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<!DOCTYPE html>
<!--[if lt IE 7]> <html class="no-js ie6" lang="en"> <![endif]-->
<!--[if IE 7]> <html class="no-js ie7" lang="en"> <![endif]-->
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<!--[if gt IE 8]><!--> <html class="no-js" lang="en"> <!--<![endif]-->
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge,chrome=1">
<title>Guide to using the AntWeb package</title>
<meta name="description" content="Guide to using the AntWeb R package">
<meta name="author" content="Karthik Ram">
<meta name="viewport" content="width=1024, user-scalable=no">
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<script src="js/modernizr.custom.js"></script>
</head>
<body class="deck-container">
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<section class="slide" id="ropensci">
<div>
<br><br><br>
<hgroup>
<img src="images/ropensci.png">
<center><h3><span style="color:#B8172F; font-size:50px">Fostering the next generation of open science with R </span><i class="ss-globe"></i></h3><br><br>
<h3>Karthik Ram (@_inundata) <br> <a href="http://nature.berkeley.edu/~kram"><br> <span style="color:#464749">Supported by: </span><br><img src="images/sloan_logo2.png"></a> </h3>
</center>
</hgroup>
</div>
</section>
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<section class="slide" id="lots_of_data">
<br><br>
<img src="images/notebook2.png" height="654" width="849">
</section>
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<section class="slide" id="notes_for_nature">
<br><br>
<img src="images/notes_for_nature.png">
</section>
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<section class="slide" id="from_sensors_too" data-duration="8000">
<br><br>
<table>
<tr>
<td><img src="images/sensors.png">
</tr>
</table>
</section>
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<section class="slide" id="science_is_closed">
<br><br>
<div>
<h1>These data are hard to get to <span style="color: #b22d28;"><i class="ss-lock"></i></span></h1>
</div>
</section>
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<section class="slide" id="science_lacks_reproducibility2">
<br><br>
<img src="images/step2.png">
</section>
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<section class="slide" id="open_science">
<br><br>
<div>
<h1>Open Science <span style="color: #59c54a;"><i class="ss-unlock"></i></span></h1>
</div>
</section>
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<section class="slide" id="sharing_increases_citations">
<br><br>
<div>
<img src="images/sharing_data.png" height="465" width="1068">
<br>
<p>Source: <i class="ss-icon ss-link"> <a href="http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0000308">PLOS, 2007</a></i></p>
</div>
</section>
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<section class="slide" id="nsf_biosketches">
<br><br>
<blockquote>Instructions for preparation of the Biographical Sketch have been revised to rename the <span style="background-color: #ebe455;">"Publications" section to "Products"</span> and amend terminology and instructions accordingly. This change makes clear that products may include, but are not limited to, publications, <span style="background-color: #ebe455;">data sets, software, patents, and copyrights.
</blockquote>
<br><i class="ss-icon ss-link"> <a href="http://www.nsf.gov/pubs/2013/nsf13004/nsf13004.jsp?WT.mc_id=USNSF_109"> Issuance of a new NSF Proposal & Award Policies and Procedures Guide (October 4<sup>th</sup>)</a></i></br>
</section>
<!-- ############## slide delimiter ############## -->
<section class="slide" id="gui_analysis_is_bad">
<h2>Why R?</h2>
<h3>The old way...</h3>
<img src="images/old-way.png">
</section>
<!-- ############## slide delimiter ############## -->
<section class="slide" id="R_is_better">
<h2>Why R?</h2>
<h3>A better way</h3><br><br>
