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<h1 class="title toc-ignore">bin-boot.R</h1>
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<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a><span class="co"># age-bin averages of influx data</span></span>
<span id="cb1-2"><a href="#cb1-2" tabindex="-1"></a><span class="co"># bootstrap-by-site confidence intervals</span></span>
<span id="cb1-3"><a href="#cb1-3" tabindex="-1"></a></span>
<span id="cb1-4"><a href="#cb1-4" tabindex="-1"></a><span class="co"># names</span></span>
<span id="cb1-5"><a href="#cb1-5" 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" tabindex="-1"></a>basename <span class="ot"><-</span> <span class="st">"nt2kb"</span> </span>
<span id="cb1-7"><a href="#cb1-7" tabindex="-1"></a></span>
<span id="cb1-8"><a href="#cb1-8" 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" 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" 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" tabindex="-1"></a>sitelist <span class="ot"><-</span> <span class="st">"v3i_nsa_globe"</span></span>
<span id="cb1-12"><a href="#cb1-12" 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" tabindex="-1"></a></span>
<span id="cb1-14"><a href="#cb1-14" tabindex="-1"></a><span class="co"># prebinning bin width</span></span>
<span id="cb1-15"><a href="#cb1-15" tabindex="-1"></a>pbw <span class="ot"><-</span> <span class="dv">10</span></span>
<span id="cb1-16"><a href="#cb1-16" tabindex="-1"></a></span>
<span id="cb1-17"><a href="#cb1-17" 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" 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>
<span id="cb1-19"><a href="#cb1-19" tabindex="-1"></a></span>
<span id="cb1-20"><a href="#cb1-20" tabindex="-1"></a><span class="co"># number of bootstrap samples/replications</span></span>
<span id="cb1-21"><a href="#cb1-21" tabindex="-1"></a>nreps <span class="ot"><-</span> <span class="dv">200</span></span>
<span id="cb1-22"><a href="#cb1-22" tabindex="-1"></a></span>
<span id="cb1-23"><a href="#cb1-23" tabindex="-1"></a><span class="co"># age bin centers</span></span>
<span id="cb1-24"><a href="#cb1-24" tabindex="-1"></a>abw <span class="ot"><-</span> <span class="dv">20</span> </span>
<span id="cb1-25"><a href="#cb1-25" tabindex="-1"></a>abinbeg <span class="ot"><-</span> <span class="sc">-</span><span class="dv">60</span> </span>
<span id="cb1-26"><a href="#cb1-26" tabindex="-1"></a>abinend <span class="ot"><-</span> <span class="dv">1950</span></span>
<span id="cb1-27"><a href="#cb1-27" tabindex="-1"></a></span>
<span id="cb1-28"><a href="#cb1-28" tabindex="-1"></a><span class="co"># array sizes</span></span>
<span id="cb1-29"><a href="#cb1-29" tabindex="-1"></a>maxrecs <span class="ot"><-</span> <span class="dv">2000</span></span>
<span id="cb1-30"><a href="#cb1-30" tabindex="-1"></a>maxreps <span class="ot"><-</span> <span class="dv">1000</span></span>
<span id="cb1-31"><a href="#cb1-31" tabindex="-1"></a></span>
<span id="cb1-32"><a href="#cb1-32" tabindex="-1"></a><span class="co"># plotting set up</span></span>
<span id="cb1-33"><a href="#cb1-33" 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">5.0</span>; ymax2 <span class="ot"><-</span> <span class="fl">5.0</span></span>
<span id="cb1-34"><a href="#cb1-34" 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="cb1-35"><a href="#cb1-35" 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="cb1-36"><a href="#cb1-36" tabindex="-1"></a>ylab<span class="ot">=</span><span class="st">"Normalized Anomalies of Transformed Influx"</span></span>
<span id="cb1-37"><a href="#cb1-37" tabindex="-1"></a></span>
<span id="cb1-38"><a href="#cb1-38" tabindex="-1"></a><span class="co"># plot output </span></span>
<span id="cb1-39"><a href="#cb1-39" tabindex="-1"></a>plotout <span class="ot"><-</span> <span class="st">"screen"</span> <span class="co"># "pdf" # </span></span>
<span id="cb1-40"><a href="#cb1-40" tabindex="-1"></a></span>
<span id="cb1-41"><a href="#cb1-41" tabindex="-1"></a><span class="co"># no changes below here</span></span>
<span id="cb1-42"><a href="#cb1-42" tabindex="-1"></a></span>
<span id="cb1-43"><a href="#cb1-43" tabindex="-1"></a><span class="co"># prebinning file name</span></span>
<span id="cb1-44"><a href="#cb1-44" tabindex="-1"></a>binname <span class="ot"><-</span> <span class="fu">paste</span>(<span class="st">"pbw"</span>, pbw_char, <span class="at">sep=</span><span class="st">""</span>)</span>
<span id="cb1-45"><a href="#cb1-45" tabindex="-1"></a></span>
<span id="cb1-46"><a href="#cb1-46" tabindex="-1"></a><span class="co"># presampled/binned files</span></span>
<span id="cb1-47"><a href="#cb1-47" tabindex="-1"></a>csvpath <span class="ot"><-</span> <span class="st">"/Projects/GPWG/GPWGv3/GCDv3Data/v3i/v3i_presamp_csv/"</span></span>
