From: Pierre Ratinaud <ratinaud@univ-tlse2.fr>
Date: Thu, 24 Mar 2016 09:18:22 +0000 (+0100)
Subject: chi2 de McNemar
X-Git-Url: http://iramuteq.org/git?p=iramuteq;a=commitdiff_plain;h=f3d845cb66abaa1e88928137d3ad4448c2997a58;hp=f1aa29b61a02454fc716775163ead02630d4a4df

chi2 de McNemar
---

diff --git a/iramuteq.py b/iramuteq.py
index ef99d20..acbff9e 100644
--- a/iramuteq.py
+++ b/iramuteq.py
@@ -1,7 +1,7 @@
 #!/bin/env python
 # -*- coding: utf-8 -*-
 #Author: Pierre Ratinaud
-#Copyright (c) 2008-2012, Pierre Ratinaud
+#Copyright (c) 2008-2016, Pierre Ratinaud
 #License: GNU GPL
 
 from optparse import OptionParser
@@ -36,6 +36,7 @@ from tableau import Tableau
 from dialog import PrefDialog
 from tabfrequence import Frequences, FreqMultiple
 from tabchi2 import ChiSquare
+from tabchi2mcnemar import McNemar
 #from tabstudent import MakeStudent
 from tabchddist import ChdCluster
 from tabafcm import DoAFCM
@@ -68,6 +69,7 @@ ID_OpenText = wx.NewId()
 ID_OnOpenAnalyse = wx.NewId()
 ID_Freq = wx.NewId()
 ID_Chi2 = wx.NewId()
+ID_Chi2mc = wx.NewId()
 ID_Student = wx.NewId()
 ID_CHDSIM = wx.NewId()
 ID_CHDReinert = wx.NewId()
@@ -185,6 +187,7 @@ images_analyses = {
         'freq' : 'frequences.png',
         'freqmulti' : 'frequences.png',
         'chi2' : 'chi2.png',
+        'chi2mcnemar' : 'chi2.png',
         'reinertmatrix' : 'reinertmatrix.png',
         'simimatrix' : 'simimatrix.png',
         'simiclustermatrix' : 'simimatrix.png',
@@ -328,6 +331,7 @@ class IraFrame(wx.Frame):
         matanalyses = [[ID_Freq, _(u"Frequencies").decode('utf8'), 'freq'],
                        [ID_FreqMulti, _(u"Multiple  Frequencies").decode('utf8'), 'freqmulti'],
                        [ID_Chi2, _(u"Chi2").decode('utf8'), 'chi2'],
+                       [ID_Chi2mc, _(u"Chi2 McNemar").decode('utf8'), 'chi2mcnemar'],
                        {'name' : _(u"Clustering").decode('utf8'),
                         'content' : [[ID_CHDReinert, _(u"Reinert's Method").decode('utf8'), 'reinertmatrix']]},
                        [ID_SIMI, _(u"Similarities Analysis").decode('utf8'), 'simimatrix'],
@@ -582,6 +586,7 @@ class IraFrame(wx.Frame):
         self.Bind(wx.EVT_MENU, self.OnFreq, id=ID_Freq)
         self.Bind(wx.EVT_MENU, self.OnFreqMulti, id=ID_FreqMulti)
         self.Bind(wx.EVT_MENU, self.OnChi2, id=ID_Chi2)
+        self.Bind(wx.EVT_MENU, self.OnChi2McNemar, id=ID_Chi2mc)
         self.Bind(wx.EVT_MENU, self.OnStudent, id=ID_Student)
         self.Bind(wx.EVT_MENU, self.OnCHDSIM, id=ID_CHDSIM)
         self.Bind(wx.EVT_MENU, self.OnCHDReinert, id=ID_CHDReinert)
@@ -969,6 +974,9 @@ Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, États-Unis."""
