documentation

*(note:from adegenet 1.4-0, these tutorials replace + the vignettes which used to be part of the package)

- Lectures - and practicals
+
+ Lectures and practicals
- globaldiv summer school 2009, Piacenza, Italie: talk - practical course
@@ -119,6 +130,8 @@ + + 1 [version with all commands]
    > practical @@ -135,6 +148,8 @@ + + 2 [version with all commands]
    > practical @@ -151,6 +166,8 @@ + + 3

- MRC methodological session: Introduction to phylogenetics:
@@ -183,6 +200,8 @@ + + Epidemiology / Public Health: Introduction to phylogenetics.
(last updated on the 15/13/2013)
@@ -203,6 +222,8 @@ + + Epidemiology / Public Health: Introduction to multivariate analysis / bacterial GWAS.
@@ -221,6 +242,8 @@ + + outbreaker
    > talk
    > practical
@@ -257,6 +280,8 @@ + + README

Deleted: www/files/adegenet-basics.pdf =================================================================== --- www/files/adegenet-basics.pdf 2014-03-14 15:18:54 UTC (rev 1159) +++ www/files/adegenet-basics.pdf 2014-03-18 15:41:43 UTC (rev 1160) @@ -1,11439 +0,0 @@ -%PDF-1.4 -%???? -1 0 obj -<< /S /GoTo /D (section.1) >> -endobj -4 0 obj -(Introduction) -endobj -5 0 obj -<< /S /GoTo /D (section.2) >> -endobj -8 0 obj -(Getting started) -endobj -9 0 obj -<< /S /GoTo /D (subsection.2.1) >> -endobj -12 0 obj -(Installing the package) -endobj -13 0 obj -<< /S /GoTo /D (subsection.2.2) >> -endobj -16 0 obj -(Getting help) -endobj -17 0 obj -<< /S /GoTo /D (section.3) >> -endobj -20 0 obj -(Object classes) -endobj -21 0 obj -<< /S /GoTo /D (subsection.3.1) >> -endobj -24 0 obj -(genind objects) -endobj -25 0 obj -<< /S /GoTo /D (subsection.3.2) >> -endobj -28 0 obj -(genpop objects) -endobj -29 0 obj -<< /S /GoTo /D (subsection.3.3) >> -endobj -32 0 obj -(Using accessors) -endobj -33 0 obj 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[TRUNCATED] To get the complete diff run: svnlook diff /svnroot/adegenet -r 1160 From noreply at r-forge.r-project.org Tue Mar 18 20:02:13 2014 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Tue, 18 Mar 2014 20:02:13 +0100 (CET) Subject: [adegenet-commits] r1161 - in www: . files Message-ID: <20140318190213.C9014186EFA@r-forge.r-project.org> Author: jombart Date: 2014-03-18 20:02:13 +0100 (Tue, 18 Mar 2014) New Revision: 1161 Added: www/files/tutorial-dapc.pdf Modified: www/documentation.html Log: added tuto on dapc Modified: www/documentation.html =================================================================== --- www/documentation.html 2014-03-18 15:41:43 UTC (rev 1160) +++ www/documentation.html 2014-03-18 19:02:13 UTC (rev 1161) @@ -49,6 +49,7 @@ + engine.

@@ -60,6 +61,7 @@ + which compiles all the manpages of the package.

@@ -71,8 +73,18 @@ introduction to the package: data classes, inputs/outputs, basic population genetics, and exploratory analyses; accessible from R by typing adegenetTutorial("basics"). + monospace; color: rgb(255, 0, 0);">adegenetTutorial("basics").

tutorial-dapc: + a tutorial for the analysis of population diversity using + Discriminant Analysis of Principal Components (DAPC); + accessible from R by typing adegenetTutorial("dapc").

adegenet-spca: spatial multivariate analysis using adegenet; includes an @@ -80,13 +92,6 @@ typing vignette("adegenet-spca").

adegenet-dapc: - analysis of the genetic structuring of populations; includes - an introduction to Discriminant Analysis of Principal - Components (DAPC); accessible from R by typing vignette("adegenet-dapc").

adegenet-genomics: introduction to the handling of genome-wide SNP data using @@ -132,6 +137,7 @@ + 1 [version with all commands]
    > practical @@ -150,6 +156,7 @@ + 2 [version with all commands]
    > practical @@ -168,6 +175,7 @@ + 3

