[adegenet-commits] r600 - in pkg: . man

Thu Apr 15 21:40:09 CEST 2010

Author: jombart
Date: 2010-04-15 21:40:08 +0200 (Thu, 15 Apr 2010)
New Revision: 600

Modified:
   pkg/DESCRIPTION
   pkg/man/H3N2.Rd
   pkg/man/adegenet.package.Rd
   pkg/man/coords.monmonier.Rd
   pkg/man/dapc.Rd
   pkg/man/dapcIllus.Rd
   pkg/man/dist.genpop.Rd
   pkg/man/eHGDP.Rd
   pkg/man/find.clusters.Rd
Log:
Done ! Compiles now, no warning, no probs. Have the give the doc a check.


Modified: pkg/DESCRIPTION
===================================================================

--- pkg/DESCRIPTION	2010-04-15 18:42:44 UTC (rev 599)
+++ pkg/DESCRIPTION	2010-04-15 19:40:08 UTC (rev 600)
@@ -2,7 +2,10 @@
 Version: 1.2-4
 Date: 2009/04/15
 Title: adegenet: a R package for the multivariate analysis of genetic markers.
-Author: Thibaut Jombart <t.jombart at imperial.ac.uk>, with contributions from Peter Solymos and Francois Balloux <f.balloux at imperial.ac.uk>
+Author:  Thibaut Jombart <t.jombart at imperial.ac.uk>
+  with contributions of: Peter Solymos, Francois Balloux
+  and contributed datasets from: Katayoun Moazami-Goudarzi, Denis Laloe,
+  Dominique Pontier, Daniel Maillard, Francois Balloux
 Maintainer: Thibaut Jombart <t.jombart at imperial.ac.uk>
 Suggests: ade4, genetics, hierfstat, spdep, tripack, ape, pegas, graph, RBGL
 Depends: methods, MASS

Modified: pkg/man/H3N2.Rd
===================================================================
--- pkg/man/H3N2.Rd	2010-04-15 18:42:44 UTC (rev 599)
+++ pkg/man/H3N2.Rd	2010-04-15 19:40:08 UTC (rev 600)
@@ -29,7 +29,7 @@
 \references{
 Jombart, T., Devillard, S. and Balloux, F.
 Discriminant analysis of principal components: a new method for the analysis of
-genetically structured populations. Submitted to \emph{PLoS genetics}.
+genetically structured populations. Submitted to \emph{Genetics}.
 }
 \examples{
 ## LOAD DATA

Modified: pkg/man/adegenet.package.Rd
===================================================================
--- pkg/man/adegenet.package.Rd	2010-04-15 18:42:44 UTC (rev 599)
+++ pkg/man/adegenet.package.Rd	2010-04-15 19:40:08 UTC (rev 600)
@@ -37,7 +37,11 @@
   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
@@ -83,11 +87,11 @@
    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 populations. Optimized boundaries can be obtained using
+   used to seek genetic boundaries among individuals or
+   populations. Optimized boundaries can be obtained using
    \code{\link{optimize.monmonier}}. Object of the class
    \code{monmonier} can be plotted and printed using the corresponding
    methods. \cr
-   - \code{\link{hybridize}}: implements hybridization between two populations. \cr
    - \code{\link{spca}}: implements Jombart et al. (in revision) spatial
    Principal Component Analysis \cr
    - \code{\link{global.rtest}}: implements Jombart et al. (2008)
@@ -101,12 +105,52 @@
    - \code{\link{scaleGen}}: generic method to scale
    \linkS4class{genind} or \linkS4class{genpop} before a principal
    component analysis \cr
+   - \code{\link{Hs}}: computes the average expected heterozygosity by
+   population in a \linkS4class{genpop}. Classically Used as a measure
+   of genetic diversity.\cr
+   - \code{\link{find.clusters}} and \code{\link{dapc}}: implements the
+   Discriminant Analysis of Principal Component (DAPC, Jombart et al.,
+   submitted A).\cr
+   - \code{\link{seqTrack}}: implements the SeqTrack algorithm for
+   recontructing transmission trees of pathogens (Jombart et al.,
+   submitted B) .\cr
 