     def OnChi2(self, event, matrix = None):
         self.analyse_matrix(ChiSquare, matrix = matrix, analyse_type = 'chi2', dlgnb = 3) 
 
+    def OnChi2McNemar(self, event, matrix = None):
+        self.analyse_matrix(McNemar, matrix = matrix, analyse_type = 'chi2mcnemar', dlgnb = 3)
+
     def OnSimiTab(self, event, matrix = None):
         self.analyse_matrix(DoSimi, matrix = matrix, analyse_type = 'simimatrix', dlgnb = 5)
 
diff --git a/openanalyse.py b/openanalyse.py
index c8089d2..a80670e 100644
--- a/openanalyse.py
+++ b/openanalyse.py
@@ -170,6 +170,6 @@ class OpenAnalyse():
             MatLayout(self.parent, corpus)
         elif self.conf['type'] == 'freq' or self.conf['type'] == 'freqmulti':
             FreqLayout(self.parent, corpus, self.conf)
-        elif self.conf['type'] == 'chi2' :
+        elif self.conf['type'] == 'chi2' or self.conf['type'] == 'chi2mcnemar':
             Chi2Layout(self.parent, corpus, self.conf)
         
diff --git a/tabchi2mcnemar.py b/tabchi2mcnemar.py
new file mode 100644
index 0000000..7270ac3
--- /dev/null
+++ b/tabchi2mcnemar.py
@@ -0,0 +1,403 @@
+#!/bin/env python
+# -*- coding: utf-8 -*-
+#Author: Pierre Ratinaud
+#Copyright (c) 2016 Pierre Ratinaud
+#License: GNU/GPL
+
+import HTML
+import os
+import string
+import wx
+import os
+import sys
+import tempfile
+from chemins import ffr,FFF
+import wx.lib.sized_controls as sc
+from time import sleep
+from functions import exec_rcode, check_Rresult
+from dialog import ChiDialog, PrefChi
+from analysematrix import AnalyseMatrix
+                    
+def make_res(line) :
+    if float(line[5]) <= 0.05 and line[6] != 'warning':
+        line.append('green')
+    elif float(line[5]) <= 0.05 and line[6] == 'warning':
+        line.append('blue')
+    else :
+        line.append('red')
+    return line
+
+def clean_line(result) :
+    return [[val for val in line if val != '**'] for line in result]
+
+def make_table(tabs, tab_title, res) :
+    return ['<br>'.join(['<font color=%s>%s</font>' % (res[i][-1], tab_title), HTML.table(tab)]) for i,tab in enumerate(tabs)]
+
+def make_restab(res) :
+    return ['<br>'.join(['<font color=%s>%s</font>'% (line[-1], u'Résultats'),HTML.table([['chi', line[3]],['p', line[5]]])]) for i,line in enumerate(res)]
+
+def make_htmlgraphs(graphs) :
+    return ['<img src=%s>' % os.path.basename(val) for val in graphs]
+
+def make_link_list(res, text) :
+    return ['<a name=back_%i></a><a href=#%i><font color=%s>%s</font></a>' % (i, i, chi[-1], text[i]) for i, chi in enumerate(res)]
+
+def make_title(res, text) :
+    return ['<a name=%i></a><br><font color=%s>%s</font><br><a href=#back_%i>retour</a><br>' % (i, val[-1], text[i], i) for i, val in enumerate(res)] 
+
+
+chioption = { 'valobs' : True,
+              'valtheo' : True,
+              'resi' : False,
+              'contrib' : True,
+              'pourcent' : False,
+              'pourcentl' : True,
+              'pourcentc' : True,
+              'graph' : True,
+              'bw' : False,
+              }
+
+class McNemar(AnalyseMatrix):
+    def doparametres(self, dlg = None):
+        if dlg is None :
+            return
+        dial = ChiDialog(self.parent, -1, u"Chi2 McNemar", chioption, self.tableau, size=(400, 350),
+                     style = wx.DEFAULT_DIALOG_STYLE
+                     )
+        dial.CenterOnParent()
+        val = dial.ShowModal()
+        if val==wx.ID_OK :     
+            self.colsel1 = dial.list_box_1.GetSelections()
+            self.colsel2 = dial.list_box_2.GetSelections()
+            if dial.chiopt :
+                chioption['valobs'] = dial.dial.check1.GetValue()
+                chioption['valtheo'] = dial.dial.check2.GetValue()
+                chioption['resi'] = dial.dial.check3.GetValue()
+                chioption['contrib'] = dial.dial.check4.GetValue()
+                chioption['pourcent'] = dial.dial.check5.GetValue()
+                chioption['pourcentl'] = dial.dial.check6.GetValue()
+                chioption['pourcentc'] = dial.dial.check7.GetValue()
+                chioption['graph'] = dial.dial.check8.GetValue()
+                chioption['bw'] = dial.dial.checkbw.GetValue()
+                dial.dial.Destroy()
+            dial.Destroy()
+            self.parametres.update(chioption)
+            self.chioption = chioption
+        else :
+            if dial.chiopt :
+                dial.dial.Destroy()
+            dial.Destroy()
+            self.parametres = None
+            
+    def doanalyse(self):
+        self.count = 1
+        keepGoing = self.dlg.Update(self.count,u"Analyse dans R...")
