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<h1 class="title toc-ignore">Composite curves and bootstrap C.I.’s via
binning <br> (bin-boot.R)</h1>
</div>
<div id="TOC">
<ul>
<li><a href="#introduction" id="toc-introduction"><span
class="toc-section-number">1</span> Introduction</a></li>
<li><a href="#set-up" id="toc-set-up"><span
class="toc-section-number">2</span> Set up</a></li>
<li><a href="#calculation-preliminaries"
id="toc-calculation-preliminaries"><span
class="toc-section-number">3</span> Calculation preliminaries</a>
<ul>
<li><a href="#initial-steps" id="toc-initial-steps"><span
class="toc-section-number">3.1</span> Initial steps</a></li>
</ul></li>
</ul>
</div>
<div id="introduction" class="section level1" number="1">
<h1><span class="header-section-number">1</span> Introduction</h1>
<p>This script (<code>binboot-curve.R</code>) fits step-like composite
curves, with bootstrapping by site confidence intervals, via binning. As
is the case with other analysis scripts, the script has two parts, a
set-up portion that changes from analysis to analysis, and a computation
part that does not change. This version reads “presampled” data.</p>
</div>
<div id="set-up" class="section level1" number="2">
<h1><span class="header-section-number">2</span> Set up</h1>
<p>The variables <code>queryname</code>, <code>basename</code> and
<code>binname</code> are used to compose the path and filenames for the
presampled data.</p>
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="co"># age-bin averages of influx data</span></span>
<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a><span class="co"># bootstrap-by-site confidence intervals</span></span>
<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a><span class="co"># names</span></span>
<span id="cb1-5"><a href="#cb1-5" aria-hidden="true" tabindex="-1"></a>queryname <span class="ot"><-</span> <span class="st">"v3i"</span> <span class="co"># </span></span>
<span id="cb1-6"><a href="#cb1-6" aria-hidden="true" tabindex="-1"></a>basename <span class="ot"><-</span> <span class="st">"nt2kb"</span> </span>
<span id="cb1-7"><a href="#cb1-7" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-8"><a href="#cb1-8" aria-hidden="true" tabindex="-1"></a><span class="co"># paths for input and output .csv files -- modify as appropriate</span></span>
<span id="cb1-9"><a href="#cb1-9" aria-hidden="true" tabindex="-1"></a>datapath <span class="ot"><-</span> <span class="st">"/Projects/GPWG/GPWGv3/GCDv3Data/v3i/"</span></span>
<span id="cb1-10"><a href="#cb1-10" aria-hidden="true" tabindex="-1"></a>sitelistpath <span class="ot"><-</span> <span class="st">"/Projects/GPWG/GPWGv3/GCDv3Data/v3i/v3i_sitelists/"</span></span>
<span id="cb1-11"><a href="#cb1-11" aria-hidden="true" tabindex="-1"></a>sitelist <span class="ot"><-</span> <span class="st">"v3i_nsa_globe"</span></span>
<span id="cb1-12"><a href="#cb1-12" aria-hidden="true" tabindex="-1"></a>outpath <span class="ot"><-</span> <span class="st">"/Projects/GPWG/GPWGv3/GCDv3Data/v3i/v3i_curves/"</span></span>
<span id="cb1-13"><a href="#cb1-13" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-14"><a href="#cb1-14" aria-hidden="true" tabindex="-1"></a><span class="co"># prebinning bin width</span></span>
<span id="cb1-15"><a href="#cb1-15" aria-hidden="true" tabindex="-1"></a>pbw <span class="ot"><-</span> <span class="dv">10</span></span>
<span id="cb1-16"><a href="#cb1-16" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-17"><a href="#cb1-17" aria-hidden="true" tabindex="-1"></a>pbw_char <span class="ot"><-</span> <span class="fu">as.character</span>(pbw)</span>