- MRC methodological session: Introduction to phylogenetics:
@@ -202,6 +210,7 @@ + Epidemiology / Public Health: Introduction to phylogenetics.
(last updated on the 15/13/2013)
@@ -224,6 +233,7 @@ + Epidemiology / Public Health: Introduction to multivariate analysis / bacterial GWAS.
@@ -244,6 +254,7 @@ + outbreaker
    > talk
    > practical
@@ -282,6 +293,7 @@ + README

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diff /svnroot/adegenet -r 1161 From noreply at r-forge.r-project.org Wed Mar 19 13:13:10 2014 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Wed, 19 Mar 2014 13:13:10 +0100 (CET) Subject: [adegenet-commits] r1162 - in www: . files Message-ID: <20140319121310.67C9F18612B@r-forge.r-project.org> Author: jombart Date: 2014-03-19 13:13:09 +0100 (Wed, 19 Mar 2014) New Revision: 1162 Added: www/files/tutorial-basics.pdf www/files/tutorial-dapc.pdf www/files/tutorial-genomics.pdf www/files/tutorial-spca.pdf Removed: www/files/tutorial-basics.pdf www/files/tutorial-dapc.pdf www/files/tutorial-spca.pdf Modified: www/acceuil.html www/documentation.html Log: adding new genomics vignette Modified: www/acceuil.html =================================================================== --- www/acceuil.html 2014-03-18 19:02:13 UTC (rev 1161) +++ www/acceuil.html 2014-03-19 12:13:09 UTC (rev 1162) @@ -39,7 +39,10 @@ - Jombart, Caitlin Collins, Ismail Ahmed, , Caitlin + Collins, Ismail Ahmed, Federico Calboli, Anne Cori, Tobias Erik Reiners, and ]

@@ -97,11 +101,13 @@ dataframe of genotypes

data import from aligned + DNA sequences to SNPs

data import from aligned + protein sequences to polymorphic sites

data export to the R packages genetics, hierfstat, LDheatmap

@@ -118,6 +124,7 @@ + manipulation

basic data information (heterozygosity, numbers of alleles, @@ -136,11 +143,13 @@ + Fst

simulation of hybridization

methods for spatial genetics: sPCA, tests + for global and local structuring, Monmonier algorithm

the genealogies @@ -161,6 +171,7 @@ + of haplotypes

Discriminant Analysis of Principal Components (DAPC)

@@ -191,6 +202,7 @@ Caitlin + Collins (caitiecollins at gmail.com), @@ -199,15 +211,18 @@ + Isma?l Ahmed (ismail.ahmed at inserm.fr), + Federico Calboli (f.calboli at imperial.ac.uk), + Anne Cori (a.cori at imperial.ac.uk), Tobias @@ -217,6 +232,7 @@ + Erik Reiners (Tobias.Reiners at Senckenberg.de), @@ -225,6 +241,7 @@ + P?ter S?lymos (solymos at ualberta.ca)
Contributors (datasets/ideas): Christophe Fraser, Katayoun Modified: www/documentation.html =================================================================== --- www/documentation.html 2014-03-18 19:02:13 UTC (rev 1161) +++ www/documentation.html 2014-03-19 12:13:09 UTC (rev 1162) @@ -50,6 +50,8 @@ + + engine.

@@ -62,42 +64,41 @@ + + which compiles all the manpages of the package.

Tutorials*

tutorial-basics: - introduction to the package: data classes, inputs/outputs, - basic population genetics, and exploratory analyses; - accessible from R by typing adegenetTutorial("basics").tutorial-basics: introduction to the + package: data classes, inputs/outputs, basic population + genetics, and exploratory analyses; accessible from R by + typing adegenetTutorial("basics").
tutorial-dapc: a tutorial for the + analysis of population diversity using Discriminant Analysis + of Principal Components (DAPC); accessible from R by + typing adegenetTutorial("dapc").
tutorial-dapc: - a tutorial for the analysis of population diversity using - Discriminant Analysis of Principal Components (DAPC); - accessible from R by typing adegenetTutorial("dapc").
adegenet-spca: - spatial multivariate analysis using adegenet; includes an - introduction to spatial PCA (sPCA); accessible from R by - typing vignette("adegenet-spca").
adegenet-genomics: - introduction to the handling of genome-wide SNP data using - adegenet; accessible from R by typing vignette("adegenet-genomics").
-
tutorial-genomics: + introduction to the genlight class for storing and handling + large genome-wide SNP data; accessible from R by typing adegenetTutorial("genomics").
adegenet-spca: spatial multivariate + analysis using adegenet; includes an introduction to spatial + PCA (sPCA); accessible from R by typing vignette("adegenet-spca").

