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<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN" "http://www.w3.org/TR/REC-html40/loose.dtd">
<html>
<head>
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<pre class="Rcode">
<span class="comment">## Estimate variogram</span>
<span id="sym1" class="symbol" onmouseover='showVariable("mdata", symIdentifiers);' onmouseout='hideVariable("mdata", symIdentifiers);'>mdata</span> <span class="assignement"><-</span> <a href="base/.readRDS.html">.readRDS</a><span class="keyword">(</span><span class="string">"monitor-data/monitor-subset.rds"</span><span class="keyword">)</span>
<span id="sym2" class="symbol" onmouseover='showVariable("mdata", symIdentifiers);' onmouseout='hideVariable("mdata", symIdentifiers);'>mdata</span><span class="keyword">$</span><span id="sym3" class="symbol" onmouseover='showVariable("LATITUDE", symIdentifiers);' onmouseout='hideVariable("LATITUDE", symIdentifiers);'>LATITUDE</span> <span class="assignement"><-</span> NULL
<span id="sym4" class="symbol" onmouseover='showVariable("mdata", symIdentifiers);' onmouseout='hideVariable("mdata", symIdentifiers);'>mdata</span><span class="keyword">$</span><span id="sym5" class="symbol" onmouseover='showVariable("LONGITUDE", symIdentifiers);' onmouseout='hideVariable("LONGITUDE", symIdentifiers);'>LONGITUDE</span> <span class="assignement"><-</span> NULL
<span id="sym6" class="symbol" onmouseover='showVariable("spmdata", symIdentifiers);' onmouseout='hideVariable("spmdata", symIdentifiers);'>spmdata</span> <span class="assignement"><-</span> <a href="base/split.html">split</a><span class="keyword">(</span><span id="sym7" class="symbol" onmouseover='showVariable("mdata", symIdentifiers);' onmouseout='hideVariable("mdata", symIdentifiers);'>mdata</span><span class="keyword">,</span> <span id="sym8" class="symbol" onmouseover='showVariable("mdata", symIdentifiers);' onmouseout='hideVariable("mdata", symIdentifiers);'>mdata</span><span class="keyword">$</span><span id="sym9" class="symbol" onmouseover='showVariable("SITEPOC", symIdentifiers);' onmouseout='hideVariable("SITEPOC", symIdentifiers);'>SITEPOC</span><span class="keyword">)</span>
<span id="sym10" class="symbol" onmouseover='showVariable("index.names", symIdentifiers);' onmouseout='hideVariable("index.names", symIdentifiers);'>index.names</span> <span class="assignement"><-</span> <a href="base/names.html">names</a><span class="keyword">(</span><span id="sym11" class="symbol" onmouseover='showVariable("spmdata", symIdentifiers);' onmouseout='hideVariable("spmdata", symIdentifiers);'>spmdata</span><span class="keyword">)</span>
<span id="sym12" class="symbol" onmouseover='showVariable("all.dates", symIdentifiers);' onmouseout='hideVariable("all.dates", symIdentifiers);'>all.dates</span> <span class="assignement"><-</span> <a href="base/seq.html">seq</a><span class="keyword">(</span><a href="base/as.Date.html">as.Date</a><span class="keyword">(</span><span class="string">"2000-01-01"</span><span class="keyword">)</span><span class="keyword">,</span> <a href="base/as.Date.html">as.Date</a><span class="keyword">(</span><span class="string">"2006-12-31"</span><span class="keyword">)</span><span class="keyword">,</span> <span class="string">"day"</span><span class="keyword">)</span>
<span id="sym13" class="symbol" onmouseover='showVariable("dateDF", symIdentifiers);' onmouseout='hideVariable("dateDF", symIdentifiers);'>dateDF</span> <span class="assignement"><-</span> <a href="base/data.frame.html">data.frame</a><span class="keyword">(</span><span class="argument">DATE</span> <span class="argument">=</span> <span id="sym14" class="symbol" onmouseover='showVariable("all.dates", symIdentifiers);' onmouseout='hideVariable("all.dates", symIdentifiers);'>all.dates</span><span class="keyword">)</span>
<span id="sym15" class="symbol" onmouseover='showVariable("pollutants", symIdentifiers);' onmouseout='hideVariable("pollutants", symIdentifiers);'>pollutants</span> <span class="assignement"><-</span> <a href="base/c.html">c</a><span class="keyword">(</span><span class="string">"SULFATE"</span><span class="keyword">,</span> <span class="string">"NITRATE"</span><span class="keyword">,</span> <span class="string">"silicon"</span><span class="keyword">,</span> <span class="string">"Elemental_Carbon"</span><span class="keyword">,</span>
<span class="string">"OC_K14"</span><span class="keyword">,</span> <span class="string">"Sodium_Ion"</span><span class="keyword">,</span> <span class="string">"AMMONIUM"</span><span class="keyword">)</span>
<span id="sym16" class="symbol" onmouseover='showVariable("ad", symIdentifiers);' onmouseout='hideVariable("ad", symIdentifiers);'>ad</span> <span class="assignement"><-</span> <a href="base/lapply.html">lapply</a><span class="keyword">(</span><span id="sym17" class="symbol" onmouseover='showVariable("spmdata", symIdentifiers);' onmouseout='hideVariable("spmdata", symIdentifiers);'>spmdata</span><span class="keyword">,</span> <span class="keyword">function</span><span class="keyword">(</span><span class="formalargs">x</span><span class="keyword">)</span> <span class="keyword">{</span>