<span id="cb1-18"><a href="#cb1-18" aria-hidden="true" tabindex="-1"></a><span class="cf">if</span> (pbw <span class="sc"><</span> <span class="dv">10</span>) pbw_char <span class="ot"><-</span> <span class="fu">paste</span>(<span class="st">"0"</span>, pbw_char, <span class="at">sep=</span><span class="st">""</span>)</span></code></pre></div>
<p>Set the number of bootstrap samples or replications:</p>
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a><span class="co"># number of bootstrap samples/replications</span></span>
<span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a>nreps <span class="ot"><-</span> <span class="dv">200</span></span></code></pre></div>
<p>Specifiy the age-bin centers, and spacing. This version uses 20-year
wide bins, with the first bin centered at -60 yr BP, or 2010 CE, and the
last at 1950 yr BP, or 1 CE.</p>
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a><span class="co"># age bin centers</span></span>
<span id="cb3-2"><a href="#cb3-2" aria-hidden="true" tabindex="-1"></a>abw <span class="ot"><-</span> <span class="dv">20</span> </span>
<span id="cb3-3"><a href="#cb3-3" aria-hidden="true" tabindex="-1"></a>abinbeg <span class="ot"><-</span> <span class="sc">-</span><span class="dv">60</span> </span>
<span id="cb3-4"><a href="#cb3-4" aria-hidden="true" tabindex="-1"></a>abinend <span class="ot"><-</span> <span class="dv">1950</span></span></code></pre></div>
<p>Set array sizes for saving bootstrap results.</p>
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb4-1"><a href="#cb4-1" aria-hidden="true" tabindex="-1"></a><span class="co"># array sizes</span></span>
<span id="cb4-2"><a href="#cb4-2" aria-hidden="true" tabindex="-1"></a>maxrecs <span class="ot"><-</span> <span class="dv">2000</span></span>
<span id="cb4-3"><a href="#cb4-3" aria-hidden="true" tabindex="-1"></a>maxreps <span class="ot"><-</span> <span class="dv">1000</span></span>
<span id="cb4-4"><a href="#cb4-4" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb4-5"><a href="#cb4-5" aria-hidden="true" tabindex="-1"></a><span class="co"># plotting set up</span></span>
<span id="cb4-6"><a href="#cb4-6" aria-hidden="true" tabindex="-1"></a>xmin <span class="ot"><-</span> <span class="dv">0</span>; xmax <span class="ot"><-</span> <span class="dv">2020</span>; ymin1 <span class="ot"><-</span> <span class="sc">-</span><span class="fl">1.0</span>; ymax1 <span class="ot"><-</span> <span class="fl">1.0</span>; ymin2 <span class="ot"><-</span> <span class="sc">-</span><span class="fl">0.5</span>; ymax2 <span class="ot"><-</span> <span class="fl">1.0</span></span>
<span id="cb4-7"><a href="#cb4-7" aria-hidden="true" tabindex="-1"></a>xlim<span class="ot">=</span><span class="fu">c</span>(xmin,xmax); ylim1<span class="ot">=</span><span class="fu">c</span>(ymin1,ymax1); ylim2 <span class="ot"><-</span> <span class="fu">c</span>(ymin2,ymax2)</span>
<span id="cb4-8"><a href="#cb4-8" aria-hidden="true" tabindex="-1"></a>xlab<span class="ot">=</span><span class="st">"Year CE"</span>; xminortick <span class="ot"><-</span> <span class="dv">50</span></span>
<span id="cb4-9"><a href="#cb4-9" aria-hidden="true" tabindex="-1"></a>ylab<span class="ot">=</span><span class="st">"Normalized Anomalies of Transformed Influx"</span></span>
<span id="cb4-10"><a href="#cb4-10" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb4-11"><a href="#cb4-11" aria-hidden="true" tabindex="-1"></a><span class="co"># plot output </span></span>
