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<!DOCTYPE html>
<html>
<head>
<title>Introduction to R</title>
<meta charset="utf-8">
<meta name="description" content="Introduction to R">
<meta name="author" content="Gabriel R. A. Margarido, Antonio Augusto Franco Garcia">
<meta name="generator" content="slidify" />
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</head>
<body style="opacity: 0">
<slides class="layout-widescreen">
<!-- LOGO SLIDE -->
<slide class="title-slide segue nobackground">
<hgroup class="auto-fadein">
<h1>Introduction to R</h1>
<h2>A primer</h2>
<p>Gabriel R. A. Margarido, Antonio Augusto Franco Garcia<br/>Department of Genetics, ESALQ/USP</p>
</hgroup>
<a href="https://github.com/augusto-garcia/R-Introduction/zipball/gh-pages" class="example">
Download
</a>
<article></article>
</slide>
<!-- SLIDES -->
<slide class="" id="slide-1" style="background:;">
<hgroup>
<h2>Outline</h2>
</hgroup>
<article data-timings="">
<ol>
<li>Introduction</li>
<li>Basic Syntax</li>
<li>Object Types</li>
<li>Graphics</li>
<li>Programming</li>
</ol>
<!---
Antonio Augusto F. Garcia
http://about.me/augusto.garcia
augusto.garcia@usp.br
-->
</article>
<!-- Presenter Notes -->
</slide>
<slide class="class" id="id" style="background:;">
<hgroup>
<h2>R Learning Curve</h2>
</hgroup>
<article data-timings="">
<p><img src="http://dl.dropboxusercontent.com/u/1968009/figures/learning-curve.jpg" alt="Learn"></p>
</article>
<!-- Presenter Notes -->
</slide>
<slide class="" id="slide-3" style="background:;">
<hgroup>
<h2>Few concepts can make a big difference</h2>
</hgroup>
<article data-timings="">
<iframe width="560" height="315" src="http://www.youtube.com/embed/5pidokakU4I" frameborder="0" allowfullscreen></iframe>
</article>
<!-- Presenter Notes -->
</slide>
<slide class="" id="slide-4" style="background:;">
<hgroup>
<h2>R</h2>
</hgroup>
<article data-timings="">
<ul>
<li>Statistics</li>
<li>Modeling</li>
<li>Graphics</li>
<li>Programming language</li>
<li>Free</li>
<li>Open Source</li>
<li>Extensible</li>
<li>DATA</li>
<li><p>"Lingua franca" of Statistics (Bioinformatics?)</p>
<p><a href="http://www.r-project.org">R Project:</a> <a href="http://www.r-project.org">http://www.r-project.org</a></p>
<p><a href="http://www.rstudio.com">RStudio:</a> <a href="http://www.rstudio.com">http://www.rstudio.com</a></p></li>
</ul>
</article>
<!-- Presenter Notes -->
</slide>
<slide class="" id="slide-5" style="background:;">
<hgroup>
<h2>But there is more!</h2>
</hgroup>
<article data-timings="">
<p><a href="http://www.foastat.org/">http://www.foastat.org/</a></p>
<p><img src="http://dl.dropboxusercontent.com/u/1968009/figures/FOAS.jpg" alt="FOAS"></p>
</article>
<!-- Presenter Notes -->
</slide>
<slide class="" id="slide-6" style="background:;">
<hgroup>
<h2>... and more!</h2>
</hgroup>
<article data-timings="">
<p><a href="http://yihui.name/knitr/">http://yihui.name/knitr/</a></p>
<p><img src="http://dl.dropboxusercontent.com/u/1968009/figures/knitrBook.jpg" alt="knitr"></p>
</article>
<!-- Presenter Notes -->
</slide>
<slide class="" id="slide-7" style="background:;">
<hgroup>
<h2>... and even more!</h2>
</hgroup>
<article data-timings="">
<p>These very slides were produced using an R package: <a href="http://slidify.org/">slidify</a></p>
<iframe width="420" height="315" src="http://www.youtube.com/embed/I95GOmLc7TA" frameborder="0" allowfullscreen></iframe>
