From noreply at r-forge.r-project.org Wed Aug 3 18:44:41 2016
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Wed, 3 Aug 2016 18:44:41 +0200 (CEST)
Subject: [adegenet-commits] r1222 - www/images
Message-ID: <20160803164441.B2879187319@r-forge.r-project.org>
Author: jombart
Date: 2016-08-03 18:44:41 +0200 (Wed, 03 Aug 2016)
New Revision: 1222
Modified:
www/images/bullet.png
Log:
new bullet
Modified: www/images/bullet.png
===================================================================
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From noreply at r-forge.r-project.org Mon Aug 8 19:25:47 2016
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Mon, 8 Aug 2016 19:25:47 +0200 (CEST)
Subject: [adegenet-commits] r1223 - in www/files: . PRstats
Message-ID: <20160808172548.05A85187C9E@r-forge.r-project.org>
Author: jombart
Date: 2016-08-08 19:25:47 +0200 (Mon, 08 Aug 2016)
New Revision: 1223
Added:
www/files/PRstats/
www/files/PRstats/Mnonsensicus1.RData
www/files/PRstats/Mnonsensicus2.RData
Log:
add PRstats files
Added: www/files/PRstats/Mnonsensicus1.RData
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Added: www/files/PRstats/Mnonsensicus2.RData
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Added: svn:mime-type
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From noreply at r-forge.r-project.org Tue Aug 9 12:32:32 2016
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Tue, 9 Aug 2016 12:32:32 +0200 (CEST)
Subject: [adegenet-commits] r1224 - www/files/PRstats
Message-ID: <20160809103232.D036918775A@r-forge.r-project.org>
Author: jombart
Date: 2016-08-09 12:32:32 +0200 (Tue, 09 Aug 2016)
New Revision: 1224
Added:
www/files/PRstats/unknown1.RData
www/files/PRstats/unknown2.RData
Log:
adding data files
Added: www/files/PRstats/unknown1.RData
===================================================================
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From noreply at r-forge.r-project.org Tue Aug 9 12:49:07 2016
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Tue, 9 Aug 2016 12:49:07 +0200 (CEST)
Subject: [adegenet-commits] r1225 - www/files
Message-ID: <20160809104907.C19EA18089A@r-forge.r-project.org>
Author: jombart
Date: 2016-08-09 12:49:07 +0200 (Tue, 09 Aug 2016)
New Revision: 1225
Added:
www/files/Mnonsensicus1.RData
www/files/Mnonsensicus2.RData
www/files/unknown1.RData
www/files/unknown2.RData
Log:
adding data files to general file directory
Added: www/files/Mnonsensicus1.RData
===================================================================
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From noreply at r-forge.r-project.org Tue Aug 9 12:55:27 2016
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Tue, 9 Aug 2016 12:55:27 +0200 (CEST)
Subject: [adegenet-commits] r1226 - in www/images: . gimp
Message-ID: <20160809105527.CA90618089A@r-forge.r-project.org>
Author: jombart
Date: 2016-08-09 12:55:27 +0200 (Tue, 09 Aug 2016)
New Revision: 1226
Modified:
www/images/acceuil.png
www/images/gimp/acceuil.xcf
Log:
updating main image
Modified: www/images/acceuil.png
===================================================================
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Modified: www/images/gimp/acceuil.xcf
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From noreply at r-forge.r-project.org Tue Aug 9 13:26:29 2016
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Tue, 9 Aug 2016 13:26:29 +0200 (CEST)
Subject: [adegenet-commits] r1227 - www
Message-ID: <20160809112629.D328718776B@r-forge.r-project.org>
Author: jombart
Date: 2016-08-09 13:26:29 +0200 (Tue, 09 Aug 2016)
New Revision: 1227
Modified:
www/acceuil.html
Log:
updated list of authors
Modified: www/acceuil.html
===================================================================
--- www/acceuil.html 2016-08-09 10:55:27 UTC (rev 1226)
+++ www/acceuil.html 2016-08-09 11:26:29 UTC (rev 1227)
@@ -43,14 +43,12 @@
and genome-wise SNP data analysis.
It is developed on Github
- by Thibaut
- Jombart, Zhian N Kamvar, Caitlin
- Collins, Roman Lustrik, Ismail Ahmed, Federico Calboli, Anne
- Cori, Tobias Erik Reiners, and P?ter S?lymos, and officially
- released on CRAN periodically.
