[adegenet-commits] r596 - in pkg: R man

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

Author: jombart
Date: 2010-04-15 19:05:01 +0200 (Thu, 15 Apr 2010)
New Revision: 596

Modified:
   pkg/R/seqTrack.R
   pkg/man/dapc.Rd
   pkg/man/find.clusters.Rd
   pkg/man/seqTrack.Rd
Log:
Trying to document everything, even in a dirty way.


Modified: pkg/R/seqTrack.R
===================================================================
--- pkg/R/seqTrack.R	2010-04-15 16:05:47 UTC (rev 595)
+++ pkg/R/seqTrack.R	2010-04-15 17:05:01 UTC (rev 596)
@@ -1123,9 +1123,9 @@
 ###############
 ## seqTrack.ml
 ###############
-seqTrack.ml <- function(aln, x.dates, best=c("min","max"), ...){
+## seqTrack.ml <- function(aln, x.dates, best=c("min","max"), ...){
 
-} # end seqTrack.ml
+## } # end seqTrack.ml
 
 
 

Modified: pkg/man/dapc.Rd
===================================================================
--- pkg/man/dapc.Rd	2010-04-15 16:05:47 UTC (rev 595)
+++ pkg/man/dapc.Rd	2010-04-15 17:05:01 UTC (rev 596)
@@ -10,6 +10,9 @@
 \alias{assignplot}
 \title{Discriminant Analysis of Principal Components (DAPC)}
 \description{
+  Important: this method is currently under review. Please email the
+  author before using it.
+  
   These functions implement the Discriminant Analysis of Principal Components
   (DAPC). See 'details' section for a succint description of the method. DAPC
   implementation calls upon \code{\link[ade4]{dudi.pca}} from the \code{ade4} package and

Modified: pkg/man/find.clusters.Rd
===================================================================
--- pkg/man/find.clusters.Rd	2010-04-15 16:05:47 UTC (rev 595)
+++ pkg/man/find.clusters.Rd	2010-04-15 17:05:01 UTC (rev 596)
@@ -7,6 +7,9 @@
 \alias{.find.sub.clusters}
 \title{find.cluster: cluster identification using successive K-means}
 \description{
+  Important: this method is currently under review. Please email the
+  author before using it.
+  
   These functions implement the clustering procedure used in Discriminant
   Analysis of Principal Components (DAPC, Jombart et al. submitted). This
   procedure consists in running successive K-means with an increasing number of

Modified: pkg/man/seqTrack.Rd
===================================================================
--- pkg/man/seqTrack.Rd	2010-04-15 16:05:47 UTC (rev 595)
+++ pkg/man/seqTrack.Rd	2010-04-15 17:05:01 UTC (rev 596)
@@ -1,28 +1,42 @@
 \name{seqTrack}
 \alias{seqTrack}
+\alias{seqTrackG}
+\alias{seqTrack.default}
+\alias{seqTrackG.default}
 \alias{plotSeqTrack}
+\alias{optimize.seqTrack}
+\alias{optimize.seqTrack.default}
+\alias{get.likelihood}
+\alias{get.likelihood.seqTrack}
+\alias{get.likelihood.seqTrack.default}
+\alias{get.result.by}
+\alias{get.consensus}
+\alias{as,seqTrack,graphNEL-method}
+\alias{coerce,seqTrack,graphNEL-method}
 \title{seqTrack algorithm}
 \description{
-  The \code{seqTrack} algorithm is currently in development. Please do
-  not use it.
+  Important: this method is currently under review. It will be
+  documented once accepted for publication.
+  Please email the author if you are interested in using it.
+
 }
-\usage{
-seqTrack(seq.names, seq.dates, W, optim = c("min", "max"), \dots)
-plotSeqTrack(x, xy, useArrows = TRUE, col = NULL, bg = "grey", add = FALSE, 
-    \dots)
-}
-\arguments{
-  \item{seq.names}{}
-  \item{seq.dates}{}
-  \item{W}{}
-  \item{optim}{}
-  \item{x}{}
-  \item{xy}{}
-  \item{useArrows}{}
-  \item{col}{}
-  \item{bg}{}
-  \item{add}{}
-  \item{\dots}{}
-  % \item{}{}
-}
+% \usage{
+% %seqTrack(seq.names, seq.dates, W, optim = c("min", "max"), \dots)
+% %plotSeqTrack(x, xy, useArrows = TRUE, col = NULL, bg = "grey", add = FALSE, 
+%  %   \dots)
+% }
+% \arguments{
+%   % \item{seq.names}{}
+%   % \item{seq.dates}{}
+%   % \item{W}{}
+%   % \item{optim}{}
+%   % \item{x}{}
+%   % \item{xy}{}
+%   % \item{useArrows}{}
+%   % \item{col}{}
+%   % \item{bg}{}
+%   % \item{add}{}
+%   % \item{\dots}{}
+%   % \item{}{}
+% }
 \author{Thibaut Jombart \email{t.jombart at imperial.ac.uk}}