*(note:from adegenet 1.4-0, these tutorials replace - the vignettes which used to be part of the package)
+ 0);">*(note: since adegenet 1.4-0, these tutorials + replace the vignettes which used to be part of the package)


Lectures and practicals
@@ -141,6 +141,7 @@ + 1 [version with all commands]
    > practical @@ -162,6 +163,7 @@ + 2 [version with all commands]
    > practical @@ -183,6 +185,7 @@ + 3

- MRC methodological session: Introduction to phylogenetics:
@@ -220,6 +223,7 @@ + Epidemiology / Public Health: Introduction to phylogenetics.
(last updated on the 15/13/2013)
@@ -245,6 +249,7 @@ + Epidemiology / Public Health: Introduction to multivariate analysis / bacterial GWAS.
@@ -268,6 +273,7 @@ + outbreaker
    > talk
    > practical
@@ -309,6 +315,7 @@ + README

Modified: www/files/tutorial-basics.pdf =================================================================== --- www/files/tutorial-basics.pdf 2014-03-19 16:36:10 UTC (rev 1163) +++ www/files/tutorial-basics.pdf 2014-03-19 16:46:17 UTC (rev 1164) @@ -202,18 +202,21 @@ << /S /GoTo /D [134 0 R /Fit ] >> endobj 138 0 obj << -/Length 1132 +/Length 1133 /Filter /FlateDecode >> stream -x??VKs?6?????????[??i??4?4??7??D?Y??????? ??]?I}?H????a????????????!?Qc?&????Jpb???MK??????LaXS,??.???%??h???O??:W&???z\???;??%???m%???9U%C?f??%\Q??@??kK?Q????Z$??m????????~-?b???????6?D;9:5?J?_??S???3K??H),??&????Z??O?up????5/FXkQt???????8-??RkZ??%?h-eR????!k??2E?i3N???/?e??????{\?8?9Q?????[?f???.??,???Ze -?8???w?????????dH?R??? -I??mE????2?f????TA????A?/?c?gt??a?Z|????????3?????aHS?.9?w??cb^? -?w]&?Iz??O?8????T??????(?x???M?[k]?]v?*?N&?..>??,????$??????9?,??Z????TP|?7?7^??iuS>??????t]V??9@?? 1????>?=3.)?cw???-@???-edA??DG?C???[b*??3?c??TC??nq`%T?(?La@e????=???q?k`???L????j??]h?.?????{P??J????p??9)?X a?v??????C3?3??ua????P c?? 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A?`?4?`?| -GX8?85??S?????\??B?FL??8D???? ?^!]??$a'?:?????=zW????????????d?:??d??0?N'???m???I?MH??X?h????\?Z>i?r?'??U??'?t?R????? ?l??\??%??X!8??Be qNI4?????Ex}??w/|??????3???"i???????C????4???t?q ??{DY?G?F???Fu??????????d_h ~l?z?"???????O$?M$y]??H?????????G.??_..???Tc?s???W_-?O?p??R?p??????????????Eo????k???9!~ %?)????????W??S?_?X????2?_K??8g???|????[?????3|??pW?????F??\????}??Q?d?????9?|"fQ???Sd???-?@??l?'j?=???*???*5??G?V???Y???O?????????\?_??^??.x???`?? -?R?L?xR?f?Py?'??\????????+y#???"????KS????u?U9?????????"??w?||W??dE??t?????%? ?????/?y??V???{?lez??XSDx?TLK????????5Y??t1|???a]>l?fwW?["{@????7?i?{?|?m?@??8??0????? ???/??????^H#D?!8(km?_Z??c?????o?6???*?-???@??O -^8w??\??F?@?? ?'1eB?A?d????}????h?/?%??<2?? -?'U??+< _?_??%Wp?s??g?=????????y(&F?P?SU?k{=????H???W??xzE? ?+???????1??r?_[11??}?y????8>???I?Q=E?S?????P????!1?K?C?E\'v?l%F????-P?T?2QblG]S3 -????k8?>??v;?-?=?C?????@???r??U???E???:"?u?%??Z??X??t?!?@???QD@?gq?N??YD?{?I??I?> f?-??cP????,A0??qx????????????N??o?|????y??IJ???^Q???????]???F??????4?+=8 ?? -D.&uQ???w?z?U?hp:?? .?9E????$K???Rg??????2IO?`???m 5B??[?XJ*?S???\g????:?y_T????aZ??\a{??:?6??!?'??dU?~?w?;8?4?Y -j??>?????s-?y?n+tr?OwK???x?K??????7W????, +x??Z?o???