[adegenet-commits] r81 - in pkg: . R man

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

Author: jombart
Date: 2008-03-28 17:46:12 +0100 (Fri, 28 Mar 2008)
New Revision: 81

Added:
   pkg/R/fstat.R
   pkg/man/fstat.Rd
Modified:
   pkg/DESCRIPTION
   pkg/TODO
   pkg/man/gstat.randtest.Rd
Log:
Added fstat function and doc.


Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION	2008-03-28 14:08:32 UTC (rev 80)
+++ pkg/DESCRIPTION	2008-03-28 16:46:12 UTC (rev 81)
@@ -9,4 +9,4 @@
 Description: Classes and functions for genetic data analysis within the multivariate framework.
 License: GPL (>=2)
 LazyLoad: yes
-Collate: classes.R auxil.R makefreq.R chooseCN.R dist.genpop.R export.R gstat.randtest.R HWE.R import.R monmonier.R coords.monmonier.R spca.R spca.rtests.R zzz.R hybridize.R
\ No newline at end of file
+Collate: classes.R auxil.R makefreq.R chooseCN.R dist.genpop.R export.R gstat.randtest.R HWE.R import.R monmonier.R coords.monmonier.R spca.R spca.rtests.R zzz.R hybridize.R fstat.R
\ No newline at end of file

Added: pkg/R/fstat.R
===================================================================
--- pkg/R/fstat.R	                        (rev 0)
+++ pkg/R/fstat.R	2008-03-28 16:46:12 UTC (rev 81)
@@ -0,0 +1,19 @@
+#################
+# fstat function
+#################
+fstat <- function(x, pop=NULL, fstonly=FALSE){
+    ## 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(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
+
+    if(fstonly) {res <- res[1,1]}
+    return(res)
+}

Modified: pkg/TODO
===================================================================
--- pkg/TODO	2008-03-28 14:08:32 UTC (rev 80)
+++ pkg/TODO	2008-03-28 16:46:12 UTC (rev 81)
@@ -38,7 +38,7 @@
 * Implement a method to merge different markers for the same individuals
 * Implement spatial weights derived from inverse spatial distances in chooseCN -- done (TJ)
 * Build accessors for marker names, indiv names, pop names, spatial coords, ...
-* Implement a Fst wrapper for genind objects
+* Implement a Fst wrapper for genind objects -- done (TJ)
 * 
 
 # TESTING:

Added: pkg/man/fstat.Rd
===================================================================
--- pkg/man/fstat.Rd	                        (rev 0)
+++ pkg/man/fstat.Rd	2008-03-28 16:46:12 UTC (rev 81)
@@ -0,0 +1,31 @@
+\encoding{UTF-8}
+\name{fstat}
+\alias{fstat}
+\title{F statistics for genind objects}
+\description{This function is a wrapper of \code{varcomp.glob} for
+  \linkS4class{genind} objects. It computes F statistics (Fst, Fis, Fit)
+  given a set of genotypes and a grouping factor.
+}
+\usage{
+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 x\@pop. 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).}
+  }
+\value{A matrix of F statistics.}
+\seealso{\code{\link[pkg:hierfstat]{varcomp.glob}},
+  \code{\link{gstat.randtest}}
+}
+\author{ Thibaut Jombart \email{jombart at biomserv.univ-lyon1.fr} }
+\examples{
+if(require(hierfstat)){
+data(nancycats)
+fstat(nancycats)
+}
+}
+\keyword{multivariate}
\ No newline at end of file

Modified: pkg/man/gstat.randtest.Rd
===================================================================
--- pkg/man/gstat.randtest.Rd	2008-03-28 14:08:32 UTC (rev 80)
+++ pkg/man/gstat.randtest.Rd	2008-03-28 16:46:12 UTC (rev 81)
@@ -44,6 +44,7 @@
 \value{Returns an object of the class \code{randtest} (package \code{ade4}).
 }
 \seealso{\code{\link[pkg:hierfstat]{g.stats.glob}},
+  \code{\link{fstat}},
   \code{\link[pkg:hierfstat]{test.g}},\code{\link[pkg:hierfstat]{test.within}},
   \code{\link[pkg:hierfstat]{test.between}},\code{\link[pkg:ade4]{as.randtest}},
   \code{\link{genind2hierfstat}}