+        self.OutFrame=tempfile.mktemp(dir=self.parent.TEMPDIR)
+        self.encode=self.parent.encode
+        self.TEMPDIR=self.parent.TEMPDIR
+        self.RPath=self.parent.PathPath.get('PATHS','rpath')
+        self.TextCroise=[]
+        for i in self.colsel1 :
+            for j in self.colsel2 :
+                self.TextCroise.append(self.tableau.colnames[i] + ' / ' + self.tableau.colnames[j])
+        rchioption = {}
+        for val in self.chioption :
+            if self.chioption[val]:
+                rchioption[val] = 'TRUE'
+            else :
+                rchioption[val] = 'FALSE'
+        txt="""
+        source("%s")
+        """%ffr(self.parent.RscriptsPath['Rfunct'])
+        txt += """
+        source("%s")
+        """ % ffr(self.parent.RscriptsPath['Rgraph'])
+        txt += """
+        doobs <- %s
+        doexp <- %s
+        docontrib <- %s
+        doresi <- %s
+        dopr <- %s
+        doprl <- %s
+        doprc <- %s
+        dograph <- %s
+        bw <- %s
+        """ % (rchioption['valobs'], rchioption['valtheo'], rchioption['contrib'], rchioption['resi'], rchioption['pourcent'], rchioption['pourcentl'], rchioption['pourcentc'], rchioption['graph'], rchioption['bw'])
+        txt+="""
+        datadm <- read.csv2("%s", encoding="%s", header = TRUE, row.names = 1, sep='\\t', quote = '"', na.string = '')
+        listres<-list()
+        listcol<-list()
+        cont<-1
+        """%(ffr(self.tableau.parametres['csvfile']), self.tableau.parametres['syscoding'])
+        if len(self.colsel1)==1:
+            strsel1=str(self.colsel1).replace(',','')
+        else:
+            strsel1=str(self.colsel1)
+        if len(self.colsel2)==1:
+            strsel2=str(self.colsel2).replace(',','')
+        else:
+            strsel2=str(self.colsel2)
+        txt+="""
+        for (i in c%s) {""" % strsel1
+        txt+="""
+            for (j in c%s) {""" % strsel2
+        txt+="""
+                tab<-table(datadm[,i+1],datadm[,j+1])
+                if (min(dim(tab)) != 1) {
+                    chi <- mcnemar.test(tab)
+                    #chi<-chisq.test(tab)
+                    CS<-colSums(tab)
+                    RS<-rowSums(tab)
+                    GT<-sum(tab)
+                    chi$observed <- tab
+                    chi$expected <- tab
+                    chi$contrib <- tab
+                    chi$residuals <- tab
+                    #chi$contrib<-(tab-chi$expected)/sqrt(chi$expected * ((1 - RS/GT) %%*%% t(1 - CS/GT)))
+                    listres[[cont]]<-chi
+                    listcol[[cont]]<-ncol(tab)
+                    cont<-cont+1
+                } else {
+                    chi <- list(observed = tab, residuals = tab, contrib = tab, statistic = 0, p.value = 1, expected = tab, message = 'pas de calcul')
+                    listres[[cont]] <- chi
+                    listcol[[cont]]<-ncol(tab)
+                    cont <- cont + 1
+                }
+            }
+        }
+        maxcol<-max(unlist(listcol))+1
+        if (maxcol<7) {maxcol<-7}
+        frameout<-matrix('*',1,maxcol)
+        count<-0
+        for (chi in listres) {
+            if (min(chi$expected)<5) {
+                att<-"warning"
+            } else {
+                att<-""
+            }
+            if ('message' %%in%% attributes(chi)$names) {
+                att <- "Ce chi2 n\'a pas été calculé"