<span id="cb1-48"><a href="#cb1-48" 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="cb1-49"><a href="#cb1-49" tabindex="-1"></a></span>
<span id="cb1-50"><a href="#cb1-50" tabindex="-1"></a><span class="co"># site list file</span></span>
<span id="cb1-51"><a href="#cb1-51" 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="cb1-52"><a href="#cb1-52" tabindex="-1"></a>sitelistfile</span>
<span id="cb1-53"><a href="#cb1-53" tabindex="-1"></a></span>
<span id="cb1-54"><a href="#cb1-54" tabindex="-1"></a><span class="co"># curve (output) path and file</span></span>
<span id="cb1-55"><a href="#cb1-55" 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="cb1-56"><a href="#cb1-56" tabindex="-1"></a></span>
<span id="cb1-57"><a href="#cb1-57" tabindex="-1"></a><span class="co"># if output folder does not exist, create it</span></span>
<span id="cb1-58"><a href="#cb1-58" 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="cb1-59"><a href="#cb1-59" 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="cb1-60"><a href="#cb1-60" tabindex="-1"></a> <span class="fu">as.character</span>(nreps), <span class="at">sep=</span><span class="st">""</span>)</span>
<span id="cb1-61"><a href="#cb1-61" 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="cb1-62"><a href="#cb1-62" tabindex="-1"></a><span class="fu">print</span>(curvecsvpath)</span>
<span id="cb1-63"><a href="#cb1-63" tabindex="-1"></a><span class="fu">print</span>(curvename)</span>
<span id="cb1-64"><a href="#cb1-64" tabindex="-1"></a><span class="fu">print</span>(curvefile)</span>
<span id="cb1-65"><a href="#cb1-65" tabindex="-1"></a></span>
<span id="cb1-66"><a href="#cb1-66" tabindex="-1"></a><span class="co"># .pdf plot of bootstrap iterations</span></span>
<span id="cb1-67"><a href="#cb1-67" tabindex="-1"></a><span class="cf">if</span> (plotout <span class="sc">==</span> <span class="st">"pdf"</span>) {</span>
<span id="cb1-68"><a href="#cb1-68" 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="cb1-69"><a href="#cb1-69" tabindex="-1"></a><span class="fu">print</span>(pdffile)</span>
<span id="cb1-70"><a href="#cb1-70" tabindex="-1"></a>}</span>
<span id="cb1-71"><a href="#cb1-71" tabindex="-1"></a><span class="co"># .png plot of bootstrap iterations</span></span>
<span id="cb1-72"><a href="#cb1-72" tabindex="-1"></a><span class="cf">if</span> (plotout <span class="sc">==</span> <span class="st">"png"</span>) {</span>
<span id="cb1-73"><a href="#cb1-73" 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="cb1-74"><a href="#cb1-74" tabindex="-1"></a> <span class="fu">print</span>(pngfile)</span>
<span id="cb1-75"><a href="#cb1-75" tabindex="-1"></a>}</span>
<span id="cb1-76"><a href="#cb1-76" tabindex="-1"></a></span>
<span id="cb1-77"><a href="#cb1-77" tabindex="-1"></a></span>
<span id="cb1-78"><a href="#cb1-78" tabindex="-1"></a><span class="co"># read the list of sites</span></span>
<span id="cb1-79"><a href="#cb1-79" tabindex="-1"></a>sites <span class="ot"><-</span> <span class="fu">read.csv</span>(sitelistfile)</span>
<span id="cb1-80"><a href="#cb1-80" tabindex="-1"></a><span class="fu">head</span>(sites)</span>
<span id="cb1-81"><a href="#cb1-81" tabindex="-1"></a>ns <span class="ot"><-</span> <span class="fu">length</span>(sites[,<span class="dv">1</span>]) <span class="co">#length(sites$ID_SITE)</span></span>
<span id="cb1-82"><a href="#cb1-82" tabindex="-1"></a>ns</span>
<span id="cb1-83"><a href="#cb1-83" tabindex="-1"></a></span>
<span id="cb1-84"><a href="#cb1-84" tabindex="-1"></a><span class="co"># arrays for data and fitted values</span></span>
<span id="cb1-85"><a href="#cb1-85" tabindex="-1"></a>age <span class="ot"><-</span> <span class="fu">matrix</span>(<span class="cn">NA</span>, <span class="at">ncol=</span>ns, <span class="at">nrow=</span>maxrecs)</span>
<span id="cb1-86"><a href="#cb1-86" tabindex="-1"></a>influx <span class="ot"><-</span> <span class="fu">matrix</span>(<span class="cn">NA</span>, <span class="at">ncol=</span>ns, <span class="at">nrow=</span>maxrecs)</span>
<span id="cb1-87"><a href="#cb1-87" tabindex="-1"></a>nsamples <span class="ot"><-</span> <span class="fu">rep</span>(<span class="dv">0</span>, maxrecs)</span>
<span id="cb1-88"><a href="#cb1-88" tabindex="-1"></a></span>
<span id="cb1-89"><a href="#cb1-89" tabindex="-1"></a><span class="co"># age bin centers</span></span>
<span id="cb1-90"><a href="#cb1-90" tabindex="-1"></a>abinage <span class="ot"><-</span> <span class="fu">seq</span>(abinbeg, abinend, <span class="at">by=</span>abw)</span>
<span id="cb1-91"><a href="#cb1-91" tabindex="-1"></a>abinage</span>
<span id="cb1-92"><a href="#cb1-92" tabindex="-1"></a>YearCE <span class="ot"><-</span> <span class="dv">1950</span> <span class="sc">-</span> abinage</span>
