[Genabel-commits] r949 - pkg/GenABEL/R

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Thu Aug 30 11:43:00 CEST 2012 

Author: yurii
Date: 2012-08-30 11:43:00 +0200 (Thu, 30 Aug 2012)
New Revision: 949

Modified:
   pkg/GenABEL/R/checkPackageVersionOnCRAN.R
   pkg/GenABEL/R/mlreg.R
   pkg/GenABEL/R/mlreg.p.R
   pkg/GenABEL/R/mmscore.R
   pkg/GenABEL/R/npsubtreated.R
   pkg/GenABEL/R/polygenic.R
   pkg/GenABEL/R/polygenic_hglm.R
Log:
fixing partial arguments match + changing default timeout for version checks to 5 sec

Modified: pkg/GenABEL/R/checkPackageVersionOnCRAN.R
===================================================================
--- pkg/GenABEL/R/checkPackageVersionOnCRAN.R	2012-08-30 09:26:00 UTC (rev 948)
+++ pkg/GenABEL/R/checkPackageVersionOnCRAN.R	2012-08-30 09:43:00 UTC (rev 949)
@@ -23,7 +23,8 @@
 #' 
 #' @author Yurii Aulchenko
 #'
-checkPackageVersionOnCRAN <- function(packageName,baseUrlCRAN="http://cran.r-project.org/web/packages/", timeout = 10)
+checkPackageVersionOnCRAN <- function(packageName,baseUrlCRAN="http://cran.r-project.org/web/packages/", 
+		timeout = 5)
 {
 	# change default timout
 	svtmo <- options("timeout")

Modified: pkg/GenABEL/R/mlreg.R
===================================================================
--- pkg/GenABEL/R/mlreg.R	2012-08-30 09:26:00 UTC (rev 948)
+++ pkg/GenABEL/R/mlreg.R	2012-08-30 09:43:00 UTC (rev 949)
@@ -101,9 +101,9 @@
 	se.effB <- chi2$sebeta
 	chi2.1df <- (chi2$beta/chi2$sebeta)^2
 	#out$lambda <- estlambda(out$chi2.1df,plot=F,prop=propPs)
-	P1df <- pchisq(chi2.1df,1,lower=F)
-	lambda <- estlambda(chi2.1df,plot=F,prop=propPs)
-	Pc1df <- pchisq(chi2.1df/lambda$est,1,lower=F)
+	P1df <- pchisq(chi2.1df,1,lower.tail=F)
+	lambda <- estlambda(chi2.1df,plot=F,proportion=propPs)
+	Pc1df <- pchisq(chi2.1df/lambda$est,1,lower.tail=F)
 	#out$call <- match.call()
 	#out$trait.type <- posttypes[ttype]
 	#class(out) <- "scan.gwaa"

Modified: pkg/GenABEL/R/mlreg.p.R
===================================================================
--- pkg/GenABEL/R/mlreg.p.R	2012-08-30 09:26:00 UTC (rev 948)
+++ pkg/GenABEL/R/mlreg.p.R	2012-08-30 09:43:00 UTC (rev 949)
@@ -91,7 +91,9 @@
 	rownames(chi2) <- gtdata at snpnames
 	chi2[abs(chi2+999.9)<1.e-6] <- NA
 	chi2.1df <- (chi2$beta/chi2$sebeta)^2
-	out <- data.frame(snpnames=gtdata at snpnames,chromosome=gtdata at chromosome,map=gtdata at map,N=chi2$N,effB=chi2$beta,se.effB=chi2$sebeta,chi2.1df=chi2.1df,P1df=pchisq(chi2.1df,1,lower=F),stringsAsFactors = FALSE)
+	out <- data.frame(snpnames=gtdata at snpnames,chromosome=gtdata at chromosome,map=gtdata at map,
+			N=chi2$N,effB=chi2$beta,se.effB=chi2$sebeta,chi2.1df=chi2.1df,
+			P1df=pchisq(chi2.1df,1,lower.tail=F),stringsAsFactors = FALSE)
 #	class(out) <- "scan.gwaa"
 	out
 }

Modified: pkg/GenABEL/R/mmscore.R
===================================================================
--- pkg/GenABEL/R/mmscore.R	2012-08-30 09:26:00 UTC (rev 948)
+++ pkg/GenABEL/R/mmscore.R	2012-08-30 09:43:00 UTC (rev 949)
@@ -72,7 +72,7 @@
 					lambda$se <- NA
 				} else {
 					if (lenn<100) warning("Number of observations < 100, Lambda estimate is unreliable")
-					lambda <- estlambda(chi2.1df,plot=FALSE,prop=propPs)
+					lambda <- estlambda(chi2.1df,plot=FALSE,proportion=propPs)
 					if (lambda$estimate<1.0 && clambda==TRUE) {
 						warning("Lambda estimated < 1, set to 1")
 						lambda$estimate <- 1.0
@@ -122,9 +122,9 @@
 		Pc1df <- pr.c1df/times
 #		out$Pc1df <- replace(out$Pc1df,(out$Pc1df==0),1/(1+times))
 	} else {
-		P1df <- pchisq(chi2.1df,1,lower=F)
-#		out$P2df <- pchisq(chi2.2df,actdf,lower=F)
-		Pc1df <- pchisq(chi2.c1df,1,lower=F)
+		P1df <- pchisq(chi2.1df,1,lower.tail=F)
+#		out$P2df <- pchisq(chi2.2df,actdf,lower.tail=F)
+		Pc1df <- pchisq(chi2.c1df,1,lower.tail=F)
 	}
 	#out$lambda <- lambda
 	#out$effB <- effB #*var(h2object$residualY,na.rm=T)