+                nom_colresi<-colnames(chi$observed)
+                chi$prl <- chi$expected
+                chi$prc <- chi$expected
+                st <- sum(chi$observed)
+            } else {
+                nom_colresi<-colnames(chi$observed)
+                st <- sum(chi$observed)
+                sc <- colSums(chi$observed)
+                sr <- rowSums(chi$observed)
+                chi$prl <- round((chi$observed/sr)*100,2)
+                chi$prc <- t(round((t(chi$observed)/sc)*100,2))
+            }
+            fileout<-paste('histo_',count,sep='')
+            fileout<-paste(fileout,'.png',sep='')
+            count<-count+1
+            fileout<-file.path("%s",fileout)
+            if (max(nchar(colnames(chi$observed)))>15) {
+                leg <- 1:length(colnames(chi$observed))
+            } else {
+                leg <- colnames(chi$observed)
+            }
+            if (dograph) {
+                width<-ncol(chi$observed)*100
+                if (width < 350) {width <- 350}
+                open_file_graph(fileout,width = width, height = 300)
+                par(mar=c(0,0,0,0))
+                layout(matrix(c(1,2),1,2, byrow=TRUE),widths=c(3,1))
+                par(mar=c(2,2,1,0))
+                par(cex=0.8)
+                if (!bw) colors <- rainbow(length(rownames(chi$observed)))
+                else colors <- gray.colors(length(rownames(chi$observed)))
+                barplot(chi$prl,names.arg = leg, beside=TRUE,border=NA, col=colors)
+                par(mar=c(0,0,0,0))
+                par(cex=0.8)
+                plot(0, axes = FALSE, pch = '')
+                legend(x = 'center' , rownames(chi$observed), fill = colors)
+                dev.off()
+            }
+            chi$prl <- cbind(chi$prl, total = rowSums(chi$prl))
+            chi$prc <- rbind(chi$prc, total = colSums(chi$prc))
+            chi$observed<-rbind(chi$observed,total=colSums(chi$observed))
+            chi$observed<-cbind(chi$observed,total=rowSums(chi$observed))
+            chi$pr <- round((chi$observed/st)*100,2)
+            chi$expected<-rbind(chi$expected,total=colSums(chi$expected))
+            chi$expected<-cbind(chi$expected,total=rowSums(chi$expected))
+            chi$expected<-round(chi$expected,digits=2)
+            chi$residuals<-round(chi$residuals,digits=2)
+            chi$contrib<-round(chi$contrib, digits=2)
+            nom_col<-colnames(chi$observed)
+           
+            if (ncol(chi$observed)<maxcol) {
+                for (i in 1:(maxcol-ncol(chi$observed))) {
+                    chi$observed<-cbind(chi$observed,'**')
+                    chi$pr<-cbind(chi$pr,'**')
+                    chi$prl<-cbind(chi$prl,'**')
+                    chi$prc<-cbind(chi$prc,'**')
+                    chi$expected<-cbind(chi$expected,'**')
+                    chi$residuals<-cbind(chi$residuals,'**')
+                    chi$contrib<-cbind(chi$contrib,'**')
+                    nom_col<-append(nom_col,'**')
+                    nom_colresi<-append(nom_colresi,'**')
+                }
+                chi$residuals<-cbind(chi$residuals,'**')
+                chi$contrib<-cbind(chi$contrib,'**')
+                nom_colresi<-append(nom_colresi,'**')
+                chi$prc<-cbind(chi$prc,'**')
+            } else if (ncol(chi$observed)==maxcol) {
+                chi$residuals<-cbind(chi$residuals,'**')
