[adegenet-commits] r603 - pkg/man

Fri Apr 16 13:53:49 CEST 2010

Author: jombart
Date: 2010-04-16 13:53:48 +0200 (Fri, 16 Apr 2010)
New Revision: 603

Modified:
   pkg/man/Hs.Rd
   pkg/man/adegenet.package.Rd
   pkg/man/find.clusters.Rd
   pkg/man/repool.Rd
   pkg/man/sequences.Rd
   pkg/man/sim2pop.Rd
Log:
A few changes in the doc.


Modified: pkg/man/Hs.Rd
===================================================================

--- pkg/man/Hs.Rd	2010-04-16 10:48:02 UTC (rev 602)
+++ pkg/man/Hs.Rd	2010-04-16 11:53:48 UTC (rev 603)
@@ -2,10 +2,12 @@
 \name{Hs}
 \alias{Hs}
 \title{Expected heterozygosity}
-\description{This function computes the expected heterozygosity per
-  population from \linkS4class{genpop} objects. This is possible for
-  codominant markers (\code{@type="codom"}). For haploid data, Hs still
-  provides a measure of within-population genetic diversity. 
+\description{
+  This function computes the expected heterozygosity (Hs) within
+  populations of a \linkS4class{genpop} object. This function is
+  available for codominant markers (\code{@type="codom"}) only. Hs is
+  commonly used for measuring within population genetic diversity (and
+  as such, it still has sense when computed from haploid data).
 }
 \usage{
 Hs(x, truenames=TRUE)

Modified: pkg/man/adegenet.package.Rd
===================================================================
--- pkg/man/adegenet.package.Rd	2010-04-16 10:48:02 UTC (rev 602)
+++ pkg/man/adegenet.package.Rd	2010-04-16 11:53:48 UTC (rev 603)
@@ -21,7 +21,7 @@
   package offers methods for manipulating and analyzing information
   coming from genetic markers (see below). \cr
 
-  
+
   === IMPORTING DATA ===\cr
   \code{adegenet} imports data to \linkS4class{genind} object from the
   following softwares:\cr
@@ -29,23 +29,23 @@
   - GENETIX: see \code{\link{read.genetix}}\cr
   - FSTAT: see \code{\link{read.fstat}}\cr
   - Genepop: see \code{\link{read.genepop}}\cr
-
   To import data from any of these formats, you can also use the general
   function \code{\link{import2genind}}.\cr
+
+  - DNA files: use  \code{\link[pkg]{read.dna}} from the ape package,
+  and then extract SNPs from DNA alignments using
+  \code{\link{DNAbin2genind}}. \cr
+
   It is also possible to read genotypes coded by character strings from
   a data.frame in which genotypes are in rows, markers in columns. For
   this, use \code{\link{df2genind}}. Note that \code{\link{df2genind}}
   can be used for any level of ploidy.\cr
 
-  It is possible to extract SNPs from DNA alignments stored in the ape
-  package using \code{\link{DNAbin2genind}}.
-  
 
-  
    === EXPORTING DATA ===\cr
    \code{adegenet} exports data from \linkS4class{genind} object to
    formats recognized by other R packages:\cr
-   - the genetics package: see \code{\link{genind2genotype}}\cr 
+   - the genetics package: see \code{\link{genind2genotype}}\cr
    - the hierfstat package: see \code{\link{genind2hierfstat}}\cr
 
    Genotypes can also be recoded from a \linkS4class{genind} object into
@@ -53,7 +53,7 @@
    alleles. This covers formats from many softwares like GENETIX or
    STRUCTURE. For this, see \code{\link{genind2df}}.\cr
 