<pre class="knitr"><div class="source"><span class="functioncall">glm</span><span class="keyword">(</span><span class="symbol">y</span> <span class="keyword">~</span> <span class="keyword">-</span><span class="number">1</span> <span class="keyword">+</span> <span class="symbol">a</span> <span class="keyword">+</span> <span class="symbol">c</span> <span class="keyword">+</span> <span class="symbol">z</span> <span class="keyword">+</span> <span class="symbol">a</span><span class="keyword">:</span><span class="symbol">z</span><span class="keyword">,</span> <span class="argument">data</span> <span class="argument">=</span> <span class="symbol">mydata</span><span class="keyword">,</span> <span class="argument">maxit</span> <span class="argument">=</span> <span class="number">30</span><span class="keyword">)</span></div></pre>
<br><br>
<h3>This is <u>reproducible</u>, <u>repeatable</u> and can serve as a analytic workflow.</h3>
</section>
<!-- ############## slide delimiter ############## -->
<section class="slide" id="open_science_tools">
<br><br>
<div>
<h2>Open Science needs open source tools</h2>
<img src="images/exponential_r_growth.png" height="367" width="378">
<br><br>
<p>Source: <i class="ss-icon ss-link"> <a href="http://blog.revolutionanalytics.com/2010/01/r-package-growth.html">Revolution Analytics, 2010</a>,
<a href="http://www.nature.com/nature/journal/v482/n7386/abs/nature10836.html">Nature editorial, 2012</a></i></p>
</div>
</section>
<!-- ############## slide delimiter ############## -->
<section class="slide" id="open_science_open_code">
<br>
<div>
<center><h2>Open data + code</h2></center>
<img src="images/openscience_opencode2.png" height="625" width="661">
<p>Source: <i class="ss-icon ss-link"><a href="http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2486.2012.02693.x/abstract"> Wolkovich et al. Global Change Biology, 2012</a></i>.
</p>
</div>
</section>
<!-- ############## slide delimiter ############## -->
<section class="slide" id="ropensci_main">
<br><br>
<div>
<img src="images/ropensci.png" height="118" width="301">
<br><br>
<blockquote>Enable access to scientific data repositories, full-text of articles, and science metrics and also <i>facilitate a culture shift in the scientific community.</i></blockquote>
</div>
</section>
<!-- ############## slide delimiter ############## -->
<section class="slide" id="ropensci_packages">
<br><br>
<div>
<img src="images/ropensci.png" height="118" width="301">
<br> <span style="font-size:165%; font-family:'Museo Sans'"><center>More info @ <span style="color:#3163a6;"><code>ropensci.org/packages</code></span></center></span><br>
<table cellpadding="40" cellspacing="40">
<tr>
<td> </td>
<td>
<img src="images/clear_line.png" height="1" width="250">
<pre><img src="images/line_separator_blue.png"><span style="color:#669900; font-family:'Museo Sans'; font-size:110%"><i class="ss-icon ss-box"></i> Data</span>
Treebase, Fishbase,
Flybase,
GBIF, Vertnet
Dryad, ITIS
NPN, Taxize
AntWeb</pre><br></td>
<td> </td>
<td>
<img src="images/clear_line.png" height="1" width="250"><pre><img src="images/line_separator_red.png"><span style="color:#c4a12e; font-family:'Museo Sans'; font-size:105%"><i class="ss-icon ss-notebook"></i> Journals</span>
PLOS
Springer
textmine
pensoft</pre>
</td>
<td> </td>
<td><img src="images/clear_line.png" height="1" width="250"><pre><img src="images/line_separator_green.png"><span style="color:#e2460e; font-family:'Museo Sans'; font-size:105%"><i class="ss-icon ss-list"></i> Hybrid</span>
figshare
Mendeley
DataONE,
rAltmetric, rEML,
rNEXML</pre>
</td>
</tr>
</table>
</div>
</section>
<!-- ############## slide delimiter ############## -->
<section class="slide" id="rplos">
<img src="images/plos.png" height="107" width="107" align="left"><h2>Search full text of 100k+ open access articles - <code>rplos</code></h2>
<br>
<section class="slide deck-previous" id="rplos_code"><div>
