[Forensim-help] r122 - in pkg: R man

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

Author: hindahaned
Date: 2009-07-23 18:09:41 +0200 (Thu, 23 Jul 2009)
New Revision: 122

Modified:
   pkg/R/AuxFunc.R
   pkg/R/likestim.R
   pkg/man/likestim.loc.Rd
Log:


Modified: pkg/R/AuxFunc.R
===================================================================
--- pkg/R/AuxFunc.R	2009-07-23 15:35:17 UTC (rev 121)
+++ pkg/R/AuxFunc.R	2009-07-23 16:09:41 UTC (rev 122)
@@ -6,8 +6,8 @@
 # returns the  position and the value of the maximum of a vector 
 
 findmax<-function(vec)
-	{
-	res0<-matrix(0,nrow=2,ncol=1)
+{
+	res0<-matrix(0,nrow=1,ncol=2)
 	#res0<-data.frame(res0)
 	if(all(vec==0))
 	{
@@ -15,22 +15,22 @@
 		maxval<-0
 	}
 	else{
-	xmax<-which(vec==max(vec))#car discret...
-	maxval<-vec[xmax]
+	xmax<-which(vec==max(vec))
+	maxval<-(vec[xmax])
 	}
 	#print(round(xmax))
 	res0[1,1]<-xmax
-	res0[2,1]<-maxval
+	res0[1,2]<-maxval
 	
-	rownames(res0)<-c('max','maxval')
-	colnames(res0)<-names(vec)
-	return(res0)
-	}
+	colnames(res0)<-c('max','maxval')
+	rownames(res0)<-names(vec)
+	return((res0))
+}
 
 
 
 
-#takes a matrix or a data frame in format of the  Journal of Forenis Sciences for genetic data, and returns a list of markers with their allele frequencies,
+#takes a matrix or a data frame in the format of the  Journal of Forenis Sciences for genetic data, and returns a list of markers with their allele frequencies,
 #skips the NA markers
 naomitab<-
 function(tab)

Modified: pkg/R/likestim.R
===================================================================
--- pkg/R/likestim.R	2009-07-23 15:35:17 UTC (rev 121)
+++ pkg/R/likestim.R	2009-07-23 16:09:41 UTC (rev 122)
@@ -20,7 +20,7 @@
 	#the maximum is searched in the discrete interval : 1: 6, more contributors is unlikely ?
 	locres <- as.matrix(apply(sapply(1:6,function(i) lik.loc(i,mix,freq,refpop,theta, loc)),1,findmax))
 	rownames(locres) <- c('max','maxval') 
-	return(locres)
+	return(t(locres))
 	
 }
 #likestm.loc(mix1,freq1)

Modified: pkg/man/likestim.loc.Rd
===================================================================
--- pkg/man/likestim.loc.Rd	2009-07-23 15:35:17 UTC (rev 121)
+++ pkg/man/likestim.loc.Rd	2009-07-23 16:09:41 UTC (rev 122)
@@ -25,8 +25,9 @@
   
 }
 \value{
-A matrix of dimension 2  x \code{loc}. The first row, \code{max}, gives the maximum likelihood estimation 
-of the number of contributors for each locus in column. The second row, \code{maxvalue}, gives the corresponding likelihood value.
+A matrix of dimension \code{loc} x 2. The first colum, \code{max}, gives the maximum likelihood estimation 
+of the number of contributors for each locus in row. The second column, \code{maxvalue}, 
+gives the corresponding likelihood value.
 }