<span id="cb1-93"><a href="#cb1-93" tabindex="-1"></a>YearCE</span>
<span id="cb1-94"><a href="#cb1-94" tabindex="-1"></a></span>
<span id="cb1-95"><a href="#cb1-95" tabindex="-1"></a><span class="co"># generate YearCE with a 1/2 time-step (abw) offset so step-plot type "s" registers correctly</span></span>
<span id="cb1-96"><a href="#cb1-96" tabindex="-1"></a>pltYearCE <span class="ot"><-</span> YearCE <span class="sc">+</span> (abw<span class="sc">/</span><span class="dv">2</span>)</span>
<span id="cb1-97"><a href="#cb1-97" tabindex="-1"></a>pltYearCE</span>
<span id="cb1-98"><a href="#cb1-98" tabindex="-1"></a></span>
<span id="cb1-99"><a href="#cb1-99" tabindex="-1"></a><span class="co"># array for bootstrap results</span></span>
<span id="cb1-100"><a href="#cb1-100" tabindex="-1"></a>min_age <span class="ot"><-</span> abinbeg<span class="sc">-</span>(abw<span class="sc">/</span><span class="dv">2</span>); max_age <span class="ot"><-</span> abinend <span class="co">#+(abw/2)</span></span>
<span id="cb1-101"><a href="#cb1-101" tabindex="-1"></a>nbins <span class="ot"><-</span> <span class="fu">length</span>(abinage)</span>
<span id="cb1-102"><a href="#cb1-102" tabindex="-1"></a>yfit <span class="ot"><-</span> <span class="fu">matrix</span>(<span class="cn">NA</span>, <span class="at">nrow=</span>nbins, <span class="at">ncol=</span>maxreps)</span>
<span id="cb1-103"><a href="#cb1-103" tabindex="-1"></a></span>
<span id="cb1-104"><a href="#cb1-104" tabindex="-1"></a><span class="co"># arrays for sample number tracking</span></span>
<span id="cb1-105"><a href="#cb1-105" tabindex="-1"></a>ndec <span class="ot"><-</span> <span class="fu">matrix</span>(<span class="dv">0</span>, <span class="at">ncol=</span>nbins, <span class="at">nrow=</span>ns)</span>
<span id="cb1-106"><a href="#cb1-106" tabindex="-1"></a>ndec_tot <span class="ot"><-</span> <span class="fu">rep</span>(<span class="dv">0</span>, nbins)</span>
<span id="cb1-107"><a href="#cb1-107" tabindex="-1"></a><span class="co">#xspan <- rep(0, ntarg)</span></span>
<span id="cb1-108"><a href="#cb1-108" tabindex="-1"></a>ninwin <span class="ot"><-</span> <span class="fu">matrix</span>(<span class="dv">0</span>, <span class="at">ncol=</span>nbins, <span class="at">nrow=</span>ns)</span>
<span id="cb1-109"><a href="#cb1-109" tabindex="-1"></a>ninwin_tot <span class="ot"><-</span> <span class="fu">rep</span>(<span class="dv">0</span>, nbins)</span>
<span id="cb1-110"><a href="#cb1-110" tabindex="-1"></a></span>
<span id="cb1-111"><a href="#cb1-111" tabindex="-1"></a></span>
<span id="cb1-112"><a href="#cb1-112" tabindex="-1"></a></span>
<span id="cb1-113"><a href="#cb1-113" tabindex="-1"></a><span class="co"># read and store the presample (binned) files as matrices of ages and influx values</span></span>
<span id="cb1-114"><a href="#cb1-114" tabindex="-1"></a>ii <span class="ot"><-</span> <span class="dv">0</span></span>
<span id="cb1-115"><a href="#cb1-115" tabindex="-1"></a><span class="cf">for</span> (i <span class="cf">in</span> <span class="dv">1</span><span class="sc">:</span>ns) {</span>
<span id="cb1-116"><a href="#cb1-116" tabindex="-1"></a> <span class="co">#i <- 1</span></span>
<span id="cb1-117"><a href="#cb1-117" tabindex="-1"></a> sitenum <span class="ot"><-</span> sites[i,<span class="dv">1</span>] <span class="co"># sites$ID_SITE[i]</span></span>
<span id="cb1-118"><a href="#cb1-118" tabindex="-1"></a> <span class="fu">print</span>(sitenum)</span>
<span id="cb1-119"><a href="#cb1-119" tabindex="-1"></a> siteidchar <span class="ot"><-</span> <span class="fu">as.character</span>(sitenum)</span>
<span id="cb1-120"><a href="#cb1-120" tabindex="-1"></a> <span class="cf">if</span> (sitenum <span class="sc">>=</span> <span class="dv">1</span>) siteid <span class="ot"><-</span> <span class="fu">paste</span>(<span class="st">"000"</span>, siteidchar, <span class="at">sep=</span><span class="st">""</span>)</span>
<span id="cb1-121"><a href="#cb1-121" tabindex="-1"></a> <span class="cf">if</span> (sitenum <span class="sc">>=</span> <span class="dv">10</span>) siteid <span class="ot"><-</span> <span class="fu">paste</span>(<span class="st">"00"</span>, siteidchar, <span class="at">sep=</span><span class="st">""</span>)</span>
<span id="cb1-122"><a href="#cb1-122" tabindex="-1"></a> <span class="cf">if</span> (sitenum <span class="sc">>=</span> <span class="dv">100</span>) siteid <span class="ot"><-</span> <span class="fu">paste</span>(<span class="st">"0"</span>, siteidchar, <span class="at">sep=</span><span class="st">""</span>)</span>
<span id="cb1-123"><a href="#cb1-123" tabindex="-1"></a> <span class="cf">if</span> (sitenum <span class="sc">>=</span> <span class="dv">1000</span>) siteid <span class="ot"><-</span> <span class="fu">paste</span>( siteidchar, <span class="at">sep=</span><span class="st">""</span>)</span>
