexicaltable <- lexicaltable[types, , drop = FALSE]
-        rowMargin <- rowMargin[types]
-    }
-    if (!is.null(parts)) {
-        if (is.character(parts)) {
-            if (is.null(colnames(lexicaltable))) 
-                stop("The lexical table has no col names and the \"parts\" argument is a character vector.")
-            if (!all(parts %in% colnames(lexicaltable))) 
-                stop(paste("Some requested parts are not known in the lexical table: ", 
-                  paste(parts[!(parts %in% colnames(lexicaltable))], 
-                    collapse = " ")))
-        }
-        else {
-            if (max(parts) > ncol(lexicaltable)) 
-                stop("Column index must be smaller than the number of cols.")
-            if (any(parts < 1)) 
-                stop("The col index must be greater than 0.")
-        }
-        lexicaltable <- lexicaltable[, parts, drop = FALSE]
-        colMargin <- colMargin[parts]
-    }
-    if (nrow(lexicaltable) == 0 | ncol(lexicaltable) == 0) {
-        stop("The lexical table must contains at least one row and one column.")
-    }
-    specif <- matrix(0, nrow = nrow(lexicaltable), ncol = ncol(lexicaltable))
-    for (i in 1:ncol(lexicaltable)) {
-        whiteDrawn <- lexicaltable[, i]
-        white <- rowMargin
-        black <- F - white
-        drawn <- colMargin[i]
-        independance <- (white * drawn)/F
-        specif_negative <- whiteDrawn < independance
-        specif_positive <- whiteDrawn >= independance
-        specif[specif_negative, i] <- phyper(whiteDrawn[specif_negative], 
-            white[specif_negative], black[specif_negative], drawn)
-        specif[specif_positive, i] <- phyper(whiteDrawn[specif_positive] - 
-            1, white[specif_positive], black[specif_positive], 
-            drawn)
-    }
-    dimnames(specif) <- dimnames(lexicaltable)
-    return(specif)
-}
-
-#from textometrieR
-#http://txm.sourceforge.net/doc/R/textometrieR-package.html
-#Sylvain Loiseau
-specificites <- function (lexicaltable, types = NULL, parts = NULL) 
-{
-    spe <- specificites.probabilities(lexicaltable, types, parts)
-    spelog <- matrix(0, nrow = nrow(spe), ncol = ncol(spe))
-    spelog[spe < 0.5] <- log10(spe[spe < 0.5])
-    spelog[spe > 0.5] <- abs(log10(1 - spe[spe > 0.5]))
-    spelog[spe == 0.5] <- 0
-    spelog[is.infinite(spe)] <- 0
-    spelog <- round(spelog, digits = 4)
-    rownames(spelog) <- rownames(spe)
-    colnames(spelog) <- colnames(spe)
-    return(spelog)
-}
-
 make.spec.hypergeo <- function(mat) {
-    #library(textometrieR)
-    spec <- specificites(mat)
+    library(textometry)
+    spec <- specificities(mat)
 	sumcol<-colSums(mat)
     eff_relatif<-round(t(apply(mat,1,function(x) {(x/t(as.matrix(sumcol))*1000)})),2)
+    colnames(eff_relatif) <- colnames(mat)
     out <-list()
     out[[1]]<-spec
     out[[3]]<-eff_relatif
@@ -404,6 +321,32 @@ BuildProf01<-function(x,classes) {
 	mat
 }
 
+build.prof.tgen <- function(x) {
+    nbst <- sum(x[nrow(x),])
+    totcl <- x[nrow(x),]
+    tottgen <- rowSums(x)
+    nbtgen <- nrow(x) - 1
+    chi2 <- x[1:(nrow(x)-1),]
+    pchi2 <- chi2
+    for (classe in 1:ncol(x)) {
+        for (tg in 1:nbtgen) {
+            cont <- c(x[tg, classe], tottgen[tg] - x[tg, classe], totcl[classe] - x[tg, classe], (nbst - totcl[classe]) - (tottgen[tg] - x[tg, classe]))
+            cont <- matrix(unlist(cont), nrow=2)
+            chiresult<-chisq.test(cont,correct=FALSE)
+            if (is.na(chiresult$p.value)) {
+                chiresult$p.value<-1
+                chiresult$statistic<-0
+            }
+            if (chiresult$expected[1,1] > cont[1,1]) {
+                chiresult$statistic <- chiresult$statistic * -1
+            }
+            chi2[tg,classe] <- chiresult$statistic
+            pchi2[tg,classe] <- chiresult$p.value
+        }
+    }
+    res <- list(chi2 = chi2, pchi2 = pchi2)
+}
+
 BuildProf<- function(x,dataclasse,clusternb,lim=2) {
 	####
 	#r.names<-rownames(x)