[adegenet-commits] r876 - pkg/man

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Wed May 25 18:04:28 CEST 2011 

Author: jombart
Date: 2011-05-25 18:04:27 +0200 (Wed, 25 May 2011)
New Revision: 876

Modified:
   pkg/man/adegenet.package.Rd
   pkg/man/fstat.Rd
   pkg/man/glAux.Rd
   pkg/man/gstat.randtest.Rd
   pkg/man/haploGen.Rd
   pkg/man/inbreeding.Rd
   pkg/man/seqTrack.Rd
Log:
Package passes the check. Pretty much all functionalities ready.
Need to check the doc and make new vignettes.


Modified: pkg/man/adegenet.package.Rd
===================================================================
--- pkg/man/adegenet.package.Rd	2011-05-24 10:11:31 UTC (rev 875)
+++ pkg/man/adegenet.package.Rd	2011-05-25 16:04:27 UTC (rev 876)
@@ -90,8 +90,8 @@
    - \code{\link{HWE.test.genind}}: performs HWE test for all
    populations and loci combinations \cr
    - \code{\link{pairwise.fst}}: computes simple pairwise Fst between populations\cr
-   - \code{\link{gstat.randtest}}: performs a Monte Carlo test of Goudet's G statistic, measuring
-   population structure (based on \code{\link[hierfstat]{g.stats.glob}} package \code{hierfstat}).\cr
+   % - \code{\link{gstat.randtest}}: performs a Monte Carlo test of Goudet's G statistic, measuring
+   % population structure (based on \code{\link[hierfstat]{g.stats.glob}} package \code{hierfstat}).\cr
    - \code{\link{dist.genpop}}: computes 5 genetic distances among populations. \cr
    - \code{\link{monmonier}}: implementation of the Monmonier algorithm,
    used to seek genetic boundaries among individuals or

Modified: pkg/man/fstat.Rd
===================================================================
--- pkg/man/fstat.Rd	2011-05-24 10:11:31 UTC (rev 875)
+++ pkg/man/fstat.Rd	2011-05-25 16:04:27 UTC (rev 876)
@@ -38,8 +38,8 @@
 }
 \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}}
+\seealso{\code{\link{Hs}}%, \code{\link[hierfstat]{varcomp.glob}},
+ % \code{\link{gstat.randtest}}
 }
 \references{
   Nei, M. (1973) Analysis of gene diversity in subdivided

Modified: pkg/man/glAux.Rd
===================================================================
--- pkg/man/glAux.Rd	2011-05-24 10:11:31 UTC (rev 875)
+++ pkg/man/glAux.Rd	2011-05-25 16:04:27 UTC (rev 876)
@@ -31,7 +31,8 @@
 glNA(x, alleleAsUnit = TRUE)
 glMean(x, alleleAsUnit = TRUE)
 glVar(x, alleleAsUnit = TRUE)
-glDotProd(x, center = FALSE, scale = FALSE, alleleAsUnit = FALSE)
+glDotProd(x, center = FALSE, scale = FALSE, alleleAsUnit = FALSE,
+                multicore = require("multicore"), n.cores = NULL)
 }
 \arguments{
   \item{x}{a \linkS4class{genlight} object}
@@ -44,9 +45,14 @@
   \item{scale}{a logical indicating whether SNPs should be scaled to
     unit variance.}
   \item{useC}{a logical indicating whether compiled C code should be
-    used (TRUE) or not (FALSE, default). Pure-R code is more efficient
-    for small number of individuals; C-code is expected to be more
-    efficient for thousands of individuals.}
+    used (TRUE) or not (FALSE, default).}
+  \item{multicore}{a logical indicating whether multiple cores -if
+    available- should be used for the computations (TRUE, default), or
+    not (FALSE); requires the package \code{multicore} to be installed
+    (see details); this option cannot be used alongside useCoption.}
+  \item{n.cores}{if \code{multicore} is TRUE, the number of cores to
+    be used in the computations; if NULL, then the maximum number of
+    cores available on the computer is used.}
 }
 \details{
   === On the unit of information ===