<span id="sym18" class="symbol" onmouseover='showVariable("m", symIdentifiers);' onmouseout='hideVariable("m", symIdentifiers);'>m</span> <span class="assignement"><-</span> <a href="base/merge.html">merge</a><span class="keyword">(</span><span id="sym19" class="symbol" onmouseover='showVariable("dateDF", symIdentifiers);' onmouseout='hideVariable("dateDF", symIdentifiers);'>dateDF</span><span class="keyword">,</span> <span id="sym20" class="symbol" onmouseover='showVariable("x", symIdentifiers);' onmouseout='hideVariable("x", symIdentifiers);'>x</span><span class="keyword">,</span> <span class="argument">by</span> <span class="argument">=</span> <span class="string">"DATE"</span><span class="keyword">,</span> <span class="argument">all.x</span> <span class="argument">=</span> <span class="number">TRUE</span><span class="keyword">)</span>
<a href="base/data.matrix.html">data.matrix</a><span class="keyword">(</span><span id="sym21" class="symbol" onmouseover='showVariable("m", symIdentifiers);' onmouseout='hideVariable("m", symIdentifiers);'>m</span><span class="keyword">[</span><span class="keyword">,</span> <span id="sym22" class="symbol" onmouseover='showVariable("pollutants", symIdentifiers);' onmouseout='hideVariable("pollutants", symIdentifiers);'>pollutants</span><span class="keyword">]</span><span class="keyword">)</span>
<span class="keyword">}</span><span class="keyword">)</span>
<span class="comment">## Dims: day, pollutant, site</span>
<span id="sym23" class="symbol" onmouseover='showVariable("adata", symIdentifiers);' onmouseout='hideVariable("adata", symIdentifiers);'>adata</span> <span class="assignement"><-</span> <a href="base/array.html">array</a><span class="keyword">(</span><span class="argument">dim</span> <span class="argument">=</span> <a href="base/c.html">c</a><span class="keyword">(</span><a href="base/dim.html">dim</a><span class="keyword">(</span><span id="sym24" class="symbol" onmouseover='showVariable("ad", symIdentifiers);' onmouseout='hideVariable("ad", symIdentifiers);'>ad</span><span class="keyword">[[</span><span class="number">1</span><span class="keyword">]</span><span class="keyword">]</span><span class="keyword">)</span><span class="keyword">,</span> <a href="base/length.html">length</a><span class="keyword">(</span><span id="sym25" class="symbol" onmouseover='showVariable("ad", symIdentifiers);' onmouseout='hideVariable("ad", symIdentifiers);'>ad</span><span class="keyword">)</span><span class="keyword">)</span><span class="keyword">)</span>
<span class="keyword">for</span><span class="keyword">(</span><span id="sym26" class="symbol" onmouseover='showVariable("i", symIdentifiers);' onmouseout='hideVariable("i", symIdentifiers);'>i</span> <span class="keyword">in</span> <a href="base/seq_along.html">seq_along</a><span class="keyword">(</span><span id="sym27" class="symbol" onmouseover='showVariable("ad", symIdentifiers);' onmouseout='hideVariable("ad", symIdentifiers);'>ad</span><span class="keyword">)</span><span class="keyword">)</span> <span class="keyword">{</span>
<span id="sym28" class="symbol" onmouseover='showVariable("adata", symIdentifiers);' onmouseout='hideVariable("adata", symIdentifiers);'>adata</span><span class="keyword">[</span><span class="keyword">,</span> <span class="keyword">,</span> <span id="sym29" class="symbol" onmouseover='showVariable("i", symIdentifiers);' onmouseout='hideVariable("i", symIdentifiers);'>i</span><span class="keyword">]</span> <span class="assignement"><-</span> <span id="sym30" class="symbol" onmouseover='showVariable("ad", symIdentifiers);' onmouseout='hideVariable("ad", symIdentifiers);'>ad</span><span class="keyword">[[</span><span id="sym31" class="symbol" onmouseover='showVariable("i", symIdentifiers);' onmouseout='hideVariable("i", symIdentifiers);'>i</span><span class="keyword">]</span><span class="keyword">]</span>
<span class="keyword">}</span>
<a href="base/dimnames.html">dimnames</a><span class="keyword">(</span><span id="sym32" class="symbol" onmouseover='showVariable("adata", symIdentifiers);' onmouseout='hideVariable("adata", symIdentifiers);'>adata</span><span class="keyword">)</span> <span class="assignement"><-</span> <a href="base/list.html">list</a><span class="keyword">(</span><a href="base/as.character.html">as.character</a><span class="keyword">(</span><span id="sym33" class="symbol" onmouseover='showVariable("all.dates", symIdentifiers);' onmouseout='hideVariable("all.dates", symIdentifiers);'>all.dates</span><span class="keyword">)</span><span class="keyword">,</span> <span id="sym34" class="symbol" onmouseover='showVariable("pollutants", symIdentifiers);' onmouseout='hideVariable("pollutants", symIdentifiers);'>pollutants</span><span class="keyword">,</span> <span id="sym35" class="symbol" onmouseover='showVariable("index.names", symIdentifiers);' onmouseout='hideVariable("index.names", symIdentifiers);'>index.names</span><span class="keyword">)</span>
<span id="sym36" class="symbol" onmouseover='showVariable("sitedata", symIdentifiers);' onmouseout='hideVariable("sitedata", symIdentifiers);'>sitedata</span> <span class="assignement"><-</span> <a href="base/.readRDS.html">.readRDS</a><span class="keyword">(</span><span class="string">"monitor-data/sitedata.rds"</span><span class="keyword">)</span>