<span id="cb1-124"><a href="#cb1-124" tabindex="-1"></a> </span>
<span id="cb1-125"><a href="#cb1-125" tabindex="-1"></a> inputfile <span class="ot"><-</span> <span class="fu">paste</span>(csvpath, siteid, csvname, <span class="at">sep=</span><span class="st">""</span>)</span>
<span id="cb1-126"><a href="#cb1-126" tabindex="-1"></a> <span class="fu">print</span>(inputfile)</span>
<span id="cb1-127"><a href="#cb1-127" tabindex="-1"></a> </span>
<span id="cb1-128"><a href="#cb1-128" tabindex="-1"></a> <span class="cf">if</span> (<span class="fu">file.exists</span>(inputfile)) {</span>
<span id="cb1-129"><a href="#cb1-129" tabindex="-1"></a> indata <span class="ot"><-</span> <span class="fu">read.csv</span>(inputfile)</span>
<span id="cb1-130"><a href="#cb1-130" tabindex="-1"></a> nsamp <span class="ot"><-</span> <span class="fu">length</span>(indata<span class="sc">$</span>age) <span class="co"># </span></span>
<span id="cb1-131"><a href="#cb1-131" tabindex="-1"></a> <span class="cf">if</span> (nsamp <span class="sc">></span> <span class="dv">0</span>) {</span>
<span id="cb1-132"><a href="#cb1-132" tabindex="-1"></a> ii <span class="ot"><-</span> ii<span class="sc">+</span><span class="dv">1</span></span>
<span id="cb1-133"><a href="#cb1-133" tabindex="-1"></a> age[<span class="dv">1</span><span class="sc">:</span>nsamp,ii] <span class="ot"><-</span> indata<span class="sc">$</span>age <span class="co"># </span></span>
<span id="cb1-134"><a href="#cb1-134" tabindex="-1"></a> influx[<span class="dv">1</span><span class="sc">:</span>nsamp,ii] <span class="ot"><-</span> indata<span class="sc">$</span>norman <span class="co"># indata$zt # </span></span>
<span id="cb1-135"><a href="#cb1-135" tabindex="-1"></a> nsamples[ii] <span class="ot"><-</span> nsamp</span>
<span id="cb1-136"><a href="#cb1-136" tabindex="-1"></a> }</span>
<span id="cb1-137"><a href="#cb1-137" tabindex="-1"></a> }</span>
<span id="cb1-138"><a href="#cb1-138" tabindex="-1"></a>}</span>
<span id="cb1-139"><a href="#cb1-139" tabindex="-1"></a>nsites <span class="ot"><-</span> ii</span>
<span id="cb1-140"><a href="#cb1-140" tabindex="-1"></a></span>
<span id="cb1-141"><a href="#cb1-141" tabindex="-1"></a><span class="co"># number of sites with data</span></span>
<span id="cb1-142"><a href="#cb1-142" tabindex="-1"></a>nsites</span>
<span id="cb1-143"><a href="#cb1-143" tabindex="-1"></a></span>
<span id="cb1-144"><a href="#cb1-144" tabindex="-1"></a><span class="co"># trim samples to age range</span></span>
<span id="cb1-145"><a href="#cb1-145" tabindex="-1"></a>influx[age <span class="sc">>=</span> abinend<span class="sc">+</span>abw<span class="sc">/</span><span class="dv">2</span>] <span class="ot"><-</span> <span class="cn">NA</span></span>
<span id="cb1-146"><a href="#cb1-146" tabindex="-1"></a>age[age <span class="sc">>=</span> abinend<span class="sc">+</span>abw<span class="sc">/</span><span class="dv">2</span>] <span class="ot"><-</span> <span class="cn">NA</span></span>
<span id="cb1-147"><a href="#cb1-147" tabindex="-1"></a></span>
<span id="cb1-148"><a href="#cb1-148" tabindex="-1"></a><span class="co"># censor abs(influx) values > 10</span></span>
<span id="cb1-149"><a href="#cb1-149" tabindex="-1"></a>influx[<span class="fu">abs</span>(influx) <span class="sc">>=</span> <span class="dv">10</span>] <span class="ot"><-</span> <span class="cn">NA</span></span>
<span id="cb1-150"><a href="#cb1-150" tabindex="-1"></a>age[<span class="fu">abs</span>(influx) <span class="sc">>=</span> <span class="dv">10</span>] <span class="ot"><-</span> <span class="cn">NA</span></span>
<span id="cb1-151"><a href="#cb1-151" tabindex="-1"></a></span>
<span id="cb1-152"><a href="#cb1-152" tabindex="-1"></a></span>
<span id="cb1-153"><a href="#cb1-153" tabindex="-1"></a><span class="co"># count number of sites that contributed to each fitted value</span></span>
<span id="cb1-154"><a href="#cb1-154" tabindex="-1"></a>ptm <span class="ot"><-</span> <span class="fu">proc.time</span>()</span>
<span id="cb1-155"><a href="#cb1-155" tabindex="-1"></a><span class="cf">for</span> (i <span class="cf">in</span> <span class="dv">1</span><span class="sc">:</span>nbins) {</span>
<span id="cb1-156"><a href="#cb1-156" tabindex="-1"></a> </span>
<span id="cb1-157"><a href="#cb1-157" tabindex="-1"></a> <span class="cf">for</span> (j <span class="cf">in</span> <span class="dv">1</span><span class="sc">:</span>nsites) {</span>
<span id="cb1-158"><a href="#cb1-158" tabindex="-1"></a> <span class="cf">for</span> (k <span class="cf">in</span> <span class="dv">1</span><span class="sc">:</span>nsamples[j]) {</span>