-   
+
    === MANIPULATING DATA ===\cr
    Several functions allow one to manipulate \linkS4class{genind} or
    \linkS4class{genpop} objects\cr
@@ -71,7 +71,7 @@
    - \code{\link{makefreq}}: returns a table of allelic frequencies from
    a \linkS4class{genpop} object.\cr
    - \code{\link{repool}} merges genoptypes from different
-   genetic pools into one single \linkS4class{genind} object.\cr
+   gene pools into one single \linkS4class{genind} object.\cr
    - \code{\link{propTyped}} returns the proportion of available (typed)
    data, by individual, population, and/or locus.\cr
    - \code{\link{selPopSize}} subsets data, retaining only genotypes

Modified: pkg/man/find.clusters.Rd
===================================================================
--- pkg/man/find.clusters.Rd	2010-04-16 10:48:02 UTC (rev 602)
+++ pkg/man/find.clusters.Rd	2010-04-16 11:53:48 UTC (rev 603)
@@ -106,7 +106,7 @@
     \code{data.frame} method.}
 }
 \details{
-  === ON THE SELECTION OF K ===
+  === ON THE SELECTION OF K ===\cr
   (where K is the 'optimal' number of clusters)
 
   So far, the analysis of data simulated under various population genetics
@@ -145,7 +145,7 @@
   The class \code{find.clusters} is a list with the following
   components:\cr
   \item{Kstat}{a \code{numeric} vector giving the values of the summary
-  statistics for the different values of K. Is NULLif \code{n.clust} was specified.}
+  statistics for the different values of K. Is NULL if \code{n.clust} was specified.}
   \item{stat}{a \code{numeric} value giving the value of the summary statistics
   for the retained model}
   \item{grp}{a \code{factor} giving group membership for each individual.}

Modified: pkg/man/repool.Rd
===================================================================
--- pkg/man/repool.Rd	2010-04-16 10:48:02 UTC (rev 602)
+++ pkg/man/repool.Rd	2010-04-16 11:53:48 UTC (rev 603)
@@ -1,6 +1,6 @@
 \name{repool}
 \alias{repool}
-\title{Pool several genotypes into the same dataset}
+\title{Pool several genotypes into a single dataset}
 \description{
   The function \code{repool} allows to merge genotypes from different
   \linkS4class{genind} objects into a single 'pool' (i.e. a new \linkS4class{genind}).

Modified: pkg/man/sequences.Rd
===================================================================
--- pkg/man/sequences.Rd	2010-04-16 10:48:02 UTC (rev 602)
+++ pkg/man/sequences.Rd	2010-04-16 11:53:48 UTC (rev 603)
@@ -12,7 +12,8 @@
   - alignement (seqinr package): to come...
 }
 \usage{
-DNAbin2genind(x, pop=NULL, exp.char=c("a","t","g","c"), na.char=NULL, polyThres=1/100)
+DNAbin2genind(x, pop=NULL, exp.char=c("a","t","g","c"), na.char=NULL,
+                         polyThres=1/100)
 }
 \arguments{
  \item{x}{an object containing aligned sequences.}

Modified: pkg/man/sim2pop.Rd
===================================================================
--- pkg/man/sim2pop.Rd	2010-04-16 10:48:02 UTC (rev 602)
+++ pkg/man/sim2pop.Rd	2010-04-16 11:53:48 UTC (rev 603)
@@ -16,14 +16,14 @@
   supplementary component.
 }
 \source{
-  Easypop version 2.0.1 was run with the following parameters:
-  - two diploid populations, one sex, random mating
-  - 1000 individuals per population
-  - proportion of migration: 0.002
-  - 20 loci
-  - mutation rate: 0.0001 (KAM model)
-  - maximum of 50 allelic states
-  - 1000 generations (last one taken)
+  Easypop version 2.0.1 was run with the following parameters:\cr
+  - two diploid populations, one sex, random mating\cr
+  - 1000 individuals per population\cr
+  - proportion of migration: 0.002\cr
+  - 20 loci\cr
+  - mutation rate: 0.0001 (KAM model)\cr
+  - maximum of 50 allelic states\cr
+  - 1000 generations (last one taken)\cr
 
 }
 \author{

