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<a href="index.html">About RangeShiftR</a>
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<a href="installing.html">Installing RangeShiftR</a>
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RangeShiftR tutorials
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<a href="overview_0.html">0. General package introduction</a>
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<a href="tutorial_1.html">1. Range expansion</a>
</li>
<li>
<a href="tutorial_2.html">2. Patch connectivity</a>
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<a href="tutorial_3.html">3. Dynamic landscapes & SMS paths</a>
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<a href="tutorial_4.html">4. Evolution of dispersal</a>
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<a href="appendix_tutorial_3.html">Appendix A3. Create dynamic landscapes</a>
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<h1 class="title toc-ignore">Installing RangeShiftR</h1>
</div>
<p>The <code>RangeShiftR</code> package source is publicly released on a
<a
href="https://github.com/RangeShifter/RangeShiftR-package"><em>github</em>
repository</a> as a beta version (it is not available on <em>CRAN</em>).
For further information please contact us under <a
href="mailto:[email protected]">[email protected]</a>.</p>
<div id="install-and-load-required-packages" class="section level1">
<h1>Install and load required packages</h1>
<p>As of yet, <code>RangeShiftR</code> has to be built from source by
the user. This requires the <code>R</code>-version <em>3.6.0</em> or
higher, the packages <code>Rcpp</code> <em>1.0.1</em> or higher and
<code>Rdpack</code> <em>0.7</em> or higher, as well as a functional C++
toolchain (see below). Further, the package <code>devtools</code> is
recommended for an easy installation directly from github.</p>
<p>Install these packages if you don’t have them already.</p>
<pre class="r"><code>library(Rcpp)
library(devtools)
library(Rdpack)</code></pre>
</div>
<div id="compiler-toolchain" class="section level1">
<h1>Compiler toolchain</h1>
<p>In order to build the package from source, we need to set up a
compiler toolchain. This involves installing a suitable C++ compiler and
making it available to <code>R</code>. The exact procedure depends on
your operating system as well as your R installation. Unix-based systems
like Linux or MacOS might have the toolchain set up already along with
the installation of R. You can find detailed instructions here: <a
href="https://thecoatlessprofessor.com/programming/installing-rtools-for-compiled-code-via-rcpp/"
class="uri">https://thecoatlessprofessor.com/programming/installing-rtools-for-compiled-code-via-rcpp/</a></p>
<p>Here is an outline of the information from this website:</p>
<ul>
<li><p>on Windows: the <code>Rtools</code> package on CRAN contains all
the required tools. Find installing instructions for either manual
installation (top) or from within <code>R</code> (further down) on the
website mentioned above. (Tip: Pay extra attention to steps
10/11.)<br />
If you have upgraded to <code>R</code> version <em>4</em>, make sure to
install the corresponding <code>Rtools40</code>. More information here:
<a href="https://cran.r-project.org/bin/windows/Rtools/"
class="uri">https://cran.r-project.org/bin/windows/Rtools/</a> (Tip: Pay
extra attention to the instructions on the bottom of the page, regarding
the path variable.)</p></li>
<li><p>on Linux: Install the standard <code>R</code> development
packages (e.g. on Ubuntu and Debian: <code>r-base-dev</code>).</p></li>
<li><p>on MacOS: Install the Apple Developer Tools <code>Xcode</code>
and the C++ compiler <code>clang7</code>. Find installing instructions
here (for <code>RangeShiftR</code>, the Fortran compiler
<em>gfortran</em> is not needed, so you may leave this step out): <a
href="https://thecoatlessprofessor.com/programming/r-compiler-tools-for-rcpp-on-macos/"
class="uri">https://thecoatlessprofessor.com/programming/r-compiler-tools-for-rcpp-on-macos/</a></p></li>
</ul>
<p>You can check if everything works properly by trying this in your
<code>R</code> terminal:</p>
<pre class="r"><code>Rcpp::evalCpp("2+2")</code></pre>
<pre><code>## [1] 4</code></pre>
<p>If the output is not <em>4</em>, then there is an issue with the
toolchain.</p>
<p>One common reason for this can be that <code>R</code> doesn’t find
the C++ compiler due to an inappropriately set path variable. In this
variable your system stores the paths in which to look for executables
like the compiler (e.g. <em>gcc</em> or <em>clang</em>), in the order in
which they appear in the path variable.</p>
<p>You can try and check if the path to the directory that contains your
compiler is part of the path variable.<br />
For example, on Windows 10: Go to Control panel -> System and
Security -> System -> Advanced system settings -> Environmental
variables.<br />
In the list of system variables, look for ‘Path’. If the correct path is
missing, you can add it manually:<br />
Click ‘edit’ on the ‘Path’ variable -> add the correct variable (The
two standard paths would be ‘C:\Rtools\bin’ and
‘C:\Rtools\mingw_32\bin’; you can also try moving them up on the list so
they get searched first.)</p>
</div>
<div id="install-the-rangeshiftr-package" class="section level1">
<h1>Install the RangeShiftR package</h1>
<p>Now, if all preparations are done and successful, we can install the
package directly from its public repository on <em>github</em>, using
<code>devtools</code>:</p>
<pre class="r"><code>devtools::install_github("https://github.com/RangeShifter/RangeShiftR-pkg", ref = "main", subdir="RangeShiftR")</code></pre>
<p>After successful installation, which can take a few minutes, you can
load and use the package:</p>
<pre class="r"><code>library(RangeShiftR)</code></pre>
<pre><code>## RangeshiftR version 1.0.4 (10.05.2022)
## Copyright (C) 2020-2022 Anne-Kathleen Malchow, Greta Bocedi, Stephen C.F. Palmer, Justin M.J. Travis, Damaris Zurell
##
## This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY.
## You are welcome to redistribute it and/or modify it under certain conditions;
## type 'RangeShiftR_license()' for details.</code></pre>
<p>If questions or problems remain, please let us know via the
<em>github</em> <a
href="https://github.com/RangeShifter/RangeshiftR-tutorials/discussions">Forum</a>.</p>
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<p>Anne-Kathleen Malchow, Greta Bocedi, Steve Palmer, Justin Travis & Damaris Zurell <a href="https://creativecommons.org/licenses/by-nc-nd/4.0/" >(CC BY-NC-ND 4.0)</a>. </p>
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