<span id="cb4-12"><a href="#cb4-12" aria-hidden="true" tabindex="-1"></a>plotout <span class="ot"><-</span> <span class="st">"screen"</span> <span class="co"># "pdf" # "png" # </span></span></code></pre></div>
</div>
<div id="calculation-preliminaries" class="section level1" number="3">
<h1><span class="header-section-number">3</span> Calculation
preliminaries</h1>
<div id="initial-steps" class="section level2" number="3.1">
<h2><span class="header-section-number">3.1</span> Initial steps</h2>
<p>Set various output paths and filenames.</p>
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb5-1"><a href="#cb5-1" aria-hidden="true" tabindex="-1"></a><span class="co"># no changes below here</span></span>
<span id="cb5-2"><a href="#cb5-2" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb5-3"><a href="#cb5-3" aria-hidden="true" tabindex="-1"></a><span class="co"># prebinning file name</span></span>
<span id="cb5-4"><a href="#cb5-4" aria-hidden="true" tabindex="-1"></a>binname <span class="ot"><-</span> <span class="fu">paste</span>(<span class="st">"bw"</span>, pbw_char, <span class="at">sep=</span><span class="st">""</span>)</span>
<span id="cb5-5"><a href="#cb5-5" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb5-6"><a href="#cb5-6" aria-hidden="true" tabindex="-1"></a><span class="co"># presampled/binned files</span></span>
<span id="cb5-7"><a href="#cb5-7" aria-hidden="true" tabindex="-1"></a>csvpath <span class="ot"><-</span> <span class="st">"/Projects/GPWG/GPWGv3/GCDv3Data/v3i/v3i_presamp_csv/"</span></span>
<span id="cb5-8"><a href="#cb5-8" aria-hidden="true" tabindex="-1"></a>csvname <span class="ot"><-</span> <span class="fu">paste</span>(<span class="st">"_presamp_influx_"</span>,basename,<span class="st">"_"</span>,binname,<span class="st">".csv"</span>, <span class="at">sep=</span><span class="st">""</span>)</span>
<span id="cb5-9"><a href="#cb5-9" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb5-10"><a href="#cb5-10" aria-hidden="true" tabindex="-1"></a><span class="co"># site list file</span></span>
<span id="cb5-11"><a href="#cb5-11" aria-hidden="true" tabindex="-1"></a>sitelistfile <span class="ot"><-</span> <span class="fu">paste</span>(sitelistpath, sitelist, <span class="st">".csv"</span>, <span class="at">sep=</span><span class="st">""</span>)</span>
<span id="cb5-12"><a href="#cb5-12" aria-hidden="true" tabindex="-1"></a>sitelistfile</span></code></pre></div>
<pre><code>## [1] "/Projects/GPWG/GPWGv3/GCDv3Data/v3i/v3i_sitelists/v3i_nsa_globe.csv"</code></pre>
<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb7-1"><a href="#cb7-1" aria-hidden="true" tabindex="-1"></a><span class="co"># curve (output) path and file</span></span>
<span id="cb7-2"><a href="#cb7-2" aria-hidden="true" tabindex="-1"></a>curvecsvpath <span class="ot"><-</span> <span class="fu">paste</span>(datapath,queryname,<span class="st">"_curves/"</span>,<span class="at">sep=</span><span class="st">""</span>)</span>
<span id="cb7-3"><a href="#cb7-3" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb7-4"><a href="#cb7-4" aria-hidden="true" tabindex="-1"></a><span class="co"># if output folder does not exist, create it</span></span>
<span id="cb7-5"><a href="#cb7-5" aria-hidden="true" tabindex="-1"></a><span class="fu">dir.create</span>(<span class="fu">file.path</span>(datapath, <span class="fu">paste</span>(queryname,<span class="st">"_curves/"</span>,<span class="at">sep=</span><span class="st">""</span>)), <span class="at">showWarnings=</span><span class="cn">FALSE</span>)</span>