</article>
<!-- Presenter Notes -->
</slide>
<slide class="" id="slide-8" style="background:;">
<hgroup>
<h3>Exercise</h3>
</hgroup>
<article data-timings="">
<ol>
<li>Install <a href="http://www.r-project.org">R</a></li>
<li>Install <a href="http://www.rstudio.com">RStudio</a></li>
<li>Take a look on the interface, trying to see where you are</li>
<li><p>Use R as a calculator:</p>
<pre><code class="r">10
</code></pre>
<pre><code>## [1] 10
</code></pre>
<pre><code class="r">1 + 3
</code></pre>
<pre><code>## [1] 4
</code></pre></li>
</ol>
</article>
<!-- Presenter Notes -->
</slide>
<slide class="" id="slide-9" style="background:;">
<article data-timings="">
<pre><code class="r"> 4/3
</code></pre>
<pre><code> ## [1] 1.333
</code></pre>
<pre><code class="r"> 4%%3 # modulo operator
</code></pre>
<pre><code> ## [1] 1
</code></pre>
</article>
<!-- Presenter Notes -->
</slide>
<slide class="" id="slide-10" style="background:;">
<hgroup>
<h2>You can write reports on R</h2>
</hgroup>
<article data-timings="">
<ul>
<li>Syntax: straightforward</li>
</ul>
<h3>Exercise</h3>
<ol>
<li>Download the file <a href="https://github.com/augusto-garcia/R-Introduction/blob/gh-pages/knitr_example.Rmd">knitr_example.Rmd</a>. It uses
<a href="http://www.rstudio.com/ide/docs/r_markdown">R Markdown</a>
syntax.</li>
<li>Open it on RStudio</li>
<li>Take a look on it, finding headers, lists (numbered, or items), and
R chunks</li>
<li>Try to add a few comments and R chunks</li>
<li>Compile it to produce an html report</li>
<li>(This is making usage of the amazing package <a href="http://yihui.name/knitr/">knitr</a>)</li>
<li>Use it for taking notes during this course</li>
</ol>
</article>
<!-- Presenter Notes -->
</slide>
<slide class="" id="slide-11" style="background:;">
<hgroup>
<h2>For reproducibility:</h2>
</hgroup>
<article data-timings="">
<pre><code class="r">sessionInfo()
</code></pre>
<pre><code>## R version 2.15.2 (2012-10-26)
## Platform: x86_64-pc-linux-gnu (64-bit)
##
## locale:
## [1] LC_CTYPE=pt_BR.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=pt_BR.UTF-8 LC_COLLATE=pt_BR.UTF-8
## [5] LC_MONETARY=pt_BR.UTF-8 LC_MESSAGES=pt_BR.UTF-8
## [7] LC_PAPER=C LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=pt_BR.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] parallel graphics grDevices utils datasets stats methods
## [8] base
##
## other attached packages:
## [1] sos_1.3-8 R2G2_1.0-2 qtl_1.30-4
## [4] plyr_1.8 fortunes_1.5-2 brew_1.0-6
## [7] BLR_1.3 SuppDists_1.1-9.1 slidify_0.4
## [10] RColorBrewer_1.0-5 knitr_1.5 ggplot2_0.9.3.1
##
## loaded via a namespace (and not attached):
## [1] codetools_0.2-8 colorspace_1.2-4 compiler_2.15.2 dichromat_2.0-0
## [5] digest_0.6.4 evaluate_0.5.1 formatR_0.10 grid_2.15.2
## [9] gtable_0.1.2 labeling_0.2 markdown_0.6.4 MASS_7.3-23
## [13] munsell_0.4.2 proto_0.3-10 reshape2_1.2.2 scales_0.2.3
## [17] stringr_0.6.2 tools_2.15.2 whisker_0.3-2 yaml_2.1.10
</code></pre>
</article>
<!-- Presenter Notes -->
</slide>
<slide class="segue dark quote" id="slide-12" style="background:;">
<article data-timings="">
<p><q class = 'yellow'> Reproducible research is a very important
concept. Not only in order to allow others to reproduce and understand
what you did, but also to allow others to extend your research.