+                chi$contrib<-cbind(chi$contrib,'**')
+                nom_colresi<-append(nom_colresi,'**')
+                chi$prc<-cbind(chi$prc,'**')
+            }
+            if (doobs) {
+                li<-matrix('*obs*',1,maxcol)
+                frameout<-rbind(frameout,li)
+                frameout<-rbind(frameout,nom_col)
+                frameout<-rbind(frameout,chi$observed)
+            }
+            if (doexp) {
+                li<-matrix('*exp*',1,maxcol)
+                frameout<-rbind(frameout,li)
+                frameout<-rbind(frameout,nom_col)
+                frameout<-rbind(frameout,chi$expected)
+            }
+            if (doresi) {
+                li<-matrix('*resi*',1,maxcol)
+                frameout<-rbind(frameout,li)
+                frameout<-rbind(frameout,nom_colresi)
+                frameout<-rbind(frameout,chi$residuals)
+            }
+            if (docontrib) {
+                li<-matrix('*contrib*',1,maxcol)
+                frameout<-rbind(frameout,li)
+                frameout<-rbind(frameout,nom_colresi)
+                frameout<-rbind(frameout,chi$contrib)
+            }
+            if (dopr) {
+                li<-matrix('*pr*', 1, maxcol)
+                frameout<-rbind(frameout,li)
+                frameout<-rbind(frameout,nom_col)
+                frameout<-rbind(frameout,chi$pr)
+            }
+            if (doprl) {
+                li<-matrix('*prl*', 1, maxcol)
+                frameout<-rbind(frameout,li)
+                frameout<-rbind(frameout,nom_col)
+                frameout<-rbind(frameout,chi$prl)
+            }
+            if (doprc) {
+                li<-matrix('*prc*', 1, maxcol)
+                frameout<-rbind(frameout,li)
+                frameout<-rbind(frameout,nom_colresi)
+                frameout<-rbind(frameout,chi$prc)
+            }
+            res<-c('****','chi',chi$statistic,'p',chi$p.value,att,fileout)
+            frameout<-rbind(frameout,res)
+        }
+        li<-matrix('fin_analyse',1,maxcol)
+        frameout<-rbind(frameout,li)
+        write.csv2(frameout,file="%s")
+        """ % (ffr(self.parametres['pathout']),ffr(self.OutFrame))
+        tmpfile=tempfile.mktemp(dir=self.TEMPDIR)
+        print tmpfile
+        tmpscript=open(tmpfile,'w')
+        tmpscript.write(txt)
+        tmpscript.close()
+        pid = exec_rcode(self.RPath, tmpfile, wait = False)
+        while pid.poll() == None :
+            sleep(0.2)
+        check_Rresult(self.parent, pid)            
+        self.count += 1
+        keepGoing = self.dlg.Update(self.count,u"Ecriture des résultats")
+         
+        listfileout = self.dolayout(self.chioption)
+            #listfileout=dlg.ShowChi2(ColSel1,ColSel2)
+            #parent.FreqNum += 1
+            #parent.DictTab[u"Chi2_%s*"%parent.FreqNum]=listfileout
+#             parent.newtab = wx.html.HtmlWindow(parent.nb, -1)
+#             if "gtk2" in wx.PlatformInfo:
+#                 parent.newtab.SetStandardFonts()
+#             parent.newtab.LoadPage(listfileout[len(listfileout)-1])
+#             parent.nb.AddPage(parent.newtab,u"Chi2_%s*"%parent.FreqNum)
+#             parent.nb.SetSelection(parent.nb.GetPageCount()-1)
+#             parent.ShowTab(wx.EVT_BUTTON)
+#             parent.DisEnSaveTabAs(True)
+#        self.count += 1
+#        keepGoing = self.dlg.Update(self.count,u"Fini")
