[adegenet-commits] r1228 - www/files/PRstats
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Aug 9 13:48:09 CEST 2016
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:
+<<eval=FALSE>>=
+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-MVAgroups.1.0.pdf
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Property changes on: www/files/PRstats/lecture-MVAgroups.1.0.pdf
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Added: svn:mime-type
+ application/octet-stream
Added: www/files/PRstats/lecture-MVAspatial.1.0.pdf
===================================================================
(Binary files differ)
Property changes on: www/files/PRstats/lecture-MVAspatial.1.0.pdf
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Added: svn:mime-type
+ application/octet-stream
Added: www/files/PRstats/lecture-phylo.1.0.pdf
===================================================================
(Binary files differ)
Property changes on: www/files/PRstats/lecture-phylo.1.0.pdf
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: www/files/PRstats/lecture-refresheR.1.2.pdf
===================================================================
--- www/files/PRstats/lecture-refresheR.1.2.pdf (rev 0)
+++ www/files/PRstats/lecture-refresheR.1.2.pdf 2016-08-09 11:48:09 UTC (rev 1228)
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[TRUNCATED]
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