<a href="base/row.names.html">row.names</a><span class="keyword">(</span><span id="sym37" class="symbol" onmouseover='showVariable("sitedata", symIdentifiers);' onmouseout='hideVariable("sitedata", symIdentifiers);'>sitedata</span><span class="keyword">)</span> <span class="assignement"><-</span> <span id="sym38" class="symbol" onmouseover='showVariable("sitedata", symIdentifiers);' onmouseout='hideVariable("sitedata", symIdentifiers);'>sitedata</span><span class="keyword">$</span><span id="sym39" class="symbol" onmouseover='showVariable("SITEPOC", symIdentifiers);' onmouseout='hideVariable("SITEPOC", symIdentifiers);'>SITEPOC</span>
<span id="sym40" class="symbol" onmouseover='showVariable("sitepairs", symIdentifiers);' onmouseout='hideVariable("sitepairs", symIdentifiers);'>sitepairs</span> <span class="assignement"><-</span> <a href="base/as.matrix.html">as.matrix</a><span class="keyword">(</span><a href="base/expand.grid.html">expand.grid</a><span class="keyword">(</span><span id="sym41" class="symbol" onmouseover='showVariable("sitedata", symIdentifiers);' onmouseout='hideVariable("sitedata", symIdentifiers);'>sitedata</span><span class="keyword">$</span><span id="sym42" class="symbol" onmouseover='showVariable("SITEPOC", symIdentifiers);' onmouseout='hideVariable("SITEPOC", symIdentifiers);'>SITEPOC</span><span class="keyword">,</span> <span id="sym43" class="symbol" onmouseover='showVariable("sitedata", symIdentifiers);' onmouseout='hideVariable("sitedata", symIdentifiers);'>sitedata</span><span class="keyword">$</span><span id="sym44" class="symbol" onmouseover='showVariable("SITEPOC", symIdentifiers);' onmouseout='hideVariable("SITEPOC", symIdentifiers);'>SITEPOC</span><span class="keyword">)</span><span class="keyword">)</span>
<a href="base/colnames.html">colnames</a><span class="keyword">(</span><span id="sym45" class="symbol" onmouseover='showVariable("sitepairs", symIdentifiers);' onmouseout='hideVariable("sitepairs", symIdentifiers);'>sitepairs</span><span class="keyword">)</span> <span class="assignement"><-</span> <a href="base/c.html">c</a><span class="keyword">(</span><span class="string">"site1"</span><span class="keyword">,</span> <span class="string">"site2"</span><span class="keyword">)</span>
<span id="sym46" class="symbol" onmouseover='showVariable("repeats", symIdentifiers);' onmouseout='hideVariable("repeats", symIdentifiers);'>repeats</span> <span class="assignement"><-</span> <span id="sym47" class="symbol" onmouseover='showVariable("sitepairs", symIdentifiers);' onmouseout='hideVariable("sitepairs", symIdentifiers);'>sitepairs</span><span class="keyword">[</span><span class="keyword">,</span><span class="number">1</span><span class="keyword">]</span> == <span id="sym48" class="symbol" onmouseover='showVariable("sitepairs", symIdentifiers);' onmouseout='hideVariable("sitepairs", symIdentifiers);'>sitepairs</span><span class="keyword">[</span><span class="keyword">,</span><span class="number">2</span><span class="keyword">]</span>
<span id="sym49" class="symbol" onmouseover='showVariable("sitepairs", symIdentifiers);' onmouseout='hideVariable("sitepairs", symIdentifiers);'>sitepairs</span> <span class="assignement"><-</span> <span id="sym50" class="symbol" onmouseover='showVariable("sitepairs", symIdentifiers);' onmouseout='hideVariable("sitepairs", symIdentifiers);'>sitepairs</span><span class="keyword">[</span><span class="keyword">!</span><span id="sym51" class="symbol" onmouseover='showVariable("repeats", symIdentifiers);' onmouseout='hideVariable("repeats", symIdentifiers);'>repeats</span><span class="keyword">,</span> <span class="keyword">]</span>
<span id="sym52" class="symbol" onmouseover='showVariable("key", symIdentifiers);' onmouseout='hideVariable("key", symIdentifiers);'>key</span> <span class="assignement"><-</span> <a href="base/apply.html">apply</a><span class="keyword">(</span><span id="sym53" class="symbol" onmouseover='showVariable("sitepairs", symIdentifiers);' onmouseout='hideVariable("sitepairs", symIdentifiers);'>sitepairs</span><span class="keyword">,</span> <span class="number">1</span><span class="keyword">,</span> <span class="keyword">function</span><span class="keyword">(</span><span class="formalargs">x</span><span class="keyword">)</span> <a href="base/paste.html">paste</a><span class="keyword">(</span><a href="base/sort.html">sort</a><span class="keyword">(</span><span id="sym54" class="symbol" onmouseover='showVariable("x", symIdentifiers);' onmouseout='hideVariable("x", symIdentifiers);'>x</span><span class="keyword">)</span><span class="keyword">,</span> <span class="argument">collapse</span> <span class="argument">=</span> <span class="string">""</span><span class="keyword">)</span><span class="keyword">)</span>
<span id="sym55" class="symbol" onmouseover='showVariable("sitepairs", symIdentifiers);' onmouseout='hideVariable("sitepairs", symIdentifiers);'>sitepairs</span> <span class="assignement"><-</span> <span id="sym56" class="symbol" onmouseover='showVariable("sitepairs", symIdentifiers);' onmouseout='hideVariable("sitepairs", symIdentifiers);'>sitepairs</span><span class="keyword">[</span><span class="keyword">!</span><a href="base/duplicated.html">duplicated</a><span class="keyword">(</span><span id="sym57" class="symbol" onmouseover='showVariable("key", symIdentifiers);' onmouseout='hideVariable("key", symIdentifiers);'>key</span><span class="keyword">)</span><span class="keyword">,</span> <span class="keyword">]</span>