_!?=T??????k?K???????[Y?J?f??w?C??W?:?n?9??o??E?&????"?|ss??;???TF7? ?Xbk*1.??C?l?7?/UX?5??O????4????J??C^??4?[X8??pp??\4?{8?=???z??dU?????&8{S|?s??] ?Z???N?nlv??7!???qR?pf?,??4??l??nK;'??L???)z????!??|y?q?MR&????????????vt?j??????D?:.??[Tb?RR????????o+??+Hi?r?g??U??'?t?R????? ?l??\??%??Z!8??Be qNI4?????Ex}??w/|??????3???"i???????C????4???t?q ??{DY?G?F???Fu??????????d_i ~l?z?"????????'??&??.O$Oq[???????#?z?/??vw????????o?'L??Z?P???????O=wEGok???$??w??? +?????????]??X^?i??&??(???'?'?wj???'???I???o??????3$?g??S??????????????5{?l??????j?( r???6D4???T(iH??gV2?'??_???*??B?r_??t>???w~m?s??9??5????-????g?}??%x?np?"eR???4s??>?V???U5g<g]?9?|?y?^?????0????????????;????????Z?0'+j????????????????gZ%S??1??u?5FbMu?5R1-M??L??S?dyG???i???u?????]?n??I?????Q?? ???=?w??7????;&?+??r^{(??z!????????iM???77;??m???*?-???@??#?/???a.?N#@ ?y?T?????~??~2 o????6V??f???????e???^??*???q???c??C??h?p?2?,9F ??v??Ql??T???^O&??D',R?,??d*??^b?J?,?$4?mf4???@?K+&?q1?O0?"6?Z??G???8)????? f?-??cP????,A0??qx????????????N??o?|????y??IJ???^Q???????]???F??????4?+=?!?k +D.&u?Q?????z?U??s:?? .?9E????$K???Rg??????2IO?`???m 5B??[?XJ*?S7?ia.?3?C?i??|(?fn??0-??e???_hfK???k??E??;P?y??,?5?V??\?_t???> endobj @@ -1730,10 +1720,10 @@ endobj 324 0 obj << -/CreationDate (D:20140318144239) -/ModDate (D:20140318144239) +/CreationDate (D:20140319164230) +/ModDate (D:20140319164230) /Title (R Graphics Output) -/Producer (R 3.1.0) +/Producer (R 3.0.3) /Creator (R) >> endobj @@ -2027,10 +2017,10 @@ endobj 359 0 obj << -/CreationDate (D:20140318144240) -/ModDate (D:20140318144240) +/CreationDate (D:20140319164231) +/ModDate (D:20140319164231) /Title (R Graphics Output) -/Producer (R 3.1.0) +/Producer (R 3.0.3) /Creator (R) >> endobj @@ -2163,10 +2153,10 @@ endobj 371 0 obj << -/CreationDate (D:20140318144240) -/ModDate (D:20140318144240) +/CreationDate (D:20140319164231) +/ModDate (D:20140319164231) /Title (R Graphics Output) -/Producer (R 3.1.0) +/Producer (R 3.0.3) /Creator (R) >> endobj @@ -2621,10 +2611,10 @@ endobj 424 0 obj << -/CreationDate (D:20140318144242) -/ModDate (D:20140318144242) +/CreationDate (D:20140319164235) +/ModDate (D:20140319164235) /Title (R Graphics Output) -/Producer (R 3.1.0) +/Producer (R 3.0.3) /Creator (R) >> endobj @@ -2863,19 +2853,22 @@ /ProcSet [ /PDF /Text ] >> endobj [TRUNCATED] To get the complete diff run: svnlook diff /svnroot/adegenet -r 1164 From noreply at r-forge.r-project.org Wed Mar 19 18:08:56 2014 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Wed, 19 Mar 2014 18:08:56 +0100 (CET) Subject: [adegenet-commits] r1165 - www Message-ID: <20140319170856.35C29186B3C@r-forge.r-project.org> Author: jombart Date: 2014-03-19 18:08:55 +0100 (Wed, 19 Mar 2014) New Revision: 1165 Modified: www/download.html www/news.html Log: updating website Modified: www/download.html =================================================================== --- www/download.html 2014-03-19 16:46:17 UTC (rev 1164) +++ www/download.html 2014-03-19 17:08:55 UTC (rev 1165) @@ -30,20 +30,18 @@