+ href="https://github.com/thibautjombart/adegenet">Github by Thibaut Jombart, Zhian N Kamvar, Caitlin Collins, Roman Lustrik,
+ Marie-Pauline Beugin, Brian Knaus, Peter Solymos, Vladimir Mikryukov, Klaus Schliep,
+ Ismail Ahmed, Anne Cori, Tobias Erik Reiners, Federico Calboli and P?ter S?lymos, and
+ officially released on CRAN periodically.
adegenet is described in the following publications:
From noreply at r-forge.r-project.org Tue Aug 9 13:48:09 2016
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Tue, 9 Aug 2016 13:48:09 +0200 (CEST)
Subject: [adegenet-commits] r1228 - www/files/PRstats
Message-ID: <20160809114809.E2208187936@r-forge.r-project.org>
Author: jombart
Date: 2016-08-09 13:48:09 +0200 (Tue, 09 Aug 2016)
New Revision: 1228
Added:
www/files/PRstats/bar.Rnw
www/files/PRstats/foo.Rmd
www/files/PRstats/lecture-MVA.1.0.pdf
www/files/PRstats/lecture-MVAgroups.1.0.pdf
www/files/PRstats/lecture-MVAspatial.1.0.pdf
www/files/PRstats/lecture-phylo.1.0.pdf
www/files/PRstats/lecture-refresheR.1.2.pdf
www/files/PRstats/lecture-reprosci.1.2.pdf
www/files/PRstats/practical-MVAgroups.1.0.pdf
www/files/PRstats/practical-MVAintro.1.0.pdf
www/files/PRstats/practical-MVAspatial.1.0.pdf
www/files/PRstats/practical-introphylo.1.0.pdf
Log:
adding material for Cumbrae
Added: www/files/PRstats/bar.Rnw
===================================================================
--- www/files/PRstats/bar.Rnw (rev 0)
+++ www/files/PRstats/bar.Rnw 2016-08-09 11:48:09 UTC (rev 1228)
@@ -0,0 +1,77 @@
+\documentclass[11pt]{article}
+\usepackage[utf8]{inputenc}
+\usepackage{graphicx}
+\usepackage[english]{babel}
+\usepackage{color}
+\usepackage[colorlinks=true,linkcolor=blue,citecolor=blue,urlcolor=blue]{hyperref}
+\usepackage{array}
+\usepackage{amsfonts}
+\usepackage{url}
+\usepackage{bm}
+\usepackage[margin=2.5cm]{geometry}
+\usepackage{authblk}
+
+\title{Dynamic document generation using knitr}
+
+\author{Thibaut Jombart\thanks{\texttt{thibautjombart at gmail.com}}}
+
+\affil{{\footnotesize Imperial College London \\MRC Centre for Outbreak Analysis and Modelling}}
+
+%% \date{\today}
+\date{August 20, 2016}
+
+\sloppy
+\hyphenpenalty 10000
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\begin{document}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\selectlanguage{english}
+
+\maketitle
+
+\newpage
+
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{A simple example}
+%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+This document is a \LaTeX document with some inclusions of R code.
+It can be compiled into a pdf using \textit{knitr} by typing:
+<>=
+knitr::knit2pdf("bar.Rnw")
+@
+
+We set a number of \textit{knitr} options using \texttt{opts\_chunk}:
+<<>>=
+opts_chunk$set(fig.path='figs/bar', fig.keep='high', dev='pdf',
+ fig.width=7, fig.height=7, tidy=FALSE, warning=FALSE,
+ fig.show="asis", fig.align='center',
+ out.width=".6\\textwidth")
+@
+
+Note that the instruction \texttt{\textbackslash Sexpr} can be used to include in-line values; for instance, the
+value of $\pi$ is \Sexpr{pi}.
+
+More substantial code needs to be enclosed in a chunk.
+For instance, the DAPC of the \textit{microbov} dataset:
+<<>>=
+library(adegenet)
+data(microbov)
+microbov
+dapc1 <- dapc(microbov, n.pca=30, n.da=15)
+dapc1
+summary(dapc1)
+scatter(dapc1)
+@
+
+
+\end{document}
+
Added: www/files/PRstats/foo.Rmd
===================================================================
--- www/files/PRstats/foo.Rmd (rev 0)
+++ www/files/PRstats/foo.Rmd 2016-08-09 11:48:09 UTC (rev 1228)
@@ -0,0 +1,33 @@
+
+This is a toy example of rmarkdown document
+-------------------------------------------
+
+Markdown is a very simple, yet powerful language. Most of its features can be summed up in a simple cheat sheet, such as:
+https://github.com/adam-p/markdown-here/wiki/Markdown-Cheatsheet
+
+To compile it, one can use:
+- `knitr::knit("foo.Rmd")` to produce a `.md` file
+- `knitr::knit2html("foo.Rmd")` to produce a `.html` file
+- `rmarkdown::render("foo.Rmd", "pdf_document")` to produce a `.pdf` file; this features may require other (non-R) packages installed, such as LaTeX and pandoc.