<span id="cb1-159"><a href="#cb1-159" tabindex="-1"></a> <span class="cf">if</span> (<span class="sc">!</span><span class="fu">is.na</span>(age[k,j])) {</span>
<span id="cb1-160"><a href="#cb1-160" tabindex="-1"></a> ii <span class="ot"><-</span> <span class="fu">as.integer</span>(<span class="fu">ceiling</span>((age[k,j]<span class="sc">-</span>abinbeg<span class="sc">-</span>(abw<span class="sc">/</span><span class="fl">2.0</span>))<span class="sc">/</span>abw))<span class="sc">+</span><span class="dv">1</span></span>
<span id="cb1-161"><a href="#cb1-161" tabindex="-1"></a> <span class="co">#print (c(i,j,k,ii))</span></span>
<span id="cb1-162"><a href="#cb1-162" tabindex="-1"></a> <span class="cf">if</span> (ii <span class="sc">></span> <span class="dv">0</span> <span class="sc">&&</span> ii <span class="sc"><=</span> nbins) {ndec[j,ii] <span class="ot">=</span> <span class="dv">1</span>}</span>
<span id="cb1-163"><a href="#cb1-163" tabindex="-1"></a> <span class="cf">if</span> (age[k,j] <span class="sc">>=</span> abinage[i]<span class="sc">-</span>(abw<span class="sc">/</span><span class="dv">2</span>) <span class="sc">&&</span> age[k,j] <span class="sc"><=</span> abinage[i]<span class="sc">+</span>(abw<span class="sc">/</span><span class="dv">2</span>)) {ninwin[j,i] <span class="ot">=</span> <span class="dv">1</span>}</span>
<span id="cb1-164"><a href="#cb1-164" tabindex="-1"></a> }</span>
<span id="cb1-165"><a href="#cb1-165" tabindex="-1"></a> }</span>
<span id="cb1-166"><a href="#cb1-166" tabindex="-1"></a> }</span>
<span id="cb1-167"><a href="#cb1-167" tabindex="-1"></a> ndec_tot[i] <span class="ot"><-</span> <span class="fu">sum</span>(ndec[,i])</span>
<span id="cb1-168"><a href="#cb1-168" tabindex="-1"></a> ninwin_tot[i] <span class="ot"><-</span> <span class="fu">sum</span>(ninwin[,i])</span>
<span id="cb1-169"><a href="#cb1-169" tabindex="-1"></a> <span class="co"># xspan[i] <- agemax - agemin</span></span>
<span id="cb1-170"><a href="#cb1-170" tabindex="-1"></a>}</span>
<span id="cb1-171"><a href="#cb1-171" tabindex="-1"></a><span class="fu">proc.time</span>() <span class="sc">-</span> ptm</span>
<span id="cb1-172"><a href="#cb1-172" tabindex="-1"></a><span class="fu">head</span>(<span class="fu">cbind</span>(<span class="dv">1950</span> <span class="sc">-</span> abinage, pltYearCE, abinage,ndec_tot,ninwin_tot))</span>
<span id="cb1-173"><a href="#cb1-173" tabindex="-1"></a><span class="fu">tail</span>(<span class="fu">cbind</span>(<span class="dv">1950</span> <span class="sc">-</span> abinage, pltYearCE, abinage,ndec_tot,ninwin_tot))</span>
<span id="cb1-174"><a href="#cb1-174" tabindex="-1"></a></span>
<span id="cb1-175"><a href="#cb1-175" tabindex="-1"></a>ptm <span class="ot"><-</span> <span class="fu">proc.time</span>()</span>
<span id="cb1-176"><a href="#cb1-176" tabindex="-1"></a><span class="co"># 1. reshape matrices into vectors </span></span>
<span id="cb1-177"><a href="#cb1-177" tabindex="-1"></a>x <span class="ot"><-</span> <span class="fu">as.vector</span>(age)</span>
<span id="cb1-178"><a href="#cb1-178" tabindex="-1"></a>y <span class="ot"><-</span> <span class="fu">as.vector</span>(influx)</span>
<span id="cb1-179"><a href="#cb1-179" tabindex="-1"></a>lfdata <span class="ot"><-</span> <span class="fu">data.frame</span>(x,y)</span>
<span id="cb1-180"><a href="#cb1-180" tabindex="-1"></a>lfdata <span class="ot"><-</span> <span class="fu">na.omit</span>(lfdata)</span>
<span id="cb1-181"><a href="#cb1-181" tabindex="-1"></a>lfdata <span class="ot"><-</span> lfdata[lfdata<span class="sc">$</span>x <span class="sc">>=</span> min_age <span class="sc">&</span> lfdata<span class="sc">$</span>x <span class="sc"><</span> max_age, ]</span>
<span id="cb1-182"><a href="#cb1-182" tabindex="-1"></a>x <span class="ot"><-</span> lfdata<span class="sc">$</span>x; y <span class="ot"><-</span> lfdata<span class="sc">$</span>y</span>
<span id="cb1-183"><a href="#cb1-183" tabindex="-1"></a></span>
<span id="cb1-184"><a href="#cb1-184" tabindex="-1"></a><span class="co"># average influx for each age bin</span></span>
<span id="cb1-185"><a href="#cb1-185" tabindex="-1"></a></span>
<span id="cb1-186"><a href="#cb1-186" tabindex="-1"></a>binnum <span class="ot"><-</span> <span class="fu">as.integer</span>(<span class="fu">ceiling</span>((x<span class="sc">-</span>abinbeg<span class="sc">-</span>(abw<span class="sc">/</span><span class="fl">2.0</span>))<span class="sc">/</span>abw))<span class="sc">+</span><span class="dv">1</span></span>
<span id="cb1-187"><a href="#cb1-187" tabindex="-1"></a>binave <span class="ot"><-</span> <span class="fu">tapply</span>(y, binnum, mean)</span>
<span id="cb1-188"><a href="#cb1-188" tabindex="-1"></a>binaveage <span class="ot"><-</span> <span class="fu">tapply</span>(x, binnum, mean)</span>