The current stable - version (adegenet_1.3-9) is available as:
+ version (adegenet_1.4-1) is available as:
- linux + href="http://cran.r-project.org/src/contrib/adegenet_1.4-1.tar.gz">linux + sources
- - MacOS X binary
- - Windows binary
-
-

The devel version - (adegenet_1.4-0) is also available from R-Forge's daily snapshots.
- It can be installed directly from R console using:
- install.packages("adegenet",repos="http://r-forge.r-project.org")
+ - MacOS + X binary
+ - Windows + binary
+

Patches @@ -53,6 +51,7 @@ +
Patches correct minor bugs or implement new functionnalities, and will be included into the next CRAN release. It is recommended to @@ -68,6 +67,7 @@ + a patch.
addedFeatures.R: (for adegenet @@ -81,15 +81,26 @@ monospace;">

Older versions:
+ adegenet_1.3-9
+ - linux + + sources
+ - MacOS X binary
+ - Windows binary
+
adegenet _1.3-8
- linux + sources
- MacOS + X binary
- Windows + binary

adegenet _1.3-7
Modified: www/news.html =================================================================== --- www/news.html 2014-03-19 16:46:17 UTC (rev 1164) +++ www/news.html 2014-03-19 17:08:55 UTC (rev 1165) @@ -28,20 +28,38 @@ 0, 0);">

What's next?
- Next release (1.4-1) is under development.
+ Next release (1.4-2) is under development.

Today
Current stable version of - adegenet is 1.4-0 for + adegenet is 1.4-1 for R.3.0.3.
See the current ChangeLog for a list of all modifications.

+ 18/03/2014

+ New adegenet version (1.4-1) + has been released for R-3.0.3! Releasing a + package with a new function to open tutorials that does not + actually work is arguably bad form. This version fixes release 1.4-0. See the ChangeLog file for more details.
+
+
14/03/2014

globaldiv summer school 2009, Piacenza, Italie: talk - practical course
+
+
Master 2 "Ecology, Evolution, Biometry", Lyon, France: + talk - practical course
+
+
One-week course on Genetic Data Analysis, Bogota, Colombia:

lecture 1: methodological + overview
lecture 2: finding + clusters, using cluster information
lecture 3: spatial + genetics
practical 1 [version with + all commands]
practical 2 [version with + all commands]
practical 3

MRC methodological session: Introduction to phylogenetics:

- - Master 2 "Ecology, Evolution, Biometry", Lyon, France: talk - practical course
+

RAPID-NGS workshop, M?nster (March 2013) - Outbreak analysis using ape and adegenet

practical
data (cases.csv, + alignment.fa, + update.csv)
+

- - One-week course on Genetic Data Analysis, Bogota, Colombia:
-     > lecture 1: - methodological overview
-     > lecture 2: - finding clusters, using cluster information
-     > lecture 3: - spatial genetics
-     > practical +

Imperial College - Master Modern @@ -142,70 +183,19 @@ - 1 [version - with all commands]
- > practical - - - - - - - - - - - - - - - - - - - - 2 [version - with all commands]
- > practical - - - - - - - - - - - - - - - - - - - - 3
+ Epidemiology / Public Health: Introduction to phylogenetics + (last updated on the 15/13/2013)

practical
data (usflu.fasta, usflu.annot.csv)
+

- - MRC methodological session: Introduction to phylogenetics:
-     > slides
-     > practical
-     > data (DNA - sequences, annotations)
-
- - RAPID-NGS workshop, M?nster (March 2013) - Outbreak analysis using ape and adegenet
-     > practical
-     > data (cases.csv, alignment.fa, update.csv)
-
- - Imperial College - Master Modern +

Imperial College - Master Modern @@ -224,15 +214,22 @@ - Epidemiology / Public Health: Introduction to phylogenetics.
- (last updated on the 15/13/2013)
- > practical
- > data (usflu.fasta, - usflu.annot.csv)
-
- - Imperial College - Master Modern + Epidemiology / Public Health: Introduction to multivariate + analysis / bacterial GWAS (last updated on the + 21/13/2013)