<span id="cb7-6"><a href="#cb7-6" aria-hidden="true" tabindex="-1"></a>curvename <span class="ot"><-</span> <span class="fu">paste</span>(sitelist,<span class="st">"_binboot_"</span>,basename,<span class="st">"_"</span>,binname,<span class="st">"_abw"</span>,<span class="fu">as.character</span>(abw),<span class="st">"_"</span>,</span>
<span id="cb7-7"><a href="#cb7-7" aria-hidden="true" tabindex="-1"></a> <span class="fu">as.character</span>(nreps), <span class="at">sep=</span><span class="st">""</span>)</span>
<span id="cb7-8"><a href="#cb7-8" aria-hidden="true" tabindex="-1"></a>curvefile <span class="ot"><-</span> <span class="fu">paste</span>(curvename, <span class="st">".csv"</span>, <span class="at">sep=</span><span class="st">""</span>)</span>
<span id="cb7-9"><a href="#cb7-9" aria-hidden="true" tabindex="-1"></a><span class="fu">print</span>(curvecsvpath)</span></code></pre></div>
<pre><code>## [1] "/Projects/GPWG/GPWGv3/GCDv3Data/v3i/v3i_curves/"</code></pre>
<div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb9-1"><a href="#cb9-1" aria-hidden="true" tabindex="-1"></a><span class="fu">print</span>(curvename)</span></code></pre></div>
<pre><code>## [1] "v3i_nsa_globe_binboot_nt2kb_bw10_abw20_200"</code></pre>
<div class="sourceCode" id="cb11"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb11-1"><a href="#cb11-1" aria-hidden="true" tabindex="-1"></a><span class="fu">print</span>(curvefile)</span></code></pre></div>
<pre><code>## [1] "v3i_nsa_globe_binboot_nt2kb_bw10_abw20_200.csv"</code></pre>
<p>Code block to implement writing .pdf to file:</p>
<div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb13-1"><a href="#cb13-1" aria-hidden="true" tabindex="-1"></a><span class="co"># .pdf plot of bootstrap iterations</span></span>
<span id="cb13-2"><a href="#cb13-2" aria-hidden="true" tabindex="-1"></a><span class="cf">if</span> (plotout <span class="sc">==</span> <span class="st">"pdf"</span>) {</span>
<span id="cb13-3"><a href="#cb13-3" aria-hidden="true" tabindex="-1"></a>pdffile <span class="ot"><-</span> <span class="fu">paste</span>(curvename, <span class="st">".pdf"</span>, <span class="at">sep=</span><span class="st">""</span>)</span>
<span id="cb13-4"><a href="#cb13-4" aria-hidden="true" tabindex="-1"></a><span class="fu">print</span>(pdffile)</span>
<span id="cb13-5"><a href="#cb13-5" aria-hidden="true" tabindex="-1"></a>}</span>
<span id="cb13-6"><a href="#cb13-6" aria-hidden="true" tabindex="-1"></a><span class="co"># .png plot of bootstrap iterations</span></span>
<span id="cb13-7"><a href="#cb13-7" aria-hidden="true" tabindex="-1"></a><span class="cf">if</span> (plotout <span class="sc">==</span> <span class="st">"png"</span>) {</span>
<span id="cb13-8"><a href="#cb13-8" aria-hidden="true" tabindex="-1"></a> pngfile <span class="ot"><-</span> <span class="fu">paste</span>(curvename, <span class="st">".png"</span>, <span class="at">sep=</span><span class="st">""</span>)</span>
<span id="cb13-9"><a href="#cb13-9" aria-hidden="true" tabindex="-1"></a> <span class="fu">print</span>(pngfile)</span>
<span id="cb13-10"><a href="#cb13-10" aria-hidden="true" tabindex="-1"></a>}</span></code></pre></div>
<p>Read the list of sites to be processed. Note that this is the site
list may contain sites that after transforming and presampling may have
no useful data. Those sites are ignored when the data are read in.</p>
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