<span id="cb1-189"><a href="#cb1-189" tabindex="-1"></a>bin_fit_all <span class="ot"><-</span> binave</span>
<span id="cb1-190"><a href="#cb1-190" tabindex="-1"></a>binsubs_all <span class="ot"><-</span> <span class="fu">as.integer</span>(<span class="fu">unlist</span>(<span class="fu">dimnames</span>(binave)))</span>
<span id="cb1-191"><a href="#cb1-191" tabindex="-1"></a></span>
<span id="cb1-192"><a href="#cb1-192" tabindex="-1"></a>binnum; <span class="fu">length</span>(binnum)</span>
<span id="cb1-193"><a href="#cb1-193" tabindex="-1"></a>binave; <span class="fu">length</span>(binave)</span>
<span id="cb1-194"><a href="#cb1-194" tabindex="-1"></a>binaveage; <span class="fu">length</span>(binaveage)</span>
<span id="cb1-195"><a href="#cb1-195" tabindex="-1"></a>bin_fit_all; <span class="fu">length</span>(bin_fit_all)</span>
<span id="cb1-196"><a href="#cb1-196" tabindex="-1"></a>abinage; <span class="fu">length</span>(abinage) </span>
<span id="cb1-197"><a href="#cb1-197" tabindex="-1"></a>pltYearCE; <span class="fu">length</span>(pltYearCE) </span>
<span id="cb1-198"><a href="#cb1-198" tabindex="-1"></a></span>
<span id="cb1-199"><a href="#cb1-199" tabindex="-1"></a><span class="fu">head</span>(<span class="fu">cbind</span>(<span class="dv">1950</span> <span class="sc">-</span> binaveage, pltYearCE[binsubs_all], abinage[binsubs_all], bin_fit_all))</span>
<span id="cb1-200"><a href="#cb1-200" tabindex="-1"></a><span class="fu">tail</span>(<span class="fu">cbind</span>(<span class="dv">1950</span> <span class="sc">-</span> binaveage, pltYearCE[binsubs_all], abinage[binsubs_all], bin_fit_all))</span>
<span id="cb1-201"><a href="#cb1-201" tabindex="-1"></a></span>
<span id="cb1-202"><a href="#cb1-202" tabindex="-1"></a><span class="co"># Bootstrap samples</span></span>
<span id="cb1-203"><a href="#cb1-203" tabindex="-1"></a></span>
<span id="cb1-204"><a href="#cb1-204" tabindex="-1"></a><span class="co"># Step 1 -- Set up to plot individual replications</span></span>
<span id="cb1-205"><a href="#cb1-205" tabindex="-1"></a><span class="cf">if</span> (plotout <span class="sc">==</span> <span class="st">"pdf"</span>) {<span class="fu">pdf</span>(<span class="at">file=</span><span class="fu">paste</span>(curvecsvpath,pdffile,<span class="at">sep=</span><span class="st">""</span>))}</span>
<span id="cb1-206"><a href="#cb1-206" tabindex="-1"></a><span class="cf">if</span> (plotout <span class="sc">==</span> <span class="st">"png"</span>) {<span class="fu">png</span>(<span class="at">file=</span><span class="fu">paste</span>(curvecsvpath,pngfile,<span class="at">sep=</span><span class="st">""</span>), <span class="at">res=</span><span class="dv">150</span>)}</span>
<span id="cb1-207"><a href="#cb1-207" tabindex="-1"></a><span class="fu">plot</span>(<span class="cn">NULL</span>, <span class="at">ylim=</span>ylim2, <span class="at">xlim=</span>xlim, <span class="at">ylab=</span>ylab, <span class="at">xlab=</span>xlab, <span class="at">cex.sub=</span><span class="fl">0.8</span>, <span class="at">sub=</span>curvename, <span class="at">type=</span><span class="st">"n"</span>)</span>
<span id="cb1-208"><a href="#cb1-208" tabindex="-1"></a><span class="fu">axis</span>(<span class="at">side =</span> <span class="dv">1</span>, <span class="at">at =</span> <span class="fu">seq</span>(xmin<span class="sc">-</span>xminortick, xmax<span class="sc">+</span>xminortick, <span class="at">by =</span> xminortick), <span class="at">labels =</span> <span class="cn">FALSE</span>, <span class="at">tcl =</span> <span class="sc">-</span>.<span class="dv">25</span>)</span>
<span id="cb1-209"><a href="#cb1-209" tabindex="-1"></a><span class="fu">axis</span>(<span class="at">side =</span> <span class="dv">1</span>, <span class="at">at =</span> <span class="fu">seq</span>(xmin, xmax, <span class="at">by =</span> xminortick<span class="sc">*</span><span class="dv">5</span>), <span class="at">labels =</span> <span class="cn">FALSE</span>, <span class="at">tcl =</span> <span class="sc">-</span>.<span class="dv">5</span>) </span>
<span id="cb1-210"><a href="#cb1-210" tabindex="-1"></a></span>
<span id="cb1-211"><a href="#cb1-211" tabindex="-1"></a><span class="co"># for debugging step plots</span></span>
<span id="cb1-212"><a href="#cb1-212" tabindex="-1"></a><span class="co"># plot the bin averages -- note pltYearCE offset to center the plot steps</span></span>
<span id="cb1-213"><a href="#cb1-213" tabindex="-1"></a><span class="co"># points(1950 - x, y, pch=16, cex=0.5, col=rgb(0.5,0.5,0.5,0.70))</span></span>
<span id="cb1-214"><a href="#cb1-214" tabindex="-1"></a><span class="co"># lines(bin_fit_all ~ pltYearCE, type="s", col="red", lwd=2)</span></span>
