[adegenet-commits] r1106 - pkg pkg/man www www/files

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

Author: jombart
Date: 2013-04-05 19:11:31 +0200 (Fri, 05 Apr 2013)
New Revision: 1106

Added:
   www/files/outbreakPractical.1.2.pdf
Modified:
   pkg/ChangeLog
   pkg/DESCRIPTION
   pkg/NAMESPACE
   pkg/man/adegenet.package.Rd
   pkg/man/export.Rd
   www/documentation.html
Log:
Added new tutorial for GenEpi day

Modified: pkg/ChangeLog
===================================================================
--- pkg/ChangeLog	2013-04-05 13:03:25 UTC (rev 1105)
+++ pkg/ChangeLog	2013-04-05 17:11:31 UTC (rev 1106)
@@ -1,3 +1,12 @@
+			CHANGES IN ADEGENET VERSION 1.3-7
+
+NEW FEATURES
+
+	o entirely new version of DNAbin2genind, much faster than before
+	and suitable for large alignments
+
+
+
 			CHANGES IN ADEGENET VERSION 1.3-6
 
 NEW FEATURES

Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION	2013-04-05 13:03:25 UTC (rev 1105)
+++ pkg/DESCRIPTION	2013-04-05 17:11:31 UTC (rev 1106)
@@ -1,6 +1,6 @@
 Package: adegenet
 Version: 1.3-7
-Date: 2013/01/30
+Date: 2013/04/05
 Title: adegenet: an R package for the exploratory analysis of genetic and genomic data.
 Author:  Thibaut Jombart, Ismail Ahmed, Anne Cori, Tobias Erik Reiners, Peter Solymos
 Maintainer: Thibaut Jombart <t.jombart at imperial.ac.uk>

Modified: pkg/NAMESPACE
===================================================================
--- pkg/NAMESPACE	2013-04-05 13:03:25 UTC (rev 1105)
+++ pkg/NAMESPACE	2013-04-05 17:11:31 UTC (rev 1106)
@@ -6,10 +6,11 @@
 
 # Import all packages listed as Imports or Depends
 import(
-  methods,
-  MASS,
-  ade4,
-  igraph
+       utils,
+       methods,
+       MASS,
+       ade4,
+       igraph
 )
 
 # Load DLL

Modified: pkg/man/adegenet.package.Rd
===================================================================
--- pkg/man/adegenet.package.Rd	2013-04-05 13:03:25 UTC (rev 1105)
+++ pkg/man/adegenet.package.Rd	2013-04-05 17:11:31 UTC (rev 1106)
@@ -190,8 +190,8 @@
   \tabular{ll}{
     Package: \tab adegenet\cr
     Type: \tab Package\cr
-    Version: \tab 1.3-6\cr
-    Date: \tab 2013-01-30 \cr
+    Version: \tab 1.3-7\cr
+    Date: \tab 2013-04-05 \cr
     License: \tab GPL (>=2)
   } 
 }

Modified: pkg/man/export.Rd
===================================================================
--- pkg/man/export.Rd	2013-04-05 13:03:25 UTC (rev 1105)
+++ pkg/man/export.Rd	2013-04-05 17:11:31 UTC (rev 1106)
@@ -49,19 +49,4 @@
 }
 \seealso{\code{\link{import2genind}}}
 \author{Thibaut Jombart \email{t.jombart at imperial.ac.uk} }
-\examples{
-\dontrun{
-if(require(hierfstat) & require(genetics)){
-
-obj <- read.fstat(system.file("data/diploid.dat",package="hierfstat"))
-
-X <- genind2hierfstat(obj)
-X
-
-read.fstat.data(paste(.path.package("hierfstat"),"/data/diploid.dat",sep="",collapse=""),nloc=5)
-
-genind2genotype(obj)
-}
-}
-}
 \keyword{manip}
\ No newline at end of file

