From 6036d5f43d8b2523f0c270f3bb3b5ce61b4c2044 Mon Sep 17 00:00:00 2001
From: Maxime WACK <maximewack@free.fr>
Date: Wed, 2 Jul 2014 11:47:38 +0200
Subject: [PATCH] Modified algorithm for qualitative test selection : If there
 is a warning in chisq.test, try fisher.test with workspace=1e+08. If it still
 fails, retry fisher.test with simulated p value with 1e+06 samples.

---
 R/desc_groupe.R | 7 ++++---
 cosmosR.rproj   | 2 +-
 2 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/R/desc_groupe.R b/R/desc_groupe.R
index 0cc9c74..dfc120c 100644
--- a/R/desc_groupe.R
+++ b/R/desc_groupe.R
@@ -206,12 +206,13 @@ desc_groupe <- function(table, groupe, param = character(0), html=NULL, titre=NU
           test <<- "f"
           tryCatch(
           {
-            fisher.test(table[[var]],modulo,workspace)$p.value
+            fisher.test(table[[var]],modulo,workspace=1e+08)$p.value
           },
           error=function(e)
           {
-            test <<- "X(f failed)"
-            chisq.test(table[[var]],modulo)$p.value
+            #test <<- "X(f failed)"
+            #chisq.test(table[[var]],modulo)$p.value
+            fisher.test(table[[var]],modulo,simulate.p.value = T,B = 1e+06)$p.value
           })
         },
         error=function(e)
diff --git a/cosmosR.rproj b/cosmosR.rproj
index 88c6159..c85962f 100644
--- a/cosmosR.rproj
+++ b/cosmosR.rproj
@@ -13,6 +13,6 @@ RnwWeave: Sweave
 LaTeX: pdfLaTeX
 
 BuildType: Package
-PackageInstallArgs: --no-multiarch
+PackageInstallArgs: --no-multiarch --with-keep.source
 PackageCheckArgs: --as-cran
 PackageRoxygenize: rd,collate,namespace