<span id="cb1-215"><a href="#cb1-215" tabindex="-1"></a><span class="co"># points(1950 - abinage, bin_fit_all, col="blue", pch=16, cex=0.5)</span></span>
<span id="cb1-216"><a href="#cb1-216" tabindex="-1"></a></span>
<span id="cb1-217"><a href="#cb1-217" tabindex="-1"></a><span class="fu">set.seed</span>(<span class="dv">10</span>) <span class="co"># do this to get the same sequence of random samples for each run</span></span>
<span id="cb1-218"><a href="#cb1-218" tabindex="-1"></a></span>
<span id="cb1-219"><a href="#cb1-219" tabindex="-1"></a><span class="co"># Step 2 -- Do the bootstrap iterations, and plot each age-bin curve</span></span>
<span id="cb1-220"><a href="#cb1-220" tabindex="-1"></a>ptm <span class="ot"><-</span> <span class="fu">proc.time</span>() <span class="co"># time the loop</span></span>
<span id="cb1-221"><a href="#cb1-221" tabindex="-1"></a><span class="cf">for</span> (i <span class="cf">in</span> <span class="dv">1</span><span class="sc">:</span>nreps) {</span>
<span id="cb1-222"><a href="#cb1-222" tabindex="-1"></a> <span class="fu">print</span>(i)</span>
<span id="cb1-223"><a href="#cb1-223" tabindex="-1"></a> randsitenum <span class="ot"><-</span> <span class="fu">sample</span>(<span class="fu">seq</span>(<span class="dv">1</span><span class="sc">:</span>nsites), nsites, <span class="at">replace=</span><span class="cn">TRUE</span>)</span>
<span id="cb1-224"><a href="#cb1-224" tabindex="-1"></a> <span class="co"># print(head(randsitenum))</span></span>
<span id="cb1-225"><a href="#cb1-225" tabindex="-1"></a> x <span class="ot"><-</span> <span class="fu">as.vector</span>(age[,randsitenum])</span>
<span id="cb1-226"><a href="#cb1-226" tabindex="-1"></a> y <span class="ot"><-</span> <span class="fu">as.vector</span>(influx[,randsitenum])</span>
<span id="cb1-227"><a href="#cb1-227" tabindex="-1"></a> lfdata <span class="ot"><-</span> <span class="fu">data.frame</span>(x,y)</span>
<span id="cb1-228"><a href="#cb1-228" tabindex="-1"></a> lfdata <span class="ot"><-</span> <span class="fu">na.omit</span>(lfdata)</span>
<span id="cb1-229"><a href="#cb1-229" tabindex="-1"></a> lfdata <span class="ot"><-</span> lfdata[lfdata<span class="sc">$</span>x <span class="sc">>=</span> min_age <span class="sc">&</span> lfdata<span class="sc">$</span>x <span class="sc"><</span> max_age, ]</span>
<span id="cb1-230"><a href="#cb1-230" tabindex="-1"></a> x <span class="ot"><-</span> lfdata<span class="sc">$</span>x; y <span class="ot"><-</span> lfdata<span class="sc">$</span>y</span>
<span id="cb1-231"><a href="#cb1-231" tabindex="-1"></a> </span>
<span id="cb1-232"><a href="#cb1-232" tabindex="-1"></a> binnum <span class="ot"><-</span> <span class="fu">as.integer</span>(<span class="fu">ceiling</span>((x<span class="sc">-</span>abinbeg<span class="sc">-</span>(abw<span class="sc">/</span><span class="fl">2.0</span>))<span class="sc">/</span>abw))<span class="sc">+</span><span class="dv">1</span></span>
<span id="cb1-233"><a href="#cb1-233" tabindex="-1"></a> binave <span class="ot"><-</span> <span class="fu">tapply</span>(y, binnum, mean)</span>
<span id="cb1-234"><a href="#cb1-234" tabindex="-1"></a> binaveage <span class="ot"><-</span> <span class="fu">tapply</span>(x, binnum, mean)</span>
<span id="cb1-235"><a href="#cb1-235" tabindex="-1"></a> binsubs <span class="ot"><-</span> <span class="fu">as.integer</span>(<span class="fu">unlist</span>(<span class="fu">dimnames</span>(binave)))</span>
<span id="cb1-236"><a href="#cb1-236" tabindex="-1"></a> <span class="co">#bin_fit <- binave[binsubs]</span></span>
<span id="cb1-237"><a href="#cb1-237" tabindex="-1"></a> yfit[binsubs,i] <span class="ot"><-</span> binave</span>
<span id="cb1-238"><a href="#cb1-238" tabindex="-1"></a> <span class="fu">segments</span>(pltYearCE<span class="fl">-1.9</span><span class="sc">*</span>(abw<span class="sc">/</span><span class="dv">2</span>), yfit[,i], pltYearCE<span class="fl">-0.1</span><span class="sc">*</span>(abw<span class="sc">/</span><span class="dv">2</span>), yfit[,i], <span class="at">lwd=</span><span class="fl">0.6</span>, <span class="at">col=</span><span class="fu">rgb</span>(<span class="fl">0.3</span>,<span class="fl">0.3</span>,<span class="fl">0.3</span>,<span class="fl">0.25</span>))</span>
<span id="cb1-239"><a href="#cb1-239" tabindex="-1"></a>}</span>
<span id="cb1-240"><a href="#cb1-240" tabindex="-1"></a><span class="fu">proc.time</span>() <span class="sc">-</span> ptm <span class="co"># how long?</span></span>
<span id="cb1-241"><a href="#cb1-241" tabindex="-1"></a></span>
<span id="cb1-242"><a href="#cb1-242" tabindex="-1"></a><span class="co"># Step 3 -- Plot the unresampled (initial) area averages</span></span>