<pre class="knitr"><span class="functioncall">library</span><span class="keyword">(</span><span class="symbol">rplos</span><span class="keyword">)</span>
<span class="functioncall">plot_throughtime</span><span class="keyword">(</span><span class="functioncall">list</span><span class="keyword">(</span><span class="string">"reproducible science"</span><span class="keyword">)</span><span class="keyword">,</span> <span class="number">500</span><span class="keyword">)</span></pre>
</div>
</section>
<section class="slide deck-current" id="rplos_figure">
<div>
<img src="images/plos_example.png">
</div>
</section>
</section>
<!-- ############## slide delimiter ############## -->
<section class="slide" id="dryad">
<br><br>
<img src="images/dryad.png" height="119" width="107" align="left"><h2>Accessing data behind papers - <code>dryad</code></h2>
<div>
<pre class="knitr"><span class="comment"># Get the URL for a data file</span>
<span class="symbol">dryaddat</span> <span class="assignement"><-</span> <span class="functioncall">download_url</span><span class="keyword">(</span><span class="string">"10255/dryad.1759"</span><span class="keyword">)</span>
<span class="comment"># Get a file given the URL</span>
<span class="symbol">file</span> <span class="assignement"><-</span> <span class="functioncall">dryad_getfile</span><span class="keyword">(</span><span class="symbol">dryaddat</span><span class="keyword">)</span>
</pre>
</div>
</section>
<!-- ############## slide delimiter ############## -->
<section class="slide" id="rgbif">
<img src="images/gbif.png" height="104" width="107" align="left"><h2>Mapping biodiversity data - <code>rgbif</code></h2>
<section class="slide deck-previous" id="getting_distribution_data">
<pre class="knitr">
<span class="symbol">distribution</span> <span class="assignement"><-</span> <span class="functioncall">occurrencelist</span><span class="keyword">(</span><span class="argument">sciname</span> <span class="argument">=</span> <span class="string">"Danaus plexippus"</span><span class="keyword">,</span> <span class="argument">coordinatestatus</span> <span class="argument">=</span> <span class="number">TRUE</span><span class="keyword">,</span> <span class="argument">maxresults</span> <span class="argument">=</span> <span class="number">1000</span><span class="keyword">,</span> <span class="argument">latlongdf</span> <span class="argument">=</span> <span class="number">TRUE</span><span class="keyword">)</span>
</pre></section>
<section class="slide deck-current" id="plotting_distribution_data">
<img src="images/rgbif.png" height="457" width="702">
</section>
<div>
</div>
</section>
<!-- ############## slide delimiter ############## -->
<section class="slide" id="rgbif_sdm">
<div>
<h2>Species distribution modeling</h2>
<img src="images/sdm.png">
</div>
</section>
<!-- ############## slide delimiter ############## -->
<section class="slide" id="rwbclimate">
<h2>World Bank climate knowledge portal <code>rWBclimate</code></h2>
<pre class="knitr r"><span class="hl kwd">library</span><span class="hl std">(rWBclimate)</span>
<span class="hl std">eu_basin</span> <span class="hl kwb"><-</span> <span class="hl kwd">create_map_df</span><span class="hl std">(Eur_basin)</span>
<span class="hl std">eu_basin_dat</span> <span class="hl kwb"><-</span> <span class="hl kwd">get_ensemble_temp</span><span class="hl std">(Eur_basin,</span> <span class="hl str">"annualanom"</span><span class="hl std">,</span> <span class="hl num">2080</span><span class="hl std">,</span> <span class="hl num">2100</span><span class="hl std">)</span>
</pre>
<img src="images/rWBClimate.png">
</section>
<!-- ############## slide delimiter ############## -->
<section class="slide" id="taxize">
<h2>Resolve taxonomic names</h2>
<pre class="knitr r"><span class="hl kwd">library</span><span class="hl std">(taxize)</span>