-   Adegenet also proposes several real or simulated datasets.\cr
 
+   === GRAPHICS ===\cr
+   - \code{\link{colorplot}}: plots points with associated values for up
+   to three variables represented by colors using the RGB system;
+   useful for spatial mapping of principal components.\cr
+   - \code{\link{loadingplot}}: plots loadings of variables. Useful for
+   representing the contribution of alleles to a given principal
+   component in a multivariate method. \cr
+
+
+   === SIMULATING DATA ===\cr
+   - \code{\link{hybridize}}: implements hybridization between two populations. \cr
+   - \code{\link{haploGen}}: simulates genealogies of haplotypes,
+   storing full genomes (under development). \cr
+   - \code{\link{haploPop}}: simulates populations of haplotypes, using
+   different population dynamics, storing SNPs (under development). \cr
+
+
+   === DATASETS ===\cr
+   - \code{\link{H3N2}}: Seasonal influenza (H3N2) HA segment data. \cr
+   - \code{\link{dapcIllus}}: Simulated data illustrating the DAPC. \cr
+   - \code{\link{eHGDP}}: Extended HGDP-CEPH dataset. \cr
+   - \code{\link{microbov}}: Microsatellites genotypes of 15 cattle breeds. \cr
+   - \code{\link{nancycats}}: Microsatellites genotypes of 237 cats from 17 colonies of Nancy (France). \cr
+   - \code{\link{rupica}}: Microsatellites genotypes of 335 chamois
+   (Rupicapra rupicapra) from the Bauges mountains (France).\cr
+   - \code{\link{sim2pop}}: Simulated genotypes of two georeferenced populations.\cr
+   - \code{\link{spcaIllus}}: Simulated data illustrating the sPCA. \cr
+
    For more information, visit the adegenet website by typing
    \code{adegenetWeb()}.\cr
 
+   Tutorials are available on the adegenet website, or by typing
+   \code{adegenetTutorial()}.\cr
+
+
    To cite adegenet, please use the reference given by
    \code{citation("adegenet")} (or see reference below).
  }
@@ -114,13 +158,17 @@
   \tabular{ll}{
     Package: \tab adegenet\cr
     Type: \tab Package\cr
-    Version: \tab 1.3-0\cr
-    Date: \tab 2009-04-01 \cr
+    Version: \tab 1.2-4\cr
+    Date: \tab 2009-04-15 \cr
     License: \tab GPL (>=2)
   }  
 }
-\author{Thibaut Jombart <t.jombart at imperial.ac.uk>\cr
-with contributions of Peter Solymos}
+\author{
+  Thibaut Jombart <t.jombart at imperial.ac.uk>\cr
+  with contributions of: Peter Solymos, Francois Balloux\cr
+  and contributed datasets from: Katayoun Moazami-Goudarzi, Denis Laloë,
+  Dominique Pontier, Daniel Maillard, Francois Balloux
+}
 \references{
 Jombart T. (2008) adegenet: a R package for the multivariate analysis of genetic markers
 \emph{Bioinformatics} 24: 1403-1405. doi: 10.1093/bioinformatics/btn129\cr
@@ -132,4 +180,10 @@
 }
 \keyword{manip}
 \keyword{multivariate}
-\seealso{The \code{ade4} package for multivariate analysis}
+\seealso{
+  adegenet is related to several packages, in particular:\cr
+  - \code{ade4} for multivariate analysis\cr
+  - \code{ape} for phylogenetics and DNA data handling\cr
+  - \code{pegas} for population genetics tools\cr
+}
+

Modified: pkg/man/coords.monmonier.Rd
===================================================================
--- pkg/man/coords.monmonier.Rd	2010-04-15 18:42:44 UTC (rev 599)
+++ pkg/man/coords.monmonier.Rd	2010-04-15 19:40:08 UTC (rev 600)
@@ -2,24 +2,32 @@
 \alias{coords.monmonier}
 \title{Returns original points in results paths of an object of class 'monmonier'}
 \description{
-The original implementation of \code{monmonier} in package \bold{adegenet} returns path coordinates, \code{coords.monmonier} additionally displays identities of the original points of the network, based on original coordinates.
+  The original implementation of \code{monmonier} in package
+  \bold{adegenet} returns path coordinates, \code{coords.monmonier}
+  additionally displays identities of the original points of the network,
+  based on original coordinates.
 }
 \usage{
 coords.monmonier(x)
 }
 \arguments{
-  \item{x}{an object of class \sQuote{monmonier}.}
+  \item{x}{an object of class \code{\link{monmonier}}.}
 }
 \value{
-Returns a list with elements according to the \code{x$nrun} result of the \sQuote{monmonier} object.
-Corresponding path points are in the same order as in the original object.
+  Returns a list with elements according to the \code{x$nrun} result of the \code{\link{monmonier}} object.
+  Corresponding path points are in the same order as in the original object.
 