Modified: www/documentation.html
===================================================================
--- www/documentation.html	2013-04-05 13:03:25 UTC (rev 1105)
+++ www/documentation.html	2013-04-05 17:11:31 UTC (rev 1106)
@@ -41,6 +41,8 @@
 
 
 
+
+
         engine</a>. <br>
       <br>
       <br>
@@ -101,6 +103,8 @@
 
 
 
+
+
         1</a> [<a href="files/practical-day1.1.2-allcmd.pdf">version
         with all commands</a>]<br>
           > <a href="files/practical-day2.1.3.pdf">practical
@@ -111,6 +115,8 @@
 
 
 
+
+
         2</a> [<a href="files/practical-day2.1.3-allcmd.pdf">version
         with all commands</a>]<br>
           > <a href="files/practical-day3.1.2.pdf">practical
@@ -121,6 +127,8 @@
 
 
 
+
+
         3</a><br>
       <br>
       - MRC methodological session: Introduction to phylogenetics:<br>
@@ -128,12 +136,11 @@
           > <a href="files/MRC-session2-tuto.1.3.pdf">practical</a><br>
           > data (<a href="files/usflu.fasta">DNA
         sequences</a>, <a href="files/usflu.annot.csv">annotations</a>)<br>
+      <br>
       - RAPID-NGS workshop, Münster (March 2013) - <span
         style="font-weight: bold;">Outbreak analysis using <span
-          style="font-style: italic;">adegenet </span>and <span
-          style="font-style: italic;">ape</span></span> <img
-        style="width: 80px; height: 37px;" alt="new"
-        src="images/new.png"><br>
+          style="font-style: italic;">ape </span>and</span> <span
+        style="font-weight: bold;"><span style="font-style: italic;">adegenet</span></span><br>
           > <a
         href="files/seqTrack-practical.1.3.pdf">practical</a><br>
           > data (<a
@@ -147,6 +154,8 @@
 
 
 
+
+
         Epidemiology</span> / <i>Public Health</i>: <span
         style="font-weight: bold;">Introduction to phylogenetics</span>.<img
         style=" width: 80px; height: 37px;" alt="new"
@@ -162,6 +171,8 @@
 
 
 
+
+
         Epidemiology</span> / <i>Public Health</i>: <span
         style="font-weight: bold;">Introduction to multivariate analysis
         / bacterial GWAS</span>.<img style=" width: 80px; height: 37px;"
@@ -173,7 +184,20 @@
           > data (<a
         href="files/simGWAS/simGWAS.RData">simGWAS.RData</a>)<br>
       <br>
+      - GenEpi workshop, London (April 2013) - <span
+        style="font-weight: bold;">Outbreak analysis using <span
+          style="font-style: italic;">ape, adegenet,</span> </span><b>and
+
+      </b><b><i>outbreaker</i></b> <img style=" width: 80px; height:
+        37px;" alt="new" src="images/new.png" height="37" width="80"><br>
+          > <a href="files/outbreakPractical.1.2.pdf">practical</a><br>
+          > data (<a
+        href="files/fakeOutbreak/cases.csv">cases.csv</a>, <a
+        href="files/fakeOutbreak/alignment.fa">alignment.fa</a>, <a
+        href="files/fakeOutbreak/update.csv">update.csv</a>)<br>
       <br>
+      <br>
+      <br>
       <span style="font-weight: bold; color: rgb(0, 102, 0);">Dirty
         hacks useful for teaching</span><br>
       - a small hack for installing R packages on computers without
@@ -181,6 +205,8 @@
 
 
 
+
+
       <a href="files/hackLib/README">README</a> <img style=" width:
         80px; height: 37px;" alt="new" src="images/new.png" height="37"
         width="80"><br>

Added: www/files/outbreakPractical.1.2.pdf
===================================================================
--- www/files/outbreakPractical.1.2.pdf	                        (rev 0)
+++ www/files/outbreakPractical.1.2.pdf	2013-04-05 17:11:31 UTC (rev 1106)
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+endobj
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[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/adegenet -r 1106