<span id="sym58" class="symbol" onmouseover='showVariable("sitepairs", symIdentifiers);' onmouseout='hideVariable("sitepairs", symIdentifiers);'>sitepairs</span> <span class="assignement"><-</span> <a href="base/as.data.frame.html">as.data.frame</a><span class="keyword">(</span><span id="sym59" class="symbol" onmouseover='showVariable("sitepairs", symIdentifiers);' onmouseout='hideVariable("sitepairs", symIdentifiers);'>sitepairs</span><span class="keyword">,</span> <span class="argument">stringsAsFactors</span> <span class="argument">=</span> <span class="number">FALSE</span><span class="keyword">)</span>
<span id="sym60" class="symbol" onmouseover='showVariable("dist", symIdentifiers);' onmouseout='hideVariable("dist", symIdentifiers);'>dist</span> <span class="assignement"><-</span> <a href="base/apply.html">apply</a><span class="keyword">(</span><span id="sym61" class="symbol" onmouseover='showVariable("sitepairs", symIdentifiers);' onmouseout='hideVariable("sitepairs", symIdentifiers);'>sitepairs</span><span class="keyword">,</span> <span class="number">1</span><span class="keyword">,</span> <span class="keyword">function</span><span class="keyword">(</span><span class="formalargs">x</span><span class="keyword">)</span> <span class="keyword">{</span>
<span id="sym62" class="symbol" onmouseover='showVariable("s1", symIdentifiers);' onmouseout='hideVariable("s1", symIdentifiers);'>s1</span> <span class="assignement"><-</span> <span id="sym63" class="symbol" onmouseover='showVariable("sitedata", symIdentifiers);' onmouseout='hideVariable("sitedata", symIdentifiers);'>sitedata</span><span class="keyword">[</span><span id="sym64" class="symbol" onmouseover='showVariable("x", symIdentifiers);' onmouseout='hideVariable("x", symIdentifiers);'>x</span><span class="keyword">[</span><span class="string">"site1"</span><span class="keyword">]</span><span class="keyword">,</span> <span class="keyword">]</span>
<span id="sym65" class="symbol" onmouseover='showVariable("s2", symIdentifiers);' onmouseout='hideVariable("s2", symIdentifiers);'>s2</span> <span class="assignement"><-</span> <span id="sym66" class="symbol" onmouseover='showVariable("sitedata", symIdentifiers);' onmouseout='hideVariable("sitedata", symIdentifiers);'>sitedata</span><span class="keyword">[</span><span id="sym67" class="symbol" onmouseover='showVariable("x", symIdentifiers);' onmouseout='hideVariable("x", symIdentifiers);'>x</span><span class="keyword">[</span><span class="string">"site2"</span><span class="keyword">]</span><span class="keyword">,</span> <span class="keyword">]</span>
<span class="comment">## Convert distance to miles (approximately)</span>
<span id="sym68" class="symbol" onmouseover='showVariable("yd", symIdentifiers);' onmouseout='hideVariable("yd", symIdentifiers);'>yd</span> <span class="assignement"><-</span> <span class="keyword">(</span><span id="sym69" class="symbol" onmouseover='showVariable("s1", symIdentifiers);' onmouseout='hideVariable("s1", symIdentifiers);'>s1</span><span class="keyword">$</span><span id="sym70" class="symbol" onmouseover='showVariable("LATITUDE", symIdentifiers);' onmouseout='hideVariable("LATITUDE", symIdentifiers);'>LATITUDE</span> <span class="keyword">-</span> <span id="sym71" class="symbol" onmouseover='showVariable("s2", symIdentifiers);' onmouseout='hideVariable("s2", symIdentifiers);'>s2</span><span class="keyword">$</span><span id="sym72" class="symbol" onmouseover='showVariable("LATITUDE", symIdentifiers);' onmouseout='hideVariable("LATITUDE", symIdentifiers);'>LATITUDE</span><span class="keyword">)</span> <span class="keyword">*</span> <span class="number">69.2</span>
<span id="sym73" class="symbol" onmouseover='showVariable("xd", symIdentifiers);' onmouseout='hideVariable("xd", symIdentifiers);'>xd</span> <span class="assignement"><-</span> <span class="keyword">(</span><span id="sym74" class="symbol" onmouseover='showVariable("s1", symIdentifiers);' onmouseout='hideVariable("s1", symIdentifiers);'>s1</span><span class="keyword">$</span><span id="sym75" class="symbol" onmouseover='showVariable("LONGITUDE", symIdentifiers);' onmouseout='hideVariable("LONGITUDE", symIdentifiers);'>LONGITUDE</span> <span class="keyword">-</span> <span id="sym76" class="symbol" onmouseover='showVariable("s2", symIdentifiers);' onmouseout='hideVariable("s2", symIdentifiers);'>s2</span><span class="keyword">$</span><span id="sym77" class="symbol" onmouseover='showVariable("LONGITUDE", symIdentifiers);' onmouseout='hideVariable("LONGITUDE", symIdentifiers);'>LONGITUDE</span><span class="keyword">)</span> <span class="keyword">*</span> <span class="number">69.2</span> <span class="keyword">*</span> <span class="number">0.78</span>
<a href="base/sqrt.html">sqrt</a><span class="keyword">(</span><span id="sym78" class="symbol" onmouseover='showVariable("xd", symIdentifiers);' onmouseout='hideVariable("xd", symIdentifiers);'>xd</span><span class="keyword">^</span><span class="number">2</span> <span class="keyword">+</span> <span id="sym79" class="symbol" onmouseover='showVariable("yd", symIdentifiers);' onmouseout='hideVariable("yd", symIdentifiers);'>yd</span><span class="keyword">^</span><span class="number">2</span><span class="keyword">)</span>