GenEpi workshop, London (April 2013) - Outbreak analysis using ape, adegenet, and @@ -245,58 +242,48 @@ + outbreaker

talk
practical
data (cases.csv, + alignment.fa, + update.csv)
+

Molecular Outbreak Epidemiology workshop, Stockholm, + Sweden (November 2013) - Outbreak - - - - - Epidemiology / Public Health: Introduction to multivariate analysis - / bacterial GWAS.
- (last updated on the 21/13/2013)
-     > lecture
-     > practical
-     > data (simGWAS.RData)
+ analysis using ape, + adegenet, and outbreaker

talk
practical
data (cases.csv, + alignment.fa, + update.csv)
+

Workshop "Phylogenetics and population genetics using R", + Montpellier (March 2014)

lecture 1: + Multivariate analysis of genetic data: an introduction
+
practical + 1: Population genetics and multivariate analysis of + genetic data
+

- - GenEpi workshop, London (April 2013) - Outbreak analysis using ape, adegenet, and - - - - - - - - - - - - outbreaker
-     > talk
-     > practical
-     > data (cases.csv, alignment.fa, update.csv)

- - Molecular Outbreak Epidemiology workshop, Stockholm, Sweden - (November 2013) - Outbreak - analysis using ape, adegenet, - and outbreaker

-     > talk
-     > practical
-     > data (cases.csv, alignment.fa, update.csv)

-
-
Dirty hacks useful for teaching
- a small hack for installing R packages on computers without @@ -316,6 +303,7 @@ + README

Added: www/files/montpellier/lecture-MVA.1.0.pdf =================================================================== (Binary files differ) Property changes on: www/files/montpellier/lecture-MVA.1.0.pdf ___________________________________________________________________ Added: svn:mime-type + application/octet-stream Added: www/files/montpellier/practical-MVAintro.1.0.pdf =================================================================== --- www/files/montpellier/practical-MVAintro.1.0.pdf (rev 0) +++ www/files/montpellier/practical-MVAintro.1.0.pdf 2014-03-24 17:48:06 UTC (rev 1167) @@ -0,0 +1,6201 @@ +%PDF-1.4 +%???? +1 0 obj +<< /S /GoTo /D (section.1) >> +endobj +4 0 obj +(Getting started) +endobj +5 0 obj +<< /S /GoTo /D (subsection.1.1) >> +endobj +8 0 obj +(Installing the package) +endobj +9 0 obj +<< /S /GoTo /D (subsection.1.2) >> +endobj +12 0 obj +(Getting help) +endobj +13 0 obj +<< /S /GoTo /D (section.2) >> +endobj +16 0 obj +(Reading data in) +endobj +17 0 obj +<< /S /GoTo /D (section.3) >> +endobj +20 0 obj +(First look at the data) +endobj +21 0 obj +<< /S /GoTo /D (section.4) >> +endobj +24 0 obj +(Basic population genetics analyses) +endobj +25 0 obj +<< /S /GoTo /D (subsection.4.1) >> +endobj +28 0 obj +(Testing for Hardy-Weinberg equilibrium) +endobj +29 0 obj +<< /S /GoTo /D (subsection.4.2) >> +endobj +32 0 obj +(Assessing population structure) +endobj +33 0 obj +<< /S /GoTo /D (section.5) >> +endobj +36 0 obj +(Principal Component Analysis of microbov) +endobj +37 0 obj +<< /S /GoTo /D (subsection.5.1) >> +endobj +40 0 obj +(Principal Coordinates Analysis $PCoA$) +endobj +41 0 obj +<< /S /GoTo /D (section.6) >> +endobj +44 0 obj +(To go further) +endobj +45 0 obj +<< /S /GoTo /D [46 0 R /Fit ] >> +endobj +48 0 obj << +/Length 1045 +/Filter /FlateDecode +>> +stream +x??VK??6??W9Q@??M??4h? 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=>?=:?`??;c??'?e??~??!?a???D?#?G?&}'/?^?x?I??????+?\????w?x?20;5?\?????_??????e?t???W?f^??Qs?-?m???w3????+??~???????O?~???? endstream endobj -194 0 obj << -/D [192 0 R /XYZ 69.866 758.996 null] +199 0 obj << +/D [197 0 R /XYZ 69.866 758.996 null] >> endobj -191 0 obj << -/Font << /F79 78 0 R /F18 53 0 R >> -/XObject << /Im7 189 0 R >> +196 0 obj << [TRUNCATED] To get the complete diff run: svnlook diff /svnroot/adegenet -r 1168 From noreply at r-forge.r-project.org Mon Mar 24 19:08:43 2014 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Mon, 24 Mar 2014 19:08:43 +0100 (CET) Subject: [adegenet-commits] r1169 - www/files Message-ID: <20140324180843.B806F186FF8@r-forge.r-project.org> Author: jombart Date: 2014-03-24 19:08:43 +0100 (Mon, 24 Mar 2014) New Revision: 1169 Modified: www/files/tutorial-genomics.pdf Log: new version of the genomics vignette with addition from Caitlin on glSim Modified: www/files/tutorial-genomics.pdf 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TK?rQ???? ??B?????W?a?x3a??F?u???U @@ -359,7 +473,7 @@ [TRUNCATED] To get the complete diff run: svnlook diff /svnroot/adegenet -r 1170 From noreply at r-forge.r-project.org Wed Mar 26 08:05:38 2014 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Wed, 26 Mar 2014 08:05:38 +0100 (CET) Subject: [adegenet-commits] r1171 - in www: . files/montpellier Message-ID: <20140326070538.D20BB18714F@r-forge.r-project.org> Author: jombart Date: 2014-03-26 08:05:37 +0100 (Wed, 26 Mar 2014) New Revision: 1171 Added: www/files/montpellier/lecture-MVAgroups.1.0.pdf www/files/montpellier/lecture-MVAspatial.1.0.pdf Modified: www/documentation.html www/files/montpellier/practical-MVAintro.1.0.pdf Log: added lectures for the workshop; updated website for day1 Modified: www/documentation.html =================================================================== --- www/documentation.html 2014-03-24 18:50:16 UTC (rev 1170) +++ www/documentation.html 2014-03-26 07:05:37 UTC (rev 1171) @@ -54,6 +54,7 @@ + engine.