<span class="hl std">splist</span> <span class="hl kwb"><-</span> <span class="hl kwd">c</span><span class="hl std">(</span><span class="hl str">"Helanthus annuus"</span><span class="hl std">,</span> <span class="hl str">"Pinos contorta"</span><span class="hl std">,</span> <span class="hl str">"Collomia grandiflorra"</span><span class="hl std">,</span> <span class="hl str">"Abies magnificaa"</span><span class="hl std">,</span>
<span class="hl str">"Rosa california"</span><span class="hl std">,</span> <span class="hl str">"Datura wrighti"</span><span class="hl std">,</span> <span class="hl str">"Mimulus bicolour"</span><span class="hl std">,</span> <span class="hl str">"Nicotiana glauca"</span><span class="hl std">,</span>
<span class="hl str">"Maddia sativa"</span><span class="hl std">,</span> <span class="hl str">"Bartlettia scapposa"</span><span class="hl std">)</span>
<span class="hl std">splist_tnrs</span> <span class="hl kwb"><-</span> <span class="hl kwd">tnrs</span><span class="hl std">(</span><span class="hl kwc">query</span> <span class="hl std">= splist,</span> <span class="hl kwc">getpost</span> <span class="hl std">=</span> <span class="hl str">"POST"</span><span class="hl std">,</span> <span class="hl kwc">source</span> <span class="hl std">=</span> <span class="hl str">"iPlant_TNRS"</span><span class="hl std">)</span>
</pre>
</section>
<!-- ############## slide delimiter ############## -->
<section class="slide" id="taxize0">
<h2>Taxize queries 11 different name resolution services</h2>
<pre>Encylopedia of Life
Taxonomic Name Resolution Service
Integrated Taxonomic Information Service
Phylomatic
uBio
Global Names Resolver
Global Names Index
IUCN Red List
Tropicos
Plantminer
Theplantlist dot org
Catalogue of Life
Global Invasive Species Database</pre>
</section>
<section class="slide" id="alt_metrics0">
<h2>Measure research impact in real time</h2>
<img src="images/altmetric.png" height="570" width="1131">
</section>
<!-- ############## slide delimiter ############## -->
<section class="slide" id="alt_metrics">
<br><br>
<h2>Tracking altmetrics - <code>rAltmetric, ALM</code></h2>
<div><pre class="knitr r"><span class="functioncall">library</span>(rAltmetric)</pre></div>
</pre></div><div class="source"><pre class="knitr r"><span class="functioncall">altmetrics</span>(<span class="string">"doi/10.1038/489201a"</span>)
</pre></div><div class="output"><pre class="knitr r">## Altmetrics on: "Future impact: Predicting scientific success" with altmetric_id: 942310 published in Nature.
## provider count
## 1 Facebook 1
## 2 Feeds 10
## 3 Google+ 1
## 4 Cited 179
## 5 Tweets 159
## 6 Accounts 171
</pre>
</div>
</section>
<!-- ############## slide delimiter ############## -->
<section class="slide" id="figshare">
<br><br>
<h2>Sharing unpublished data - <code>(figshare)</code></h2>
<div>
<h3 class="figshare">Using fig<b>share</b>'s <a href="http://api.figshare.com/docs/">API</a> it is now possible to share figures, data and any other object generated in <code>R</code> directly to any figshare account.</h3><br>
<pre class="knitr r"><span class="functioncall">library</span><span class="keyword">(rfigshare)</span>
<span class="functioncall">fs_auth</span><span class="keyword">()</span>
<span class="hl com"># uses api keys to login</span>
<span class="keyword">id</span> <span class="hl kwb"><-</span> <span class="functioncall">fs_create</span><span class="keyword">()</span>
<span class="functioncall">fs_upload</span><span class="keyword">(id, r_objects)</span>
</pre>
</div>
</section>
<!-- ############## slide delimiter ############## -->
<section class="slide" id="ropensci">
<div>
<br><br><br>
<hgroup>
<img src="images/antweb_main.jpg">
<center><h3><span style="color:#34495E; font-size:70px">A guide to using the Antweb package</span><i class="ss-globe"></i></h3><br><br>
<h4> <a href="https://twitter.com/_inundata">@_inundata</a> <br>