<span class="keyword">}</span><span class="keyword">)</span>
<span id="sym80" class="symbol" onmouseover='showVariable("sitepairs", symIdentifiers);' onmouseout='hideVariable("sitepairs", symIdentifiers);'>sitepairs</span><span class="keyword">$</span><span id="sym81" class="symbol" onmouseover='showVariable("distance", symIdentifiers);' onmouseout='hideVariable("distance", symIdentifiers);'>distance</span> <span class="assignement"><-</span> <span id="sym82" class="symbol" onmouseover='showVariable("dist", symIdentifiers);' onmouseout='hideVariable("dist", symIdentifiers);'>dist</span>
<span id="sym83" class="symbol" onmouseover='showVariable("getsites", symIdentifiers);' onmouseout='hideVariable("getsites", symIdentifiers);'>getsites</span> <span class="assignement"><-</span> <span class="keyword">function</span><span class="keyword">(</span><span class="formalargs">maxdist</span><span class="keyword">,</span> <span class="formalargs">mindist</span> <span class="eqformalargs">=</span> <span class="number">0</span><span class="keyword">)</span> <span class="keyword">{</span>
<a href="base/with.html">with</a><span class="keyword">(</span><span id="sym84" class="symbol" onmouseover='showVariable("sitepairs", symIdentifiers);' onmouseout='hideVariable("sitepairs", symIdentifiers);'>sitepairs</span><span class="keyword">,</span> <span id="sym85" class="symbol" onmouseover='showVariable("distance", symIdentifiers);' onmouseout='hideVariable("distance", symIdentifiers);'>distance</span> <= <span id="sym86" class="symbol" onmouseover='showVariable("maxdist", symIdentifiers);' onmouseout='hideVariable("maxdist", symIdentifiers);'>maxdist</span> <span class="keyword">&</span> <span id="sym87" class="symbol" onmouseover='showVariable("distance", symIdentifiers);' onmouseout='hideVariable("distance", symIdentifiers);'>distance</span> <span class="keyword">>=</span> <span id="sym88" class="symbol" onmouseover='showVariable("mindist", symIdentifiers);' onmouseout='hideVariable("mindist", symIdentifiers);'>mindist</span><span class="keyword">)</span>
<span class="keyword">}</span>
<span id="sym89" class="symbol" onmouseover='showVariable("plotsites", symIdentifiers);' onmouseout='hideVariable("plotsites", symIdentifiers);'>plotsites</span> <span class="assignement"><-</span> <span class="keyword">function</span><span class="keyword">(</span><span class="formalargs">maxdist</span><span class="keyword">,</span> <span class="formalargs">mindist</span> <span class="eqformalargs">=</span> <span class="number">0</span><span class="keyword">,</span> <span class="formalargs">add</span> <span class="eqformalargs">=</span> <span class="number">FALSE</span><span class="keyword">,</span> <span class="formalargs">...</span><span class="keyword">)</span> <span class="keyword">{</span>
<span id="sym90" class="symbol" onmouseover='showVariable("p", symIdentifiers);' onmouseout='hideVariable("p", symIdentifiers);'>p</span> <span class="assignement"><-</span> <a href="NA/getsites.html">getsites</a><span class="keyword">(</span><span id="sym91" class="symbol" onmouseover='showVariable("maxdist", symIdentifiers);' onmouseout='hideVariable("maxdist", symIdentifiers);'>maxdist</span><span class="keyword">,</span> <span id="sym92" class="symbol" onmouseover='showVariable("mindist", symIdentifiers);' onmouseout='hideVariable("mindist", symIdentifiers);'>mindist</span><span class="keyword">)</span>
<span id="sym93" class="symbol" onmouseover='showVariable("p", symIdentifiers);' onmouseout='hideVariable("p", symIdentifiers);'>p</span> <span class="assignement"><-</span> <a href="base/unique.html">unique</a><span class="keyword">(</span><a href="base/unlist.html">unlist</a><span class="keyword">(</span><span id="sym94" class="symbol" onmouseover='showVariable("p", symIdentifiers);' onmouseout='hideVariable("p", symIdentifiers);'>p</span><span class="keyword">)</span><span class="keyword">)</span>
<span class="keyword">if</span><span class="keyword">(</span><span class="keyword">!</span><span id="sym95" class="symbol" onmouseover='showVariable("add", symIdentifiers);' onmouseout='hideVariable("add", symIdentifiers);'>add</span><span class="keyword">)</span>
<a href="base/with.html">with</a><span class="keyword">(</span><span id="sym96" class="symbol" onmouseover='showVariable("sitedata", symIdentifiers);' onmouseout='hideVariable("sitedata", symIdentifiers);'>sitedata</span><span class="keyword">[</span><span id="sym97" class="symbol" onmouseover='showVariable("p", symIdentifiers);' onmouseout='hideVariable("p", symIdentifiers);'>p</span><span class="keyword">,</span> <span class="keyword">]</span><span class="keyword">,</span> <a href="graphics/plot.html">plot</a><span class="keyword">(</span><span id="sym98" class="symbol" onmouseover='showVariable("LONGITUDE", symIdentifiers);' onmouseout='hideVariable("LONGITUDE", symIdentifiers);'>LONGITUDE</span><span class="keyword">,</span> <span id="sym99" class="symbol" onmouseover='showVariable("LATITUDE", symIdentifiers);' onmouseout='hideVariable("LATITUDE", symIdentifiers);'>LATITUDE</span><span class="keyword">,</span> <span id="sym100" class="symbol" onmouseover='showVariable("...", symIdentifiers);' onmouseout='hideVariable("...", symIdentifiers);'>...</span><span class="keyword">)</span><span class="keyword">)</span>