@@ -70,6 +71,7 @@ + which compiles all the manpages of the package.

@@ -183,6 +185,7 @@ + Epidemiology / Public Health: Introduction to phylogenetics (last updated on the 15/13/2013) @@ -215,6 +218,7 @@ + Epidemiology / Public Health: Introduction to multivariate analysis / bacterial GWAS (last updated on the @@ -242,6 +246,7 @@ + outbreaker

talk
Molecular Outbreak Epidemiology workshop, Stockholm, Sweden (November 2013) - Outbreak + analysis using ape, adegenet, and outbreaker

@@ -268,17 +274,21 @@

Workshop "Phylogenetics and population genetics using R", - Montpellier (March 2014)
Workshop "Phylogenetics and + population genetics using R", Montpellier (March + 2014)

lecture 1: - Multivariate analysis of genetic data: an introduction
+
Multivariate analysis of genetic data: an introduction [lecture, + practical]
practical - 1: Population genetics and multivariate analysis of - genetic data
+
Multivariate analysis of genetic data: exploring group + diversity [lecture, practical]
Multivariate analysis of genetic data: uncovering spatial + structures [lecture, practical]
+

@@ -304,6 +314,7 @@ + README

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Author: jombart Date: 2014-03-26 23:45:26 +0100 (Wed, 26 Mar 2014) New Revision: 1173 Modified: www/documentation.html Log: updated website for day 2 Modified: www/documentation.html =================================================================== --- www/documentation.html 2014-03-26 11:31:09 UTC (rev 1172) +++ www/documentation.html 2014-03-26 22:45:26 UTC (rev 1173) @@ -55,6 +55,7 @@ + engine.

@@ -72,6 +73,7 @@ + which compiles all the manpages of the package.

@@ -186,6 +188,7 @@ + Epidemiology / Public Health: Introduction to phylogenetics (last updated on the 15/13/2013) @@ -219,6 +222,7 @@ + Epidemiology / Public Health: Introduction to multivariate analysis / bacterial GWAS (last updated on the @@ -247,6 +251,7 @@ + outbreaker

talk

Outbreak + analysis using ape, adegenet,

and

outbreaker

practical

Multivariate analysis of genetic data: exploring group - diversity [lecture, practical]
+ diversity [lecture, + practical]
Multivariate analysis of genetic data: uncovering spatial structures [lecture, practical]
@@ -315,6 +323,7 @@ + README