-  \item{run1 (run2, ...)}{for each run, a list containing a matrix giving the original points in the network 
-  (\code{first} and \code{second}, indicating neighbouring pairs) which are divided by the path (path coordinates are stored in columns \code{x.hw} and \code{y.hw}. \code{first} and \code{second} are integers referring to the row numbers in the \code{x$xy} matrix of the original \sQuote{monmonier} object.}
-
+  run1 (run2, ...): for each run, a list containing a matrix giving the
+  original points in the network (\code{first} and \code{second},
+  indicating pairs of neighbours). Path coordinates are stored in
+  columns \code{x.hw} and \code{y.hw}. \code{first} and \code{second}
+  are integers referring to the row numbers in the \code{x$xy} matrix of
+  the original \code{\link{monmonier}} object.
 }
 \author{Peter Solymos, \email{Solymos.Peter at aotk.szie.hu}, \url{http://www.univet.hu/users/psolymos/personal/}}
-\seealso{\code{\link{monmonier}}}
+\seealso{
+  \code{\link{monmonier}}
+}
 \examples{
 
 \dontrun{

Modified: pkg/man/dapc.Rd
===================================================================
--- pkg/man/dapc.Rd	2010-04-15 18:42:44 UTC (rev 599)
+++ pkg/man/dapc.Rd	2010-04-15 19:40:08 UTC (rev 600)
@@ -156,7 +156,7 @@
     of DAPC.}
 
 
-  \cr=== other outputs ===\cr
+  === other outputs ===\cr
   Other functions have different outputs:\cr
   - \code{summary.dapc} returns a list with 6 components: \code{n.dim} (number
   of retained DAPC axes), \code{n.pop} (number of groups/populations),
@@ -170,7 +170,7 @@
 \references{
 Jombart, T., Devillard, S. and Balloux, F.
 Discriminant analysis of principal components: a new method for the analysis of
-genetically structured populations. Submitted to \emph{PLoS genetics}.
+genetically structured populations. Submitted to \emph{Genetics}.
 }
 \seealso{
   - \code{\link{find.clusters}}: to identify clusters without prior.

Modified: pkg/man/dapcIllus.Rd
===================================================================
--- pkg/man/dapcIllus.Rd	2010-04-15 18:42:44 UTC (rev 599)
+++ pkg/man/dapcIllus.Rd	2010-04-15 19:40:08 UTC (rev 600)
@@ -2,7 +2,7 @@
 \name{dapcIllus}
 \alias{dapcIllus}
 \docType{data}
-\title{Simulated data illustrating the dapc}
+\title{Simulated data illustrating the DAPC}
 \description{
   Datasets illustrating the Discriminant Analysis of Principal
   Components (DAPC, Jombart et al. submitted).\cr
@@ -43,7 +43,7 @@
 \references{
    Jombart, T., Devillard, S. and Balloux, F.  Discriminant analysis of
    principal components: a new method for the analysis of genetically
-   structured populations. Submitted to \emph{PLoS genetics}.
+   structured populations. Submitted to \emph{Genetics}.
 }
 \examples{
 if(require(MASS) & require(ade4)){

Modified: pkg/man/dist.genpop.Rd
===================================================================
--- pkg/man/dist.genpop.Rd	2010-04-15 18:42:44 UTC (rev 599)
+++ pkg/man/dist.genpop.Rd	2010-04-15 19:40:08 UTC (rev 600)
@@ -9,8 +9,8 @@
   (see details).\cr
   
   A non-euclidian distance can be transformed into an Euclidian one
-  using \code{\link[pkg:ade4]{cailliez}} in order to perform a
-  Principal Coordinate Analysis \code{\link[pkg:ade4]{dudi.pco}} (both
+  using \code{\link[ade4]{cailliez}} in order to perform a
+  Principal Coordinate Analysis \code{\link[ade4]{dudi.pco}} (both
   functions in \code{ade4}). \cr
   
   The function \code{dist.genpop} is based on former \code{dist.genet}

Modified: pkg/man/eHGDP.Rd
===================================================================
--- pkg/man/eHGDP.Rd	2010-04-15 18:42:44 UTC (rev 599)
+++ pkg/man/eHGDP.Rd	2010-04-15 19:40:08 UTC (rev 600)
@@ -51,7 +51,7 @@
 
 [5] Jombart, T., Devillard, S. and Balloux, F.  Discriminant analysis of
 principal components: a new method for the analysis of genetically
-structured populations. Submitted to \emph{PLoS genetics}.
+structured populations. Submitted to \emph{Genetics}.
 }
 \examples{
 \dontrun{

Modified: pkg/man/find.clusters.Rd
===================================================================
--- pkg/man/find.clusters.Rd	2010-04-15 18:42:44 UTC (rev 599)
+++ pkg/man/find.clusters.Rd	2010-04-15 19:40:08 UTC (rev 600)
@@ -154,7 +154,7 @@
 \references{
 Jombart, T., Devillard, S. and Balloux, F.
 Discriminant analysis of principal components: a new method for the analysis of
-genetically structured populations. Submitted to \emph{PLoS genetics}.
+genetically structured populations. Submitted to \emph{Genetics}.
 }
 \seealso{
   - \code{\link{dapc}}: implements the DAPC.