<span class="keyword">else</span>
<a href="base/with.html">with</a><span class="keyword">(</span><span id="sym101" class="symbol" onmouseover='showVariable("sitedata", symIdentifiers);' onmouseout='hideVariable("sitedata", symIdentifiers);'>sitedata</span><span class="keyword">[</span><span id="sym102" class="symbol" onmouseover='showVariable("p", symIdentifiers);' onmouseout='hideVariable("p", symIdentifiers);'>p</span><span class="keyword">,</span> <span class="keyword">]</span><span class="keyword">,</span> <a href="graphics/points.html">points</a><span class="keyword">(</span><span id="sym103" class="symbol" onmouseover='showVariable("LONGITUDE", symIdentifiers);' onmouseout='hideVariable("LONGITUDE", symIdentifiers);'>LONGITUDE</span><span class="keyword">,</span> <span id="sym104" class="symbol" onmouseover='showVariable("LATITUDE", symIdentifiers);' onmouseout='hideVariable("LATITUDE", symIdentifiers);'>LATITUDE</span><span class="keyword">,</span> <span id="sym105" class="symbol" onmouseover='showVariable("...", symIdentifiers);' onmouseout='hideVariable("...", symIdentifiers);'>...</span><span class="keyword">)</span><span class="keyword">)</span>
<span class="keyword">}</span>
<span class="comment">## Compute variances</span>
<span id="sym106" class="symbol" onmouseover='showVariable("vars", symIdentifiers);' onmouseout='hideVariable("vars", symIdentifiers);'>vars</span> <span class="assignement"><-</span> <a href="base/t.html">t</a><span class="keyword">(</span> <a href="base/mapply.html">mapply</a><span class="keyword">(</span><span class="keyword">function</span><span class="keyword">(</span><span class="formalargs">site1</span><span class="keyword">,</span> <span class="formalargs">site2</span><span class="keyword">)</span> <span class="keyword">{</span>
<span id="sym107" class="symbol" onmouseover='showVariable("d", symIdentifiers);' onmouseout='hideVariable("d", symIdentifiers);'>d</span> <span class="assignement"><-</span> <span id="sym108" class="symbol" onmouseover='showVariable("adata", symIdentifiers);' onmouseout='hideVariable("adata", symIdentifiers);'>adata</span><span class="keyword">[</span><span class="keyword">,</span> <span class="keyword">,</span> <span id="sym109" class="symbol" onmouseover='showVariable("site1", symIdentifiers);' onmouseout='hideVariable("site1", symIdentifiers);'>site1</span><span class="keyword">]</span> <span class="keyword">-</span> <span id="sym110" class="symbol" onmouseover='showVariable("adata", symIdentifiers);' onmouseout='hideVariable("adata", symIdentifiers);'>adata</span><span class="keyword">[</span><span class="keyword">,</span> <span class="keyword">,</span> <span id="sym111" class="symbol" onmouseover='showVariable("site2", symIdentifiers);' onmouseout='hideVariable("site2", symIdentifiers);'>site2</span><span class="keyword">]</span>
<a href="base/diag.html">diag</a><span class="keyword">(</span><a href="stats/var.html">var</a><span class="keyword">(</span><span id="sym112" class="symbol" onmouseover='showVariable("d", symIdentifiers);' onmouseout='hideVariable("d", symIdentifiers);'>d</span><span class="keyword">,</span> <span class="argument">use</span> <span class="argument">=</span> <span class="string">"pairwise"</span><span class="keyword">)</span><span class="keyword">)</span>
<span class="keyword">}</span><span class="keyword">,</span> <span id="sym113" class="symbol" onmouseover='showVariable("sitepairs", symIdentifiers);' onmouseout='hideVariable("sitepairs", symIdentifiers);'>sitepairs</span><span class="keyword">[</span><span class="keyword">,</span> <span class="number">1</span><span class="keyword">]</span><span class="keyword">,</span> <span id="sym114" class="symbol" onmouseover='showVariable("sitepairs", symIdentifiers);' onmouseout='hideVariable("sitepairs", symIdentifiers);'>sitepairs</span><span class="keyword">[</span><span class="keyword">,</span> <span class="number">2</span><span class="keyword">]</span><span class="keyword">)</span><span class="keyword">)</span>
<span class="comment">## Covariances</span>
<span id="sym115" class="symbol" onmouseover='showVariable("covs", symIdentifiers);' onmouseout='hideVariable("covs", symIdentifiers);'>covs</span> <span class="assignement"><-</span> <a href="base/t.html">t</a><span class="keyword">(</span> <a href="base/mapply.html">mapply</a><span class="keyword">(</span><span class="keyword">function</span><span class="keyword">(</span><span class="formalargs">site1</span><span class="keyword">,</span> <span class="formalargs">site2</span><span class="keyword">)</span> <span class="keyword">{</span>