+
+    def dolayout(self, option):
+        ListFile=[False]
+        file=open(self.OutFrame,'rU')
+        content=file.readlines()
+        file.close()
+        lcont = [line.replace('"','').replace('\n','').split(';') for line in content]
+    
+        lcont.pop(0)
+        lcont.pop(0)
+        
+        allcoord = []
+        names = []
+
+        res = [chi for chi in lcont if chi[0]=='res']
+        res = [make_res(line) for line in res]
+        coord_res = [i for i,chi in enumerate(lcont) if chi[0]=='res']
+        if option['valobs']:
+            allcoord.append([i for i,chi in enumerate(lcont) if chi[1]=='*obs*'])
+            names.append(u'Valeurs observées')
+        if option['valtheo'] :
+            allcoord.append([i for i,chi in enumerate(lcont) if chi[1]=='*exp*'])
+            names.append(u'Valeurs théoriques')
+        if option['resi'] :
+            allcoord.append([i for i,chi in enumerate(lcont) if chi[1]=='*resi*'])
+            names.append(u'Residuals')
+        if option['contrib'] :
+            allcoord.append([i for i,chi in enumerate(lcont) if chi[1]=='*contrib*'])
+            names.append(u'Contributions a posteriori')
+        if option['pourcent'] : 
+            allcoord.append([i for i,chi in enumerate(lcont) if chi[1]=='*pr*'])
+            names.append(u'Pourcentages')
+        if option['pourcentl'] :
+            allcoord.append([i for i,chi in enumerate(lcont) if chi[1]=='*prl*'])
+            names.append(u'Pourcentages en ligne')
+        if option['pourcentc'] :
+            allcoord.append([i for i,chi in enumerate(lcont) if chi[1]=='*prc*'])
+            names.append(u'Pourcentages en colonne')
+    
+        allcoord.append(coord_res)
+        allhtml = [[clean_line(lcont[allcoord[i][j]+1:allcoord[i+1][j]]) for j, line in enumerate(allcoord[i])] for i, tab in enumerate(allcoord) if i!=len(allcoord)-1]
+        allhtml = [make_table(val,names[i],res) for i,val in enumerate(allhtml)]
+        links = make_link_list(res, self.TextCroise)
+        html_res = make_restab(res)
+        allhtml.insert(0,html_res)
+        titles = make_title(res, self.TextCroise)
+        allhtml.insert(0,titles)
+        
+        if option['graph'] :
+            graphs = [line[7] for line in res]
+            ListFile += graphs
+            html_graphs = make_htmlgraphs(graphs)
+            allhtml.append(html_graphs)
+
+        header=u"""
+        <html>\n
+        <meta http-equiv="content-Type" content="text/html; charset=%s" />\n
+        <body>\n
+        <h1>Test du Chi2</h1>\n
+        <br>
+        <table border=1><tr><td>
+        Légende : <br>
+        <font color=green>p &lt;= 0.05</font><br>
+        <font color=blue>p &lt;= 0.05 mais il y a des valeurs théoriques &lt; 5</font><br>
+        <font color=red>p &gt; 0.05</font>
+        </td></tr></table><br><br>
+        """%self.parent.SysEncoding
+
+        pretxt = '<br>\n'.join(links)+'<br><hr><br>\n'
+        txt = '<br><hr><br>\n'.join(['<br><br>'.join([tab[i] for tab in allhtml]) for i,val in enumerate(res)])
+        txt = header + pretxt + txt + '\n</body></html>'
+
+        fileout=os.path.join(self.parametres['pathout'],'resultats-chi2.html')
+        with open(fileout, 'w') as f :
+            f.write(txt)
+        ListFile.append(fileout)         
+        return ListFile
\ No newline at end of file