<span id="cb1-243"><a href="#cb1-243" tabindex="-1"></a><span class="fu">lines</span>(pltYearCE[binsubs_all], bin_fit_all, <span class="at">type=</span><span class="st">"s"</span>, <span class="at">lwd=</span><span class="dv">1</span>, <span class="at">col=</span><span class="st">"red"</span>)</span>
<span id="cb1-244"><a href="#cb1-244" tabindex="-1"></a><span class="fu">segments</span>(pltYearCE[nbins]<span class="sc">-</span>abw, bin_fit_all[nbins], pltYearCE[nbins], bin_fit_all[nbins], <span class="at">lwd=</span><span class="dv">1</span>, <span class="at">col=</span><span class="st">"red"</span>)</span>
<span id="cb1-245"><a href="#cb1-245" tabindex="-1"></a><span class="co">#points(pltYearCE[binsubs_all], bin_fit_all, pch="_", cex=0.8, col="blue")</span></span>
<span id="cb1-246"><a href="#cb1-246" tabindex="-1"></a></span>
<span id="cb1-247"><a href="#cb1-247" tabindex="-1"></a><span class="co"># Step 4 -- Find and add bootstrap CIs</span></span>
<span id="cb1-248"><a href="#cb1-248" tabindex="-1"></a>yfit975 <span class="ot"><-</span> <span class="fu">apply</span>(yfit, <span class="dv">1</span>, <span class="cf">function</span>(x) <span class="fu">quantile</span>(x,<span class="at">prob=</span><span class="fl">0.975</span>, <span class="at">na.rm=</span>T))</span>
<span id="cb1-249"><a href="#cb1-249" tabindex="-1"></a>yfit025 <span class="ot"><-</span> <span class="fu">apply</span>(yfit, <span class="dv">1</span>, <span class="cf">function</span>(x) <span class="fu">quantile</span>(x,<span class="at">prob=</span><span class="fl">0.025</span>, <span class="at">na.rm=</span>T))</span>
<span id="cb1-250"><a href="#cb1-250" tabindex="-1"></a>yfit50 <span class="ot"><-</span> <span class="fu">apply</span>(yfit, <span class="dv">1</span>, <span class="cf">function</span>(x) <span class="fu">quantile</span>(x,<span class="at">prob=</span><span class="fl">0.500</span>, <span class="at">na.rm=</span>T))</span>
<span id="cb1-251"><a href="#cb1-251" tabindex="-1"></a></span>
<span id="cb1-252"><a href="#cb1-252" tabindex="-1"></a><span class="fu">lines</span>(pltYearCE, yfit975, <span class="at">type=</span><span class="st">"s"</span>, <span class="at">lwd=</span><span class="fl">0.5</span>, <span class="at">col=</span><span class="st">"red"</span>)</span>
<span id="cb1-253"><a href="#cb1-253" tabindex="-1"></a><span class="fu">segments</span>(pltYearCE[nbins]<span class="sc">-</span>abw, yfit975[nbins], pltYearCE[nbins], yfit975[nbins], <span class="at">lwd=</span><span class="dv">1</span>, <span class="at">col=</span><span class="st">"red"</span>)</span>
<span id="cb1-254"><a href="#cb1-254" tabindex="-1"></a><span class="fu">lines</span>(pltYearCE, yfit025, <span class="at">type=</span><span class="st">"s"</span>, <span class="at">lwd=</span><span class="fl">0.5</span>, <span class="at">col=</span><span class="st">"red"</span>)</span>
<span id="cb1-255"><a href="#cb1-255" tabindex="-1"></a><span class="fu">segments</span>(pltYearCE[nbins]<span class="sc">-</span>abw, yfit025[nbins], pltYearCE[nbins], yfit025[nbins], <span class="at">lwd=</span><span class="dv">1</span>, <span class="at">col=</span><span class="st">"red"</span>)</span>
<span id="cb1-256"><a href="#cb1-256" tabindex="-1"></a></span>
<span id="cb1-257"><a href="#cb1-257" tabindex="-1"></a><span class="cf">if</span> (plotout <span class="sc">==</span> <span class="st">"pdf"</span>) {<span class="fu">dev.off</span>()}</span>
<span id="cb1-258"><a href="#cb1-258" tabindex="-1"></a><span class="cf">if</span> (plotout <span class="sc">==</span> <span class="st">"png"</span>) {<span class="fu">dev.off</span>()}</span>
<span id="cb1-259"><a href="#cb1-259" tabindex="-1"></a>curveout <span class="ot"><-</span> <span class="fu">data.frame</span>(<span class="fu">cbind</span>(abinage, <span class="dv">1950</span><span class="sc">-</span>abinage, bin_fit_all, yfit975, yfit025, ndec_tot, ninwin_tot))</span>
<span id="cb1-260"><a href="#cb1-260" tabindex="-1"></a><span class="fu">colnames</span>(curveout) <span class="ot"><-</span> <span class="fu">c</span>(<span class="st">"age"</span>, <span class="st">"YearCE"</span>, <span class="st">"bin_ave"</span>, <span class="st">"cu95"</span>, <span class="st">"cl95"</span>, <span class="st">"nsites"</span>, <span class="st">"ninwin"</span>)</span>
<span id="cb1-261"><a href="#cb1-261" tabindex="-1"></a>outputfile <span class="ot"><-</span> <span class="fu">paste</span>(curvecsvpath, curvefile, <span class="at">sep=</span><span class="st">""</span>)</span>
<span id="cb1-262"><a href="#cb1-262" tabindex="-1"></a><span class="fu">write.table</span>(curveout, outputfile, <span class="at">col.names=</span><span class="cn">TRUE</span>, <span class="at">row.names=</span><span class="cn">FALSE</span>, <span class="at">sep=</span><span class="st">","</span>)</span></code></pre></div>
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