[adegenet-commits] r969 - in pkg: . man

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

Author: jombart
Date: 2011-11-10 11:41:01 +0100 (Thu, 10 Nov 2011)
New Revision: 969

Modified:
   pkg/ChangeLog
   pkg/man/fstat.Rd
   pkg/man/read.fstat.Rd
   pkg/man/read.genetix.Rd
Log:
Updated doc; ChangeLog ready for new release.


Modified: pkg/ChangeLog
===================================================================
--- pkg/ChangeLog	2011-11-10 10:31:19 UTC (rev 968)
+++ pkg/ChangeLog	2011-11-10 10:41:01 UTC (rev 969)
@@ -2,14 +2,19 @@
 
 BUG FIXES
 
-	o
+	o replaced calls to multicore:::detectCores with
+	parallel:::detectCores (the former gives unexpected results on
+	some platforms).
 
-NEW FEATURES
+	o documentation update: fstat function is no longer available due
+	to removal of hierfstat package from CRAN.
 
-	o
+	o documentation update: doc now specifies that read.genepop and
+	read.fstat are meant for diploid data only, with guidelines for
+	haploid data.
 
+	
 
-
 			CHANGES IN ADEGENET VERSION 1.3-1
 
 BUG FIXES

Modified: pkg/man/fstat.Rd
===================================================================
--- pkg/man/fstat.Rd	2011-11-10 10:31:19 UTC (rev 968)
+++ pkg/man/fstat.Rd	2011-11-10 10:41:01 UTC (rev 969)
@@ -7,22 +7,19 @@
 \alias{pairwise.fst}
 \title{F statistics for genind objects}
 \description{
-  The function \code{fstat} computes a global Fst, while
   \code{pairwise.fst} computes Nei's pairwise Fst between all pairs of
-  populations. Both functions are designed for \linkS4class{genind}
-  objects.
-
-  \code{fstat} is wrapper for \code{varcomp.glob} from package
-  \code{hierfstat} for \linkS4class{genind} objects. It computes F statistics (Fst, Fis, Fit)
-  given a set of genotypes and a grouping factor.
-
-  \code{pairwise.fst} is an implementation of Nei's Fst in which
-  heretozygosities are weighted by group sizes (see details).
+  populations using a \linkS4class{genind} object. Heretozygosities are
+  weighted by group sizes (see details).
+  
+  The former function \code{fstat} was a wrapper for \code{varcomp.glob}
+  from the package \code{hierfstat}. Unfortunately, this package was
+  removed from CRAN due to maintaining issues. For a replacement, see
+  the function \code{Fst} in the \code{pagas} package.!
 }
 \usage{
-fstat(x, pop=NULL, fstonly=FALSE)
-
 pairwise.fst(x, pop=NULL, res.type=c("dist","matrix"), truenames=TRUE)
+
+fstat(x, pop=NULL, fstonly=FALSE)
 }
 \arguments{
   \item{x}{an object of class \linkS4class{genind}.}
@@ -60,15 +57,6 @@
 ## pairwise Fst
 mat.fst <- pairwise.fst(nancycats, res.type="matrix")
 mat.fst
-
-
-## using hierfstat (if available)
-if(require(hierfstat)){
-data(nancycats)
-
-## Fst, Fis, Fit
-fstat(nancycats)
 }
 }
-}
 \keyword{multivariate}
\ No newline at end of file

Modified: pkg/man/read.fstat.Rd
===================================================================
--- pkg/man/read.fstat.Rd	2011-11-10 10:31:19 UTC (rev 968)
+++ pkg/man/read.fstat.Rd	2011-11-10 10:41:01 UTC (rev 969)
@@ -4,7 +4,12 @@
 \title{ Reading data from Fstat}
 \description{
  The function \code{read.fstat} reads Fstat data files (.dat) and
- convert them into a \linkS4class{genind} object. 
+ convert them into a \linkS4class{genind} object.
+
+ Note: \code{read.fstat} is meant for DIPLOID DATA ONLY. Haploid
+ data with the Hierfstat format can be read into R using
+ \code{read.table} or \code{read.csv} after removing headers and 'POP'
+ lines, and then converted using \code{\link{df2genind}}.
 }
 \usage{
 read.fstat(file,missing=NA,quiet=FALSE)

Modified: pkg/man/read.genetix.Rd
===================================================================
--- pkg/man/read.genetix.Rd	2011-11-10 10:31:19 UTC (rev 968)
+++ pkg/man/read.genetix.Rd	2011-11-10 10:41:01 UTC (rev 969)
@@ -4,7 +4,12 @@
 \title{ Reading data from GENETIX}
 \description{
   The function \code{read.genetix} reads GENETIX data files (.gtx) and
-  convert them into a \linkS4class{genind} object. 
+  convert them into a \linkS4class{genind} object.
+
+  Note: \code{read.genetix} is meant for DIPLOID DATA ONLY. Haploid
+  data with the GENETIX format can be read into R using
+  \code{read.table} or \code{read.csv} after removing headers and 'POP'
+  lines, and then converted using \code{\link{df2genind}}.
 }
 \usage{
 read.genetix(file=NULL,missing=NA,quiet=FALSE)