Modified: pkg/man/gstat.randtest.Rd
===================================================================
--- pkg/man/gstat.randtest.Rd	2011-05-24 10:11:31 UTC (rev 875)
+++ pkg/man/gstat.randtest.Rd	2011-05-25 16:04:27 UTC (rev 876)
@@ -43,10 +43,10 @@
 }
 \value{Returns an object of the class \code{randtest} (package \code{ade4}).
 }
-\seealso{\code{\link[hierfstat]{g.stats.glob}},
+\seealso{%\code{\link[hierfstat]{g.stats.glob}},
   \code{\link{fstat}},
-  \code{\link[hierfstat]{test.g}},\code{\link[hierfstat]{test.within}},
-  \code{\link[hierfstat]{test.between}},\code{\link[ade4]{as.randtest}},
+  %\code{\link[hierfstat]{test.g}}%,\code{\link[hierfstat]{test.within}},
+  %\code{\link[hierfstat]{test.between}},\code{\link[ade4]{as.randtest}},
   \code{\link{genind2hierfstat}}
 }
 \author{ Thibaut Jombart \email{t.jombart at imperial.ac.uk} }

Modified: pkg/man/haploGen.Rd
===================================================================
--- pkg/man/haploGen.Rd	2011-05-24 10:11:31 UTC (rev 875)
+++ pkg/man/haploGen.Rd	2011-05-25 16:04:27 UTC (rev 876)
@@ -101,7 +101,7 @@
   \item{n}{an integer indicating the number of haplotypes to be retained
     in the sample}
   \item{from, to}{arguments of the conversion function, for converting a
-    \code{haploGen} object into a \code{\link[graph]{graphNEL-class}}.}
+    \code{haploGen} object into a \code{graphNEL-class}.}
   \item{tz, origin}{ aguments to be passed to \code{\link{as.POSIXct}}
     (see ?as.POSIXct)}
   \item{\dots}{further arguments to be passed to other methods}
@@ -142,7 +142,7 @@
   \code{install.packages("ape")}
 
   - for various purposes including plotting, converting genealogies to
-  graphs (\code{\link[graph]{graphNEL-class}} class) can be useful. This requires the
+  graphs (\code{graphNEL-class} class) can be useful. This requires the
   packages graph, and possibly Rgraphviz for plotting. These packages are
   not on CRAN, but on Bioconductor. To install them, use:\cr
   source("http://bioconductor.org/biocLite.R")\cr
@@ -153,7 +153,7 @@
 
 
   === Converting haploGen objects to graphs ===\cr
-  \code{haploGen} objects can be converted to \code{\link[graph]{graphNEL-class}}
+  \code{haploGen} objects can be converted to \code{graphNEL-class}
   objects, which can in turn be plotted and manipulated using classical
   graph tools. Simply use 'as(x, "graphNEL")' where 'x' is a
   \code{haploGen} object. This functionality requires the \code{graph}

Modified: pkg/man/inbreeding.Rd
===================================================================
--- pkg/man/inbreeding.Rd	2011-05-24 10:11:31 UTC (rev 875)
+++ pkg/man/inbreeding.Rd	2011-05-25 16:04:27 UTC (rev 876)
@@ -37,8 +37,8 @@
   \code{\link{inbreeding.ml}}: a maximum-likelihood estimation of
   inbreeding.
   
-  \code{\link{Hs}}, \code{\link[hierfstat]{varcomp.glob}},
-  \code{\link{gstat.randtest}}
+  \code{\link{Hs}}%, \code{\link[hierfstat]{varcomp.glob}},
+%  \code{\link{gstat.randtest}}
 }
 \references{
   Brown AR, Hosken DJ, Balloux F, et al. 2009 Genetic variation,

Modified: pkg/man/seqTrack.Rd
===================================================================
--- pkg/man/seqTrack.Rd	2011-05-24 10:11:31 UTC (rev 875)
+++ pkg/man/seqTrack.Rd	2011-05-25 16:04:27 UTC (rev 876)
@@ -133,7 +133,7 @@
 
   
   === Converting seqTrack objects to graphs ===\cr
-  seqTrack objects can be converted to \code{\link[graph]{graphNEL-class}} objects,
+  seqTrack objects can be converted to \code{graphNEL-class} objects,
   which can in turn be plotted and manipulated using classical graph
   tools. Simply use 'as(x, "graphNEL")' where 'x' is a seqTrack
   object. This functionality requires the \code{graph} package. Note

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