Modified: pkg/GenABEL/R/npsubtreated.R
===================================================================
--- pkg/GenABEL/R/npsubtreated.R	2012-08-30 09:26:00 UTC (rev 948)
+++ pkg/GenABEL/R/npsubtreated.R	2012-08-30 09:43:00 UTC (rev 949)
@@ -12,7 +12,7 @@
 	
 	if (increase) x1$y.obs <- (-1)*x1$y.obs
 
-	ord <- sort.int(x1$y.obs,dec=T,index=T)$ix
+	ord <- sort.int(x1$y.obs,decreasing=T,index.return=T)$ix
 	x1 <- x1[ord,]
 	subtr <- mean(x1$y.obs)
 	x1$y.1 <- x1$y.obs - subtr

Modified: pkg/GenABEL/R/polygenic.R
===================================================================
--- pkg/GenABEL/R/polygenic.R	2012-08-30 09:26:00 UTC (rev 948)
+++ pkg/GenABEL/R/polygenic.R	2012-08-30 09:43:00 UTC (rev 949)
@@ -280,9 +280,9 @@
 	tmp <- t(relmat)
 	relmat[upper.tri(relmat)] <- tmp[upper.tri(tmp)]
 	rm(tmp);gc()
-	if (llfun=="polylik") eigres <- eigen(ginv(relmat),symm=TRUE)
+	if (llfun=="polylik") eigres <- eigen(ginv(relmat),symmetric=TRUE)
 	else if (llfun=="polylik_eigen") {
-		eigres <- eigen(relmat,symm=TRUE)
+		eigres <- eigen(relmat,symmetric=TRUE)
 		if (any(eigres$values<0)) {
 			#eigres$values <- abs(eigres$values)
 			warning("some eigenvalues <=0, taking ABS for det; try option llfun='polylik'")
@@ -362,7 +362,7 @@
 # 
 #				iSigma <- ginv(h2*relmat + (1-h2)*diag(x=1,ncol=length(y),nrow=length(y)))
 # start new
-				if (llfun=="polylik") eigres <- eigen(relmat,symm=TRUE) # ensure eigres contain eigen of RelMat (not Inv(RelMat))
+				if (llfun=="polylik") eigres <- eigen(relmat,symmetric=TRUE) # ensure eigres contain eigen of RelMat (not Inv(RelMat))
 				es <- (eigres$value*h2+1.-h2)*parsave[npar]*sdy*sdy
 				iSigma <- (eigres$vec) %*% diag(1./es,ncol=length(es)) %*% t(eigres$vec)
 # END new
@@ -479,7 +479,7 @@
 	if (fglschecks && missing(fixh2)) { 
 		ginvsig <- iSigma # already computed it in FGLS checks
 	} else {
-		if (llfun=="polylik") eigres <- eigen(relmat,symm=TRUE) # ensure eigres contain eigen of RelMat (not Inv(RelMat))
+		if (llfun=="polylik") eigres <- eigen(relmat,symmetric=TRUE) # ensure eigres contain eigen of RelMat (not Inv(RelMat))
 		es <- tvar*(eigres$value*h2+1.-h2)
 		#print(es[1:5])
 		#print(eigres$vec[1:5,1:5])

Modified: pkg/GenABEL/R/polygenic_hglm.R
===================================================================
--- pkg/GenABEL/R/polygenic_hglm.R	2012-08-30 09:26:00 UTC (rev 948)
+++ pkg/GenABEL/R/polygenic_hglm.R	2012-08-30 09:43:00 UTC (rev 949)
@@ -166,7 +166,7 @@
 	#out$ProfLogLik <- res_hglm$ProfLogLik
 	
 	logdetSigma <- sum(log(eigen(Sigma, only.values = TRUE)$values))
-	temp <- determinant(t(desmat)%*%out$InvSigma%*%desmat, log = TRUE)
+	temp <- determinant(t(desmat)%*%out$InvSigma%*%desmat, logarithm = TRUE)
 	out$ProfLogLik <- as.numeric(- .5*logdetSigma 
 					- .5*t(out$residualY[mids])%*%out$InvSigma%*%out$residualY[mids]
 					- .5*temp$modulus*temp$sign)

More information about the Genabel-commits mailing list