Programs with 'point and click' menus are not in line with this
concept.</q></p>
</article>
<!-- Presenter Notes -->
</slide>
<slide class="" id="slide-13" style="background:;">
<hgroup>
<h2>R syntax</h2>
</hgroup>
<article data-timings="">
<pre><code class="r">10 > 2
</code></pre>
<pre><code>## [1] TRUE
</code></pre>
<pre><code class="r">(3 * 2) == 5 # caution: '==' is different than '='
</code></pre>
<pre><code>## [1] FALSE
</code></pre>
<pre><code class="r">"Hello, world"
</code></pre>
<pre><code>## [1] "Hello, world"
</code></pre>
</article>
<!-- Presenter Notes -->
</slide>
<slide class="" id="slide-14" style="background:;">
<hgroup>
<h2>Variables</h2>
</hgroup>
<article data-timings="">
<pre><code class="r">a <- 100
a
</code></pre>
<pre><code>## [1] 100
</code></pre>
<pre><code class="r">a * 8
</code></pre>
<pre><code>## [1] 800
</code></pre>
<pre><code class="r">a <- 20
a <- "New string"
a
</code></pre>
<pre><code>## [1] "New string"
</code></pre>
</article>
<!-- Presenter Notes -->
</slide>
<slide class="" id="slide-15" style="background:;">
<hgroup>
<h2>Functions</h2>
</hgroup>
<article data-timings="">
<pre><code class="r">log(100)
</code></pre>
<pre><code>## [1] 4.605
</code></pre>
<pre><code class="r">log10(100)
</code></pre>
<pre><code>## [1] 2
</code></pre>
<pre><code class="r">sequence(5)
</code></pre>
<pre><code>## [1] 1 2 3 4 5
</code></pre>
<pre><code class="r">seq(from = 0, to = 1, by = 0.2)
</code></pre>
<pre><code>## [1] 0.0 0.2 0.4 0.6 0.8 1.0
</code></pre>
</article>
<!-- Presenter Notes -->
</slide>
<slide class="" id="slide-16" style="background:;">
<hgroup>
<h3>Exercise</h3>
</hgroup>
<article data-timings="">
<ol>
<li>Compute the square root of all numbers from 7 to 1458.</li>
<li>Compute the square root of all even numbers from 7 to 1458.</li>
</ol>
</article>
<!-- Presenter Notes -->
</slide>
<slide class="" id="slide-17" style="background:;">
<hgroup>
<h2>Help!</h2>
</hgroup>
<article data-timings="">
<pre><code class="r">help(seq)
`?`(seq)
help.search("histogram")
</code></pre>
<h3>Exercise</h3>
<ol>
<li>Find help about the function plot()</li>
</ol>
</article>
<!-- Presenter Notes -->
</slide>
<slide class="" id="slide-18" style="background:;">
<hgroup>
<h2>RSeek</h2>
</hgroup>
<article data-timings="">
<p><a href="http://www.rseek.org/">http://www.rseek.org/</a></p>
<p><img src="http://dl.dropboxusercontent.com/u/1968009/figures/RSeek.jpg" alt="rseek"></p>
</article>
<!-- Presenter Notes -->
</slide>
<slide class="" id="slide-19" style="background:;">
<hgroup>
<h3>Exercise</h3>
</hgroup>
<article data-timings="">
<ol>
<li>Find R packages for "linkage mapping"</li>
<li>Find R packages for "QTL mapping"</li>
<li>"Genomic selection"</li>
<li class = '..'>(your choice)</li>
</ol>
</article>
<!-- Presenter Notes -->
</slide>
<slide class="" id="slide-20" style="background:;">
<hgroup>
<h2>Install and load packages</h2>
</hgroup>
<article data-timings="">
<ul>
<li>Repositories: your choice, but closer is better</li>
</ul>
<pre><code class="r">install.packages()
</code></pre>
<pre><code class="r">install.packages("fortunes")
</code></pre>
<pre><code class="r">library("fortunes")
fortune()
</code></pre>
<pre><code>##
## I cannot remember if I have been using 14 or 14, I think it was 14 and I
## am not near the machine to check.
## -- John Kane (confused about his SPSS version)
## R-help (April 2007)
</code></pre>
</article>
<!-- Presenter Notes -->
</slide>
<slide class="" id="slide-21" style="background:;">
<hgroup>
<h2>More help</h2>
</hgroup>
<article data-timings="">
<pre><code class="r">install.packages("sos")
</code></pre>
<pre><code class="r">library("sos")
findFn("qtl")
</code></pre>
<pre><code>## found 633 matches; retrieving 20 pages, 400 matches.