ropensci.github.io/antweb-guide
</h4>
</center>
</hgroup>
</div>
</section>
<!-- ############## slide delimiter ############## -->
<!--begin.rcode options, echo = FALSE
knitr::opts_chunk$set(
comment = " ",
error = FALSE,
tidy = FALSE)
end.rcode-->
<section class="slide" id="installing_package">
<br><br>
<h2>Installing the package</h2>
<!--begin.rcode installing, eval = FALSE, message = FALSE, fig.align = 'center', cache = TRUE
install.packages("AntWeb", dependencies = TRUE)
# Requires R version 3.0.1 or higher
end.rcode-->
</section>
<section class="slide" id="AntWeb_sources">
<br><br>
<h2>Unique taxa in the data source</h2>
<!--begin.rcode families, message = FALSE, fig.align = 'center', cache = TRUE
library(AntWeb)
families <- aw_unique(rank = "subfamily")
head(families)
nrow(families)
end.rcode-->
</section>
<section class="slide" id="AntWeb_sources1">
<br><br>
<h2>Unique taxa in the data source</h2>
<!--begin.rcode genera, message = FALSE, fig.align = 'center', cache = TRUE
library(AntWeb)
genera <- aw_unique(rank = "genus")
head(genera)
nrow(genera)
end.rcode-->
</section>
<section class="slide" id="AntWeb_sources2">
<br><br>
<h2>Unique taxa in the data source</h2>
<!--begin.rcode species, message = FALSE, fig.align = 'center', cache = TRUE
library(AntWeb)
species <- aw_unique(rank = "species")
head(species)
nrow(species)
end.rcode-->
</section>
<section class="slide" id="data_by_code">
<br><br>
<h2>Download data by any catalog number</h2>
<!--begin.rcode catalog_number, message = FALSE, fig.align = 'center', cache = TRUE
data_by_code <- aw_code(occurrenceid = "CAS:ANTWEB:alas188691")
data_by_code
end.rcode-->
</section>
<section class="slide" id="crematogaster">
<br><br>
<h2>Download data with bounding boxes</h2>
<!--begin.rcode crematogaster, message = FALSE, eval = FALSE, fig.align = 'center', cache = TRUE
bbox <- "6.7117,-87.7867,13.2595,-76.9277" # Central America
crematogaster <- aw_data_all(genus = "crematogaster", bbox = bbox)
aw_map(crematogaster)
end.rcode-->
<a href="AntWeb_species_map.html"><img src="images/crematogaster_ca.png"></a>
</section>
<section class="slide" id="all_data">
<br><br>
<h2>Download all available data on a taxonomic group</h2>
<!--begin.rcode all_data_retrive, message = FALSE, eval = FALSE, fig.align = 'center', cache = TRUE
crematogaster <- aw_data_all(genus = "crematogaster", georeferenced = TRUE)
end.rcode-->
<!--begin.rcode load_data, echo = FALSE, message = FALSE, fig.align = 'center', cache = TRUE
crematogaster <- read.csv("crem_data.csv")
end.rcode-->
</section>
<section class="slide" id="search_by_coord">
<br><br>
<h2>Search around specific coordinates with an error radius</h2>
<!--begin.rcode coords, message = FALSE, eval = TRUE, fig.align = 'center', cache = TRUE
san_andres <- aw_coords("12.54,-81.72", r = 10)
# Search around the San Andres Island.
nrow(san_andres$data)
end.rcode-->
<img src="images/san_andres.png">
</section>
<section class="slide" id="find_images">
<br><br>
<h2>Find recent images</h2>
<!--begin.rcode images, message = FALSE, eval = TRUE, fig.align = 'center', cache = TRUE
last_five_days <- aw_images(since = 5)
end.rcode-->
</section>
<!-- ############## closing slide ############## -->
<section class="slide" id="outro">
<div>
<hgroup>
<h1>ropensci.org/AntWeb</h1>
<h2><a href="http://GitHub.com/ropensci" style="color:#010101;"> ropensci on GitHub</a><br>
<a href="http://twitter.com/ropensci" style="color:#79cef7;"> @ropensci on Twitter </a><br>
Questions or comments to: karthik dot ram at berkeley dot edu
<h2>To navigate this presentation, type <span style="color:#e64b65;font-style:bold; text-shadow: none"><b>M</a></span> to see all slides. <br><b><span style="color:#e64b65;font-style:bold; text-shadow: none"><b>G</a></span> to go to a specific slide</h2>
</hgroup>
</div>
</section>
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