<span id="sym116" class="symbol" onmouseover='showVariable("cc", symIdentifiers);' onmouseout='hideVariable("cc", symIdentifiers);'>cc</span> <span class="assignement"><-</span> <a href="stats/cov.html">cov</a><span class="keyword">(</span><span id="sym117" class="symbol" onmouseover='showVariable("adata", symIdentifiers);' onmouseout='hideVariable("adata", symIdentifiers);'>adata</span><span class="keyword">[</span><span class="keyword">,</span> <span class="keyword">,</span> <span id="sym118" class="symbol" onmouseover='showVariable("site1", symIdentifiers);' onmouseout='hideVariable("site1", symIdentifiers);'>site1</span><span class="keyword">]</span><span class="keyword">,</span> <span id="sym119" class="symbol" onmouseover='showVariable("adata", symIdentifiers);' onmouseout='hideVariable("adata", symIdentifiers);'>adata</span><span class="keyword">[</span><span class="keyword">,</span> <span class="keyword">,</span> <span id="sym120" class="symbol" onmouseover='showVariable("site2", symIdentifiers);' onmouseout='hideVariable("site2", symIdentifiers);'>site2</span><span class="keyword">]</span><span class="keyword">,</span> <span class="argument">use</span> <span class="argument">=</span> <span class="string">"pairwise"</span><span class="keyword">)</span>
<a href="base/diag.html">diag</a><span class="keyword">(</span><span id="sym121" class="symbol" onmouseover='showVariable("cc", symIdentifiers);' onmouseout='hideVariable("cc", symIdentifiers);'>cc</span><span class="keyword">)</span>
<span class="keyword">}</span><span class="keyword">,</span> <span id="sym122" class="symbol" onmouseover='showVariable("sitepairs", symIdentifiers);' onmouseout='hideVariable("sitepairs", symIdentifiers);'>sitepairs</span><span class="keyword">[</span><span class="keyword">,</span> <span class="number">1</span><span class="keyword">]</span><span class="keyword">,</span> <span id="sym123" class="symbol" onmouseover='showVariable("sitepairs", symIdentifiers);' onmouseout='hideVariable("sitepairs", symIdentifiers);'>sitepairs</span><span class="keyword">[</span><span class="keyword">,</span> <span class="number">2</span><span class="keyword">]</span><span class="keyword">)</span><span class="keyword">)</span>
<a href="base/colnames.html">colnames</a><span class="keyword">(</span><span id="sym124" class="symbol" onmouseover='showVariable("covs", symIdentifiers);' onmouseout='hideVariable("covs", symIdentifiers);'>covs</span><span class="keyword">)</span> <span class="assignement"><-</span> <a href="base/paste.html">paste</a><span class="keyword">(</span><a href="base/colnames.html">colnames</a><span class="keyword">(</span><span id="sym125" class="symbol" onmouseover='showVariable("covs", symIdentifiers);' onmouseout='hideVariable("covs", symIdentifiers);'>covs</span><span class="keyword">)</span><span class="keyword">,</span> <span class="string">"c"</span><span class="keyword">,</span> <span class="argument">sep</span> <span class="argument">=</span> <a href="."><span class="string">"."</span></a><span class="keyword">)</span>
<span class="comment">## Correlations (for plotting)</span>
<span id="sym126" class="symbol" onmouseover='showVariable("cors", symIdentifiers);' onmouseout='hideVariable("cors", symIdentifiers);'>cors</span> <span class="assignement"><-</span> <a href="base/t.html">t</a><span class="keyword">(</span> <a href="base/mapply.html">mapply</a><span class="keyword">(</span><span class="keyword">function</span><span class="keyword">(</span><span class="formalargs">site1</span><span class="keyword">,</span> <span class="formalargs">site2</span><span class="keyword">)</span> <span class="keyword">{</span>
<span id="sym127" class="symbol" onmouseover='showVariable("cc", symIdentifiers);' onmouseout='hideVariable("cc", symIdentifiers);'>cc</span> <span class="assignement"><-</span> <a href="stats/cor.html">cor</a><span class="keyword">(</span><span id="sym128" class="symbol" onmouseover='showVariable("adata", symIdentifiers);' onmouseout='hideVariable("adata", symIdentifiers);'>adata</span><span class="keyword">[</span><span class="keyword">,</span> <span class="keyword">,</span> <span id="sym129" class="symbol" onmouseover='showVariable("site1", symIdentifiers);' onmouseout='hideVariable("site1", symIdentifiers);'>site1</span><span class="keyword">]</span><span class="keyword">,</span> <span id="sym130" class="symbol" onmouseover='showVariable("adata", symIdentifiers);' onmouseout='hideVariable("adata", symIdentifiers);'>adata</span><span class="keyword">[</span><span class="keyword">,</span> <span class="keyword">,</span> <span id="sym131" class="symbol" onmouseover='showVariable("site2", symIdentifiers);' onmouseout='hideVariable("site2", symIdentifiers);'>site2</span><span class="keyword">]</span><span class="keyword">,</span> <span class="argument">use</span> <span class="argument">=</span> <span class="string">"pairwise"</span><span class="keyword">)</span>
<a href="base/diag.html">diag</a><span class="keyword">(</span><span id="sym132" class="symbol" onmouseover='showVariable("cc", symIdentifiers);' onmouseout='hideVariable("cc", symIdentifiers);'>cc</span><span class="keyword">)</span>