## 2 3 4 5 6 7 8 9 10
## 11 12 13 14 15 16 17 18 19 20
##
## Downloaded 354 links in 33 packages.
</code></pre>
</article>
<!-- Presenter Notes -->
</slide>
<slide class="" id="slide-22" style="background:;">
<hgroup>
<h2>SOS!</h2>
</hgroup>
<article data-timings="">
<pre><code class="r">findFn("metabolomic")
</code></pre>
<pre><code>## found 65 matches; retrieving 4 pages
## 2 3 4
## Downloaded 63 links in 16 packages.
</code></pre>
<pre><code class="r">findFn("qtl mapping metabolomic")
</code></pre>
<pre><code>## found 2 matches
## Downloaded 2 links in 1 packages.
</code></pre>
</article>
<!-- Presenter Notes -->
</slide>
<slide class="" id="slide-23" style="background:;">
<hgroup>
<h2>Packages on your computer</h2>
</hgroup>
<article data-timings="">
<pre><code class="r">installed.packages()
</code></pre>
<pre><code>## Package
## bitops "bitops"
## BLR "BLR"
## colorspace "colorspace"
## devtools "devtools"
## dichromat "dichromat"
## digest "digest"
## evaluate "evaluate"
## formatR "formatR"
## fortunes "fortunes"
## ggplot2 "ggplot2"
## gtable "gtable"
## highr "highr"
## httr "httr"
## knitr "knitr"
## labeling "labeling"
## markdown "markdown"
## memoise "memoise"
## munsell "munsell"
## plyr "plyr"
## proto "proto"
## qtl "qtl"
## R2G2 "R2G2"
## RColorBrewer "RColorBrewer"
## RCurl "RCurl"
## reshape2 "reshape2"
## scales "scales"
## slidify "slidify"
## slidifyLibraries "slidifyLibraries"
## stringr "stringr"
## SuppDists "SuppDists"
## whisker "whisker"
## yaml "yaml"
## base "base"
## boot "boot"
## class "class"
## cluster "cluster"
## codetools "codetools"
## compiler "compiler"
## datasets "datasets"
## foreign "foreign"
## graphics "graphics"
## grDevices "grDevices"
## grid "grid"
## KernSmooth "KernSmooth"
## lattice "lattice"
## MASS "MASS"
## Matrix "Matrix"
## methods "methods"
## mgcv "mgcv"
## nlme "nlme"
## nnet "nnet"
## parallel "parallel"
## rpart "rpart"
## spatial "spatial"
## splines "splines"
## stats "stats"
## stats4 "stats4"
## survival "survival"
## tcltk "tcltk"
## tools "tools"
## utils "utils"
## LibPath
## bitops "/home/augusto/R/x86_64-pc-linux-gnu-library/2.15"
## BLR "/home/augusto/R/x86_64-pc-linux-gnu-library/2.15"
## colorspace "/home/augusto/R/x86_64-pc-linux-gnu-library/2.15"
## devtools "/home/augusto/R/x86_64-pc-linux-gnu-library/2.15"
## dichromat "/home/augusto/R/x86_64-pc-linux-gnu-library/2.15"
## digest "/home/augusto/R/x86_64-pc-linux-gnu-library/2.15"
## evaluate "/home/augusto/R/x86_64-pc-linux-gnu-library/2.15"
## formatR "/home/augusto/R/x86_64-pc-linux-gnu-library/2.15"
## fortunes "/home/augusto/R/x86_64-pc-linux-gnu-library/2.15"
## ggplot2 "/home/augusto/R/x86_64-pc-linux-gnu-library/2.15"
## gtable "/home/augusto/R/x86_64-pc-linux-gnu-library/2.15"
## highr "/home/augusto/R/x86_64-pc-linux-gnu-library/2.15"
## httr "/home/augusto/R/x86_64-pc-linux-gnu-library/2.15"
## knitr "/home/augusto/R/x86_64-pc-linux-gnu-library/2.15"
## labeling "/home/augusto/R/x86_64-pc-linux-gnu-library/2.15"
## markdown "/home/augusto/R/x86_64-pc-linux-gnu-library/2.15"
## memoise "/home/augusto/R/x86_64-pc-linux-gnu-library/2.15"
## munsell "/home/augusto/R/x86_64-pc-linux-gnu-library/2.15"
## plyr "/home/augusto/R/x86_64-pc-linux-gnu-library/2.15"
## proto "/home/augusto/R/x86_64-pc-linux-gnu-library/2.15"
## qtl "/home/augusto/R/x86_64-pc-linux-gnu-library/2.15"
## R2G2 "/home/augusto/R/x86_64-pc-linux-gnu-library/2.15"
## RColorBrewer "/home/augusto/R/x86_64-pc-linux-gnu-library/2.15"
## RCurl "/home/augusto/R/x86_64-pc-linux-gnu-library/2.15"
## reshape2 "/home/augusto/R/x86_64-pc-linux-gnu-library/2.15"
## scales "/home/augusto/R/x86_64-pc-linux-gnu-library/2.15"
## slidify "/home/augusto/R/x86_64-pc-linux-gnu-library/2.15"
## slidifyLibraries "/home/augusto/R/x86_64-pc-linux-gnu-library/2.15"
## stringr "/home/augusto/R/x86_64-pc-linux-gnu-library/2.15"
## SuppDists "/home/augusto/R/x86_64-pc-linux-gnu-library/2.15"
## whisker "/home/augusto/R/x86_64-pc-linux-gnu-library/2.15"
## yaml "/home/augusto/R/x86_64-pc-linux-gnu-library/2.15"
## base "/usr/lib/R/library"
## boot "/usr/lib/R/library"
## class "/usr/lib/R/library"
## cluster "/usr/lib/R/library"
## codetools "/usr/lib/R/library"
## compiler "/usr/lib/R/library"
## datasets "/usr/lib/R/library"
## foreign "/usr/lib/R/library"
## graphics "/usr/lib/R/library"
## grDevices "/usr/lib/R/library"
## grid "/usr/lib/R/library"
## KernSmooth "/usr/lib/R/library"
## lattice "/usr/lib/R/library"
## MASS "/usr/lib/R/library"
## Matrix "/usr/lib/R/library"
## methods "/usr/lib/R/library"
## mgcv "/usr/lib/R/library"
## nlme "/usr/lib/R/library"
## nnet "/usr/lib/R/library"
## parallel "/usr/lib/R/library"
## rpart "/usr/lib/R/library"
## spatial "/usr/lib/R/library"
## splines "/usr/lib/R/library"
## stats "/usr/lib/R/library"
## stats4 "/usr/lib/R/library"
## survival "/usr/lib/R/library"
## tcltk "/usr/lib/R/library"
## tools "/usr/lib/R/library"
## utils "/usr/lib/R/library"
## Version Priority
## bitops "1.0-6" NA
## BLR "1.3" NA
## colorspace "1.2-4" NA
## devtools "1.4.1" NA
## dichromat "2.0-0" NA
## digest "0.6.4" NA
## evaluate "0.5.1" NA
## formatR "0.10" NA
## fortunes "1.5-2" NA
## ggplot2 "0.9.3.1" NA
## gtable "0.1.2" NA
## highr "0.3" NA
## httr "0.2" NA
## knitr "1.5" NA
## labeling "0.2" NA
## markdown "0.6.4" NA
## memoise "0.1" NA
## munsell "0.4.2" NA
## plyr "1.8" NA
## proto "0.3-10" NA
## qtl "1.30-4" NA
## R2G2 "1.0-2" NA
## RColorBrewer "1.0-5" NA
## RCurl "1.95-4.1" NA
## reshape2 "1.2.2" NA
## scales "0.2.3" NA
## slidify "0.4" NA
## slidifyLibraries "0.3.1" NA
## stringr "0.6.2" NA
## SuppDists "1.1-9.1" NA
## whisker "0.3-2" NA
## yaml "2.1.10" NA
## base "2.15.2" "base"
## boot "1.3-7" "recommended"
## class "7.3-5" "recommended"
## cluster "1.14.3" "recommended"
## codetools "0.2-8" "recommended"
## compiler "2.15.2" "base"
## datasets "2.15.2" "base"
## foreign "0.8-52" "recommended"
## graphics "2.15.2" "base"
## grDevices "2.15.2" "base"
## grid "2.15.2" "base"
## KernSmooth "2.23-8" "recommended"
## lattice "0.20-13" "recommended"
## MASS "7.3-23" "recommended"
## Matrix "1.0-11" "recommended"
## methods "2.15.2" "base"
## mgcv "1.7-22" "recommended"
## nlme "3.1-108" "recommended"
## nnet "7.3-5" "recommended"
## parallel "2.15.2" "base"
## rpart "4.1-0" "recommended"
## spatial "7.3-5" "recommended"
## splines "2.15.2" "base"
## stats "2.15.2" "base"
## stats4 "2.15.2" "base"
## survival "2.37-2" "recommended"
## tcltk "2.15.2" "base"
## tools "2.15.2" "base"
## utils "2.15.2" "base"
## Depends
## bitops NA
## BLR "R (>= 2.10), SuppDists"
## colorspace "R (>= 2.13.0), methods"
## devtools "R (>= 2.15)"
## dichromat "R (>= 2.10), stats"
## digest "R (>= 2.4.1)"
## evaluate "R (>= 2.14.0)"
## formatR NA
## fortunes NA
## ggplot2 "R (>= 2.14), stats, methods"
## gtable "R (>= 2.14), grid"
## highr NA
## httr NA
## knitr "R (>= 2.14.1)"
## labeling NA
## markdown "R (>= 2.11.1)"
## memoise NA
## munsell NA
## plyr "R (>= 2.11.0)"
## proto NA
## qtl "R (>= 2.14.0), graphics, stats, parallel, utils"
## R2G2 NA
## RColorBrewer "R (>= 2.0.0)"
## RCurl "R (>= 2.7.0), methods, bitops"
## reshape2 NA
## scales "R (>= 2.12), methods"
## slidify "\nR (>= 2.15.0)"
## slidifyLibraries NA
## stringr "R (>= 2.14)"
## SuppDists NA
## whisker NA
## yaml NA
## base NA
## boot "R (>= 2.14.0), graphics, stats"
## class "R (>= 2.5.0), stats, utils"
## cluster "R (>= 2.10.0), stats, graphics, utils"
## codetools "R (>= 2.1)"
## compiler NA
## datasets NA
## foreign "R (>= 2.14.0), stats"
## graphics NA
## grDevices NA
## grid NA
## KernSmooth "R (>= 2.5.0), stats"
## lattice "R (>= 2.15.1)"
## MASS "R (>= 2.14.0), grDevices, graphics, stats, utils"
## Matrix "R (>= 2.15.0), stats, methods, utils, lattice"
## methods NA
## mgcv "R (>= 2.14.0), stats, graphics"
## nlme "graphics, stats, R (>= 2.14.0), R (< 3.0.0)"
## nnet "R (>= 2.5.0), stats, utils"
## parallel NA
## rpart "R (>= 2.14.0), graphics, stats, grDevices"
## spatial "R (>= 2.5.0), graphics, stats, utils"
## splines NA
## stats NA
## stats4 "methods, graphics, stats"
## survival "stats, utils, graphics, splines, R (>= 2.13.0)"
## tcltk NA
## tools NA
## utils NA
## Imports
## bitops NA
## BLR NA
## colorspace NA
## devtools "httr, RCurl, utils, tools, methods, memoise, whisker,\nevaluate, digest"
## dichromat NA
## digest NA
## evaluate "stringr (>= 0.4)"
## formatR NA
## fortunes "utils"
## ggplot2 "plyr (>= 1.7.1), digest, grid, gtable (>= 0.1.1), reshape2,\nscales (>= 0.2.3), proto, MASS"
## gtable NA
## highr NA
## httr "RCurl (>= 1.95-0), stringr (>= 0.6.1), digest, tools"
## knitr "evaluate (>= 0.4.7), digest, formatR (>= 0.9), highr (>= 0.2),\nmarkdown (>= 0.6.3), stringr (>= 0.6), tools"
## labeling NA
## markdown NA
## memoise "digest"
## munsell "colorspace"
## plyr NA
## proto NA
## qtl NA
## R2G2 NA
## RColorBrewer NA
## RCurl "methods"
## reshape2 "plyr (>= 1.5), stringr, lattice"
## scales "RColorBrewer, stringr, dichromat, munsell (>= 0.2), plyr (>=\n1.2), labeling"
## slidify "\nknitr (>= 0.1),\nmarkdown,\nstringr,\nyaml,\nwhisker"
## slidifyLibraries NA
## stringr NA
## SuppDists NA
## whisker NA
## yaml NA
## base NA
## boot NA
## class "MASS"
## cluster NA
## codetools NA
## compiler NA
## datasets NA
## foreign "methods, utils"
## graphics "grDevices"
## grDevices NA
## grid "grDevices"
## KernSmooth NA
## lattice "grid, grDevices, graphics, stats, utils"
## MASS NA
## Matrix "graphics, grid"
## methods "utils"
## mgcv "nlme, methods, Matrix"
## nlme "lattice"
## nnet NA
## parallel NA
## rpart NA
## spatial NA
## splines "graphics, stats"