+
+
+### Including R inputs and outputs
+```{r, echo=FALSE}
+opts_chunk$set(fig.path="figs/foo-")
+```
+In the following, we load the `microbov` dataset and run a DAPC on it:
+```{r, dapc}
+library(adegenet)
+data(microbov)
+microbov
+dapc1 <- dapc(microbov, n.pca=30, n.da=15)
+dapc1
+```
+
+
+
+```{r, results}
+summary(dapc1)
+scatter(dapc1)
+```
+
Added: www/files/PRstats/lecture-MVA.1.0.pdf
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Added: www/files/PRstats/lecture-refresheR.1.2.pdf
===================================================================
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+&F1^f?g??A?????! 5^)8l????t?? (??[??e??????-? ???? 5???xQ?P_???=????#?4????/6o?QZR?u???????%???t?j????????$ ?b]\???i ???4?" ??J?pd*? ?H?x $?<9?(?y?_?! .\?x??%K?-[6g??_|?????c??SM?*????4O?=?
Author: jombart
Date: 2016-08-09 14:08:58 +0200 (Tue, 09 Aug 2016)
New Revision: 1229
Modified:
www/documentation.html
Log:
putting material online for Cumbrae
Modified: www/documentation.html
===================================================================
--- www/documentation.html 2016-08-09 11:48:09 UTC (rev 1228)
+++ www/documentation.html 2016-08-09 12:08:58 UTC (rev 1229)
@@ -88,6 +88,7 @@
+
engine.
@@ -108,8 +109,7 @@
Tutorials* 
+ font-family: Helvetica,Arial,sans-serif;">Tutorials*
Up-to-date tutorials are
now hosted on Github:
@@ -228,6 +229,7 @@
+
Epidemiology / Public Health: Introduction to phylogenetics
(last updated on the 15/13/2013)
@@ -286,6 +288,7 @@
+
Epidemiology / Public Health: Introduction to multivariate
analysis / bacterial GWAS (last updated on the
@@ -340,6 +343,7 @@
+
outbreaker
- talk
@@ -380,6 +384,7 @@
+
analysis using ape,
adegenet, and outbreaker
@@ -459,6 +464,7 @@
+
all commands
]
- An introduction to Genome Wise Association Studies (GWAS)
[
- Multivariate analysis of genetic data: an introduction [lecture,
- practical,
- practical
-
-
-
- with all commands]
+ practical]
+
- Multivariate analysis of genetic data: exploring group
diversity [lecture,
- practical,
- practical
-
- with all commands]
+ practical]
- An introduction to Genome Wise Association Studies (GWAS)
[Multivariate analysis of genetic data: uncovering spatial
structures [lecture,
- practical]
+ practical]
+
+
Workshop "Exploratory
methods for population genetics using R" - Barcelona
- (October 2015)
+ (October 2015)
+ Workshop "Genetic data
+ analysis with R" - Cumbrae (August 2016)
+ - Introduction to phylogenetics [lecture, practical]
+
+ - R refresher [lecture]
+
+ - Multivariate analysis of genetic data: an introduction [lecture, practical,
+ practical with all commands]
+ - Multivariate analysis of genetic data: exploring group
+ diversity [lecture,
+ practical,
+ practical with all commands]
+ - Multivariate analysis of genetic data: uncovering spatial
+ structures [lecture,
+ practical]
+ - Reproducible science using R [lecture,
+ foo.Rmd, bar.Rnw]
+
+
.
