[adegenet-commits] r970 - in pkg: . R man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Nov 10 12:24:20 CET 2011
Author: jombart
Date: 2011-11-10 12:24:20 +0100 (Thu, 10 Nov 2011)
New Revision: 970
Modified:
pkg/DESCRIPTION
pkg/R/fstat.R
pkg/man/adegenet.package.Rd
pkg/man/fstat.Rd
Log:
Final changes.
Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION 2011-11-10 10:41:01 UTC (rev 969)
+++ pkg/DESCRIPTION 2011-11-10 11:24:20 UTC (rev 970)
@@ -1,6 +1,6 @@
Package: adegenet
Version: 1.3-2
-Date: 2011/09/01
+Date: 2011/11/11
Title: adegenet: an R package for the exploratory analysis of genetic and genomic data.
Author: Thibaut Jombart <t.jombart at imperial.ac.uk>
with contributions of: Ismail Ahmed <ismail.ahmed at inserm.fr>, Peter Solymos
Modified: pkg/R/fstat.R
===================================================================
--- pkg/R/fstat.R 2011-11-10 10:41:01 UTC (rev 969)
+++ pkg/R/fstat.R 2011-11-10 11:24:20 UTC (rev 970)
@@ -1,35 +1,32 @@
-#################
-# fstat function
-#################
-#
-# Wrapper for fst estimator from hierfstat package
-#
-fstat <- function(x, pop=NULL, fstonly=FALSE){
- cat("\nSorry, hierfstat package has been disabled - this function will be restored in a future release.\n")
- return(invisible())
- ## ## misc checks
- ## if(!is.genind(x)) stop("x is not a valid genind object")
- ## if(!require(hierfstat)) stop("hierfstat package is required. Please install it.")
- ## if(x at ploidy != as.integer(2)) stop("not implemented for non-diploid genotypes")
- ## checkType(x)
+## #################
+## # fstat function
+## #################
+## #
+## # Wrapper for fst estimator from hierfstat package
+## #
+## fstat <- function(x, pop=NULL, fstonly=FALSE){
+## cat("\nSorry, hierfstat package has been disabled - this function will be restored in a future release.\n")
+## return(invisible())
+## ## ## misc checks
+## ## if(!is.genind(x)) stop("x is not a valid genind object")
+## ## if(!require(hierfstat)) stop("hierfstat package is required. Please install it.")
+## ## if(x at ploidy != as.integer(2)) stop("not implemented for non-diploid genotypes")
+## ## checkType(x)
- ## if(is.null(pop)) pop <- x at pop
- ## if(is.null(pop)) stop("no pop factor provided")
- ## if(length(pop)!=nrow(x at tab)) stop("pop has a wrong length.")
+## ## if(is.null(pop)) pop <- x at pop
+## ## if(is.null(pop)) stop("no pop factor provided")
+## ## if(length(pop)!=nrow(x at tab)) stop("pop has a wrong length.")
- ## ## computations
- ## dat <- genind2hierfstat(x)[,-1]
- ## res <- varcomp.glob(levels=data.frame(pop), loci=dat)$F
+## ## ## computations
+## ## dat <- genind2hierfstat(x)[,-1]
+## ## res <- varcomp.glob(levels=data.frame(pop), loci=dat)$F
- ## if(fstonly) {res <- res[1,1]}
- ## return(res)
-}
+## ## if(fstonly) {res <- res[1,1]}
+## ## return(res)
+## }
-
-
-
###############
## pairwise.fst
###############
Modified: pkg/man/adegenet.package.Rd
===================================================================
--- pkg/man/adegenet.package.Rd 2011-11-10 10:41:01 UTC (rev 969)
+++ pkg/man/adegenet.package.Rd 2011-11-10 11:24:20 UTC (rev 970)
@@ -78,7 +78,10 @@
alleles. This covers formats from many softwares like GENETIX or
STRUCTURE. For this, see \code{\link{genind2df}}.\cr
+ Also note that the \code{pegas} package imports \linkS4class{genind}
+ objects using the function \code{as.loci}.
+
=== MANIPULATING DATA ===\cr
Several functions allow one to manipulate \linkS4class{genind} or
\linkS4class{genpop} objects\cr
@@ -188,7 +191,7 @@
Package: \tab adegenet\cr
Type: \tab Package\cr
Version: \tab 1.3-2\cr
- Date: \tab 2011-09-01 \cr
+ Date: \tab 2011-11-11 \cr
License: \tab GPL (>=2)
}
}
@@ -226,8 +229,8 @@
\seealso{
adegenet is related to several packages, in particular:\cr
- \code{ade4} for multivariate analysis\cr
+ - \code{pegas} for population genetics tools\cr
- \code{ape} for phylogenetics and DNA data handling\cr
- - \code{pegas} for population genetics tools\cr
- \code{seqinr} for handling nucleic and proteic sequences\cr
}
Modified: pkg/man/fstat.Rd
===================================================================
--- pkg/man/fstat.Rd 2011-11-10 10:41:01 UTC (rev 969)
+++ pkg/man/fstat.Rd 2011-11-10 11:24:20 UTC (rev 970)
@@ -1,7 +1,6 @@
\encoding{UTF-8}
\name{F statistics}
\alias{fstat}
-\alias{Fst}
\alias{FST}
\alias{fst}
\alias{pairwise.fst}
@@ -10,34 +9,29 @@
\code{pairwise.fst} computes Nei's pairwise Fst between all pairs of
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.!
+
+ The function \code{fstat} is no longer available as the package
+ \code{hierfstat} has been removed from CRAN. For Fst, Fis and Fit, use
+ the function \code{Fst} from the \code{pagas} package (see example).
}
\usage{
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}.}
\item{pop}{a factor giving the 'population' of each individual. If NULL,
pop is seeked from \code{pop(x)}. Note that the term population refers in
fact to any grouping of individuals'.}
- \item{fstonly}{a logical stating whether only the Fst value should be
- returned (TRUE) instead of all F statistics (FALSE, default).}
\item{res.type}{the type of result to be returned: a \code{dist} object, or a
symmetric matrix}
\item{truenames}{a logical indicating whether true labels (as opposed
to generic labels) should be used to name the output.}
}
\value{
- A vector, a matrix, or a dist object containing F statistics.}
-\seealso{\code{\link{Hs}}%, \code{\link[hierfstat]{varcomp.glob}},
- % \code{\link{gstat.randtest}}
+ A vector, a matrix, or a dist object containing F statistics.
}
+\seealso{\code{\link{Hs}}
+}
\references{
Nei, M. (1973) Analysis of gene diversity in subdivided
populations. Proc Natl Acad Sci USA, 70: 3321-3323
@@ -58,5 +52,19 @@
mat.fst <- pairwise.fst(nancycats, res.type="matrix")
mat.fst
}
+
+## Fst, Fis, Fit
+if(require(pegas)){
+data(nancycats)
+
+## conversion to pegas's format
+as.loci(nancycats)
+
+## use Fst from pegas
+fsttab <- Fst(as.loci(nancycats))
+
+## average over loci
+apply(fsttab, 2, mean)
}
+}
\keyword{multivariate}
\ No newline at end of file
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