## stats NA
## stats4 NA
## survival NA
## tcltk NA
## tools NA
## utils NA
## LinkingTo
## bitops NA
## BLR NA
## colorspace NA
## devtools NA
## dichromat NA
## digest NA
## evaluate NA
## formatR NA
## fortunes NA
## ggplot2 NA
## gtable NA
## highr NA
## httr NA
## knitr NA
## labeling NA
## markdown NA
## memoise NA
## munsell NA
## plyr NA
## proto NA
## qtl NA
## R2G2 NA
## RColorBrewer NA
## RCurl NA
## reshape2 NA
## scales NA
## slidify NA
## slidifyLibraries NA
## stringr NA
## SuppDists NA
## whisker NA
## yaml NA
## base NA
## boot NA
## class NA
## cluster NA
## codetools NA
## compiler NA
## datasets NA
## foreign NA
## graphics NA
## grDevices NA
## grid NA
## KernSmooth NA
## lattice NA
## MASS NA
## Matrix NA
## methods NA
## mgcv NA
## nlme NA
## nnet NA
## parallel NA
## rpart NA
## spatial NA
## splines NA
## stats NA
## stats4 NA
## survival NA
## tcltk NA
## tools NA
## utils NA
## Suggests
## bitops NA
## BLR NA
## colorspace "KernSmooth, MASS, kernlab, mvtnorm, vcd, tcltk, dichromat"
## devtools "testthat (>= 0.7), roxygen2, BiocInstaller, Rcpp (>= 0.10.0),\nMASS, knitr, rstudio"
## dichromat NA
## digest NA
## evaluate "testthat, ggplot2"
## formatR "codetools, gWidgetsRGtk2, testit, knitr"
## fortunes NA
## ggplot2 "quantreg, Hmisc, mapproj, maps, hexbin, maptools, multcomp,\nnlme, testthat"
## gtable "testthat, plyr"
## highr "knitr, testit"
## httr "rjson, XML, testthat, png, jpeg, Rook"
## knitr "testit, rgl, codetools, XML, RCurl"
## labeling NA
## markdown "knitr, RCurl"
## memoise NA
## munsell "ggplot2 (>= 0.9.2)"
## plyr "abind, testthat (>= 0.2), tcltk, foreach, doMC, itertools,\niterators"
## proto "graph, Rgraphviz"
## qtl NA
## R2G2 NA
## RColorBrewer NA
## RCurl "Rcompression, XML"
## reshape2 "testthat"
## scales "testthat"
## slidify NA
## slidifyLibraries NA
## stringr "testthat (>= 0.3)"
## SuppDists NA
## whisker "markdown"
## yaml "testthat"
## base NA
## boot "MASS, survival"
## class NA
## cluster "MASS"
## codetools NA
## compiler NA
## datasets NA
## foreign NA
## graphics NA
## grDevices NA
## grid "lattice"
## KernSmooth "MASS"
## lattice "grid, KernSmooth, MASS"
## MASS "lattice, nlme, nnet, survival"
## Matrix "expm, MASS"
## methods NA
## mgcv "nlme (>= 3.1-64), splines, Matrix, parallel"
## nlme "Hmisc, MASS"
## nnet "MASS"
## parallel NA
## rpart "survival"
## spatial "MASS"
## splines NA
## stats NA
## stats4 NA
## survival NA
## tcltk NA
## tools NA
## utils NA
## Enhances OS_type
## bitops NA NA
## BLR NA NA
## colorspace NA NA
## devtools NA NA
## dichromat NA NA
## digest NA NA
## evaluate NA NA
## formatR NA NA
## fortunes NA NA
## ggplot2 "sp" NA
## gtable NA NA
## highr NA NA
## httr NA NA
## knitr NA NA
## labeling NA NA
## markdown NA NA
## memoise NA NA
## munsell NA NA
## plyr NA NA
## proto NA NA
## qtl NA NA
## R2G2 NA NA
## RColorBrewer NA NA
## RCurl NA NA
## reshape2 NA NA
## scales NA NA
## slidify NA NA
## slidifyLibraries NA NA
## stringr NA NA
## SuppDists NA NA
## whisker NA NA
## yaml NA NA
## base NA NA
## boot NA NA
## class NA NA
## cluster NA NA
## codetools NA NA
## compiler NA NA
## datasets NA NA
## foreign NA NA
## graphics NA NA
## grDevices NA NA
## grid NA NA