From noreply at r-forge.r-project.org Thu Mar 27 10:38:22 2014 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Thu, 27 Mar 2014 10:38:22 +0100 (CET) Subject: [adegenet-commits] r1174 - www/files/montpellier Message-ID: <20140327093822.CF207187283@r-forge.r-project.org> Author: jombart Date: 2014-03-27 10:38:22 +0100 (Thu, 27 Mar 2014) New Revision: 1174 Modified: www/files/montpellier/practical-MVAgroups.1.0.pdf Log: Added new version of the tutorial with supplementary exercises for the hungry wolves Modified: www/files/montpellier/practical-MVAgroups.1.0.pdf =================================================================== --- www/files/montpellier/practical-MVAgroups.1.0.pdf 2014-03-26 22:45:26 UTC (rev 1173) +++ www/files/montpellier/practical-MVAgroups.1.0.pdf 2014-03-27 09:38:22 UTC (rev 1174) @@ -46,12 +46,18 @@ << /S /GoTo /D (section.3) >> endobj 32 0 obj -(To go further) +(Supplementary exercise) endobj 33 0 obj -<< /S /GoTo /D [34 0 R /Fit ] >> +<< /S /GoTo /D (section.4) >> endobj -36 0 obj << +36 0 obj +(To go further) +endobj +37 0 obj +<< /S /GoTo /D [38 0 R /Fit ] >> +endobj +40 0 obj << /Length 1096 /Filter /FlateDecode >> @@ -60,126 +66,135 @@ ?/%? 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????N???>?u?????c?Kz???=s?/?o?l????|??????y??????^d]???p?s?~???:;???/;]??7|?????W????p???????Q?o?H?!?????V????sn??Ys}?????????~4??]? =>?=:?`??;c??'?e??~??!?a???D?#?G?&}'/?^?x?I??????+?\????w?x?20;5?\?????_??????e?t???W?f^??Qs?-?m???w3????+??~???????O?~???? endstream endobj -163 0 obj << -/D [161 0 R /XYZ 69.866 758.996 null] +168 0 obj << +/D [166 0 R /XYZ 69.866 758.996 null] >> endobj -160 0 obj << -/Font << /F78 68 0 R /F17 40 0 R >> -/XObject << /Im8 159 0 R >> +165 0 obj << +/Font << /F78 73 0 R /F17 44 0 R >> +/XObject << /Im8 164 0 R >> /ProcSet [ /PDF /Text ] >> endobj -176 0 obj << +181 0 obj << /Length 1171 [TRUNCATED] To get the complete diff run: svnlook diff /svnroot/adegenet -r 1174 From noreply at r-forge.r-project.org Thu Mar 27 11:36:04 2014 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Thu, 27 Mar 2014 11:36:04 +0100 (CET) Subject: [adegenet-commits] r1175 - in www/images: . gimp Message-ID: <20140327103604.3C8D8187241@r-forge.r-project.org> Author: jombart Date: 2014-03-27 11:36:03 +0100 (Thu, 27 Mar 2014) New Revision: 1175 Modified: www/images/acceuil.png www/images/gimp/acceuil.xcf Log: updated main figure for 1.4-1 Modified: www/images/acceuil.png =================================================================== (Binary files differ) Modified: www/images/gimp/acceuil.xcf =================================================================== (Binary files differ) From noreply at r-forge.r-project.org Thu Mar 27 22:24:35 2014 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Thu, 27 Mar 2014 22:24:35 +0100 (CET) Subject: [adegenet-commits] r1176 - www Message-ID: <20140327212435.9C745187180@r-forge.r-project.org> Author: jombart Date: 2014-03-27 22:24:35 +0100 (Thu, 27 Mar 2014) New Revision: 1176 Modified: www/documentation.html Log: added the last lecture and practical for the last day Modified: www/documentation.html =================================================================== --- www/documentation.html 2014-03-27 10:36:03 UTC (rev 1175) +++ www/documentation.html 2014-03-27 21:24:35 UTC (rev 1176) @@ -56,6 +56,7 @@ + engine.

@@ -74,6 +75,7 @@ + which compiles all the manpages of the package.

@@ -189,6 +191,7 @@ + Epidemiology / Public Health: Introduction to phylogenetics (last updated on the 15/13/2013)

Public Health

Introduction to multivariate analysis / bacterial GWAS

outbreaker

talk

ape, adegenet,

and

outbreaker

practical

Multivariate analysis of genetic data: uncovering spatial - structures [lecture, practical]
+ structures [lecture, + practical]

README