@@ -123,6 +124,7 @@
+
@@ -230,6 +232,7 @@
+
Epidemiology / Public Health: Introduction to phylogenetics
(last updated on the 15/13/2013)
@@ -289,6 +292,7 @@
+
Epidemiology / Public Health: Introduction to multivariate
analysis / bacterial GWAS (last updated on the
@@ -344,6 +348,7 @@
+
outbreaker
- talk
@@ -385,6 +390,7 @@
+
analysis using ape,
adegenet, and outbreaker
@@ -465,6 +471,7 @@
+
all commands]
- An introduction to Genome Wise Association Studies (GWAS)
[practical]
+
- Multivariate analysis of genetic data: exploring group
diversity [
- Multivariate analysis of genetic data: an introduction [lecture, practical,
- practical with all commands]
+ href="files/PRstats/practical-MVAintro.1.0.pdf">practical]
+
- Multivariate analysis of genetic data: exploring group
diversity [lecture,
practical,
- practical with all commands]
+ practical
+ with all commands]
- Multivariate analysis of genetic data: uncovering spatial
structures [lecture,
From noreply at r-forge.r-project.org Fri Aug 19 13:22:29 2016
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Fri, 19 Aug 2016 13:22:29 +0200 (CEST)
Subject: [adegenet-commits] r1232 - www
Message-ID: <20160819112229.597A3186D06@r-forge.r-project.org>
Author: jombart
Date: 2016-08-19 13:22:29 +0200 (Fri, 19 Aug 2016)
New Revision: 1232
Modified:
www/documentation.html
Log:
fixing links to Leuven practicals - GWAS
Modified: www/documentation.html
===================================================================
--- www/documentation.html 2016-08-18 15:39:51 UTC (rev 1231)
+++ www/documentation.html 2016-08-19 11:22:29 UTC (rev 1232)
@@ -475,9 +475,9 @@
all commands]
- An introduction to Genome Wise Association Studies (GWAS)
[lecture,
+href="files/Leuven2014/Lecture-Day4-%20Genome-Wide%20Association%20Studies.pptx">lecture,
practical]
+href="files/Leuven2014/practical-GWAS.pdf">practical]
- Multivariate analysis of genetic data: uncovering spatial
structures [lecture,
From noreply at r-forge.r-project.org Tue Aug 23 08:05:17 2016
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Tue, 23 Aug 2016 08:05:17 +0200 (CEST)
Subject: [adegenet-commits] r1233 - in www: . files files/Lausanne2016
Message-ID: <20160823060517.C48C518008D@r-forge.r-project.org>
Author: jombart
Date: 2016-08-23 08:05:16 +0200 (Tue, 23 Aug 2016)
New Revision: 1233
Added:
www/files/Lausanne2016/
www/files/Lausanne2016/lecture-MVA.1.0.pdf
www/files/Lausanne2016/lecture-MVAgroups.1.0.pdf
www/files/Lausanne2016/practical-MVAgroups.1.0-allCmds.pdf
www/files/Lausanne2016/practical-MVAgroups.1.0.pdf
Modified:
www/documentation.html
Log:
adding course material for Lausanne
Modified: www/documentation.html
===================================================================
--- www/documentation.html 2016-08-19 11:22:29 UTC (rev 1232)
+++ www/documentation.html 2016-08-23 06:05:16 UTC (rev 1233)
@@ -90,6 +90,7 @@
+
engine.
@@ -125,6 +126,7 @@
+
@@ -233,6 +235,7 @@
+
Epidemiology / Public Health: Introduction to phylogenetics
(last updated on the 15/13/2013)
@@ -293,6 +296,7 @@
+
Epidemiology / Public Health: Introduction to multivariate
analysis / bacterial GWAS (last updated on the
@@ -349,6 +353,7 @@
+
outbreaker
- talk
@@ -391,6 +396,7 @@
+
analysis using ape,
adegenet, and outbreaker
@@ -472,12 +478,12 @@
+
all commands]
- An introduction to Genome Wise Association Studies (GWAS)
[lecture,
- practical]
+ practical]
- Multivariate analysis of genetic data: uncovering spatial
structures [lecture,
@@ -500,8 +506,7 @@
- Multivariate analysis of genetic data: exploring group
diversity [lecture,
- practical]
+ practical]
- An introduction to Genome Wise Association Studies (GWAS)
[practical]
+
- Multivariate analysis of genetic data: exploring group
diversity [lecture,
practical,
practical
+
with all commands]
- Multivariate analysis of genetic data: uncovering spatial
structures [foo.Rmd, bar.Rnw]
+ - Workshop "Genetic data
+ analysis with R" - Cumbrae (August 2016)
+ - Multivariate analysis of genetic data: an introduction [lecture]
+
+ - Multivariate analysis of genetic data: exploring group
+ diversity [lecture,
+ practical,
+ practical with all commands]
-
-
Dirty hacks useful for
teaching
Genetic data
analysis with R" - Cumbrae (August 2016)
- - Workshop "Genetic data
- analysis with R" - Cumbrae (August 2016) Workshop "Population genomics using R" - Lausanne
+ (August 2016)
- Multivariate analysis of genetic data: an introduction [