[Genabel-commits] r1087 - in pkg/GenABEL: . R

[noreply at r-forge.r-project.org]

Author: yurii
Date: 2013-01-18 20:37:08 +0100 (Fri, 18 Jan 2013)
New Revision: 1087

Modified:
   pkg/GenABEL/CHANGES.LOG
   pkg/GenABEL/DESCRIPTION
   pkg/GenABEL/R/ztransform.R
   pkg/GenABEL/R/zzz.R
Log:
fixing bug in ztransform; version change

Modified: pkg/GenABEL/CHANGES.LOG
===================================================================
--- pkg/GenABEL/CHANGES.LOG	2013-01-18 19:32:15 UTC (rev 1086)
+++ pkg/GenABEL/CHANGES.LOG	2013-01-18 19:37:08 UTC (rev 1087)
@@ -1,3 +1,9 @@
+***  v. 1.7-3 (2013.01.18)
+
+(2013.01.18)
+Fixing bug in ztransform (if NA is present and formula used, NA's are kicked out)
+Changed the version number
+
 ***  v. 1.7-3 (2013.01.09)
 
 (2013.01.09)

Modified: pkg/GenABEL/DESCRIPTION
===================================================================
--- pkg/GenABEL/DESCRIPTION	2013-01-18 19:32:15 UTC (rev 1086)
+++ pkg/GenABEL/DESCRIPTION	2013-01-18 19:37:08 UTC (rev 1087)
@@ -1,8 +1,8 @@
 Package: GenABEL
 Type: Package
 Title: genome-wide SNP association analysis
-Version: 1.7-3
-Date: 2013-01-09
+Version: 1.7-4
+Date: 2013-01-18
 Author: GenABEL project developers
 Contact: GenABEL project developers <genabel.project at gmail.com>
 Maintainer: Yurii Aulchenko <yurii at bionet.nsc.ru>

Modified: pkg/GenABEL/R/ztransform.R
===================================================================
--- pkg/GenABEL/R/ztransform.R	2013-01-18 19:32:15 UTC (rev 1086)
+++ pkg/GenABEL/R/ztransform.R	2013-01-18 19:37:08 UTC (rev 1087)
@@ -31,14 +31,16 @@
 	}
 	
 	if (is(formula,"formula")) {
-		mf <- model.frame(formula,data,na.action=na.omit,drop.unused.levels=TRUE)
+#		mf <- model.frame(formula,data,na.action=na.omit,drop.unused.levels=TRUE)
+		mf <- model.frame(formula,data,na.action=na.pass,drop.unused.levels=TRUE)
+		mids <- complete.cases(mf)
+		mf <- mf[mids,]
 		y <- model.response(mf)
 		desmat <- model.matrix(formula,mf)
 		lmf <- glm.fit(desmat,y,family=family)
 #		if (wasdata) 
 #			mids <- rownames(data) %in% rownames(mf)
 #		else 
-		mids <- complete.cases(desmat,y)
 		resid <- lmf$resid
 #		print(formula)
 	} else if (is(formula,"numeric") || is(formula,"integer") || is(formula,"double")) {

Modified: pkg/GenABEL/R/zzz.R
===================================================================
--- pkg/GenABEL/R/zzz.R	2013-01-18 19:32:15 UTC (rev 1086)
+++ pkg/GenABEL/R/zzz.R	2013-01-18 19:37:08 UTC (rev 1087)
@@ -4,8 +4,8 @@
 	#pkgDescription <- packageDescription(pkg)
 	#pkgVersion <- pkgDescription$Version
 	#pkgDate <- pkgDescription$Date
-	pkgVersion <- "1.7-3"
-	pkgDate <- "January 09, 2013"
+	pkgVersion <- "1.7-4"
+	pkgDate <- "January 18, 2013"
 	welcomeMessage <- paste(pkg," v. ",pkgVersion," (",pkgDate,") loaded\n",sep="")
 	# check if CRAN version is the same as loaded
 	cranVersion <- try( checkPackageVersionOnCRAN(pkg) )