[adegenet-commits] r652 - pkg/man

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

Author: jombart
Date: 2010-07-14 13:13:54 +0200 (Wed, 14 Jul 2010)
New Revision: 652

Modified:
   pkg/man/H3N2.Rd
   pkg/man/adegenet.package.Rd
   pkg/man/dapc.Rd
   pkg/man/dapcIllus.Rd
   pkg/man/eHGDP.Rd
Log:
Updated references.
One check and submission.


Modified: pkg/man/H3N2.Rd
===================================================================
--- pkg/man/H3N2.Rd	2010-07-14 10:59:18 UTC (rev 651)
+++ pkg/man/H3N2.Rd	2010-07-14 11:13:54 UTC (rev 652)
@@ -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{Genetics}.
+genetically structured populations. Submitted to \emph{BMC genetics}.
 }
 \examples{
 ## LOAD DATA

Modified: pkg/man/adegenet.package.Rd
===================================================================
--- pkg/man/adegenet.package.Rd	2010-07-14 10:59:18 UTC (rev 651)
+++ pkg/man/adegenet.package.Rd	2010-07-14 11:13:54 UTC (rev 652)
@@ -110,10 +110,10 @@
    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
+   submitted).\cr
    - \code{\link{seqTrack}}: implements the SeqTrack algorithm for
    recontructing transmission trees of pathogens (Jombart et al.,
-   submitted B) .\cr
+   2010) .\cr
 
 
    === GRAPHICS ===\cr
@@ -128,7 +128,7 @@
    === 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
+   storing full genomes. \cr
    - \code{\link{haploPop}}: simulates populations of haplotypes, using
    different population dynamics, storing SNPs (under development). \cr
 
@@ -170,13 +170,21 @@
   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
-  
-See adegenet website: \url{http://adegenet.r-forge.r-project.org/}\cr
+  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
 
-Please post your questions on 'the adegenet forum': adegenet-forum at lists.r-forge.r-project.org
+  Jombart T, Eggo R, Dodd P, Balloux F (2010) Reconstructing disease
+  outbreaks from genetic data: a graph approach. \emph{Heredity}. doi:
+  10.1038/hdy.2010.78.\cr
 
+  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{BMC genetics}.\cr
+
+  See adegenet website: \url{http://adegenet.r-forge.r-project.org/}\cr
+
+  Please post your questions on 'the adegenet forum': adegenet-forum at lists.r-forge.r-project.org
+
 }
 \keyword{manip}
 \keyword{multivariate}

Modified: pkg/man/dapc.Rd
===================================================================
--- pkg/man/dapc.Rd	2010-07-14 10:59:18 UTC (rev 651)
+++ pkg/man/dapc.Rd	2010-07-14 11:13:54 UTC (rev 652)
@@ -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{Genetics}.
+genetically structured populations. Submitted to \emph{BMC genetics}.
 }
 \seealso{
   - \code{\link{find.clusters}}: to identify clusters without prior.

Modified: pkg/man/dapcIllus.Rd
===================================================================
--- pkg/man/dapcIllus.Rd	2010-07-14 10:59:18 UTC (rev 651)
+++ pkg/man/dapcIllus.Rd	2010-07-14 11:13:54 UTC (rev 652)
@@ -25,7 +25,7 @@
 \source{
   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{BMC genetics}.
 
 }
 \author{

Modified: pkg/man/eHGDP.Rd
===================================================================
--- pkg/man/eHGDP.Rd	2010-07-14 10:59:18 UTC (rev 651)
+++ pkg/man/eHGDP.Rd	2010-07-14 11:13:54 UTC (rev 652)
@@ -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{Genetics}.
+structured populations. Submitted to \emph{BMC genetics}.
 }
 \examples{
 \dontrun{