<span class="keyword">}</span><span class="keyword">,</span> <span id="sym133" class="symbol" onmouseover='showVariable("sitepairs", symIdentifiers);' onmouseout='hideVariable("sitepairs", symIdentifiers);'>sitepairs</span><span class="keyword">[</span><span class="keyword">,</span> <span class="number">1</span><span class="keyword">]</span><span class="keyword">,</span> <span id="sym134" class="symbol" onmouseover='showVariable("sitepairs", symIdentifiers);' onmouseout='hideVariable("sitepairs", symIdentifiers);'>sitepairs</span><span class="keyword">[</span><span class="keyword">,</span> <span class="number">2</span><span class="keyword">]</span><span class="keyword">)</span><span class="keyword">)</span>
<a href="base/colnames.html">colnames</a><span class="keyword">(</span><span id="sym135" class="symbol" onmouseover='showVariable("cors", symIdentifiers);' onmouseout='hideVariable("cors", symIdentifiers);'>cors</span><span class="keyword">)</span> <span class="assignement"><-</span> <a href="base/paste.html">paste</a><span class="keyword">(</span><a href="base/colnames.html">colnames</a><span class="keyword">(</span><span id="sym136" class="symbol" onmouseover='showVariable("cors", symIdentifiers);' onmouseout='hideVariable("cors", symIdentifiers);'>cors</span><span class="keyword">)</span><span class="keyword">,</span> <a href="r"><span class="string">"r"</span></a><span class="keyword">,</span> <span class="argument">sep</span> <span class="argument">=</span> <a href="."><span class="string">"."</span></a><span class="keyword">)</span>
<span id="sym137" class="symbol" onmouseover='showVariable("means", symIdentifiers);' onmouseout='hideVariable("means", symIdentifiers);'>means</span> <span class="assignement"><-</span> <a href="base/t.html">t</a><span class="keyword">(</span> <a href="base/mapply.html">mapply</a><span class="keyword">(</span><span class="keyword">function</span><span class="keyword">(</span><span class="formalargs">site1</span><span class="keyword">,</span> <span class="formalargs">site2</span><span class="keyword">)</span> <span class="keyword">{</span>
<span id="sym138" class="symbol" onmouseover='showVariable("s", symIdentifiers);' onmouseout='hideVariable("s", symIdentifiers);'>s</span> <span class="assignement"><-</span> <span class="keyword">(</span><span id="sym139" class="symbol" onmouseover='showVariable("adata", symIdentifiers);' onmouseout='hideVariable("adata", symIdentifiers);'>adata</span><span class="keyword">[</span><span class="keyword">,</span> <span class="keyword">,</span> <span id="sym140" class="symbol" onmouseover='showVariable("site1", symIdentifiers);' onmouseout='hideVariable("site1", symIdentifiers);'>site1</span><span class="keyword">]</span> <span class="keyword">+</span> <span id="sym141" class="symbol" onmouseover='showVariable("adata", symIdentifiers);' onmouseout='hideVariable("adata", symIdentifiers);'>adata</span><span class="keyword">[</span><span class="keyword">,</span> <span class="keyword">,</span> <span id="sym142" class="symbol" onmouseover='showVariable("site2", symIdentifiers);' onmouseout='hideVariable("site2", symIdentifiers);'>site2</span><span class="keyword">]</span><span class="keyword">)</span> <span class="keyword">/</span> <span class="number">2</span>
<a href="base/colMeans.html">colMeans</a><span class="keyword">(</span><span id="sym143" class="symbol" onmouseover='showVariable("s", symIdentifiers);' onmouseout='hideVariable("s", symIdentifiers);'>s</span><span class="keyword">,</span> <span class="argument">na.rm</span> <span class="argument">=</span> <span class="number">TRUE</span><span class="keyword">)</span>
<span class="keyword">}</span><span class="keyword">,</span> <span id="sym144" class="symbol" onmouseover='showVariable("sitepairs", symIdentifiers);' onmouseout='hideVariable("sitepairs", symIdentifiers);'>sitepairs</span><span class="keyword">[</span><span class="keyword">,</span> <span class="number">1</span><span class="keyword">]</span><span class="keyword">,</span> <span id="sym145" class="symbol" onmouseover='showVariable("sitepairs", symIdentifiers);' onmouseout='hideVariable("sitepairs", symIdentifiers);'>sitepairs</span><span class="keyword">[</span><span class="keyword">,</span> <span class="number">2</span><span class="keyword">]</span><span class="keyword">)</span><span class="keyword">)</span>
<a href="base/colnames.html">colnames</a><span class="keyword">(</span><span id="sym146" class="symbol" onmouseover='showVariable("means", symIdentifiers);' onmouseout='hideVariable("means", symIdentifiers);'>means</span><span class="keyword">)</span> <span class="assignement"><-</span> <a href="base/paste.html">paste</a><span class="keyword">(</span><a href="base/colnames.html">colnames</a><span class="keyword">(</span><span id="sym147" class="symbol" onmouseover='showVariable("means", symIdentifiers);' onmouseout='hideVariable("means", symIdentifiers);'>means</span><span class="keyword">)</span><span class="keyword">,</span> <span class="string">"m"</span><span class="keyword">,</span> <span class="argument">sep</span> <span class="argument">=</span> <a href="."><span class="string">"."</span></a><span class="keyword">)</span>
<span id="sym148" class="symbol" onmouseover='showVariable("nobs", symIdentifiers);' onmouseout='hideVariable("nobs", symIdentifiers);'>nobs</span> <span class="assignement"><-</span> <a href="base/mapply.html">mapply</a><span class="keyword">(</span><span class="keyword">function</span><span class="keyword">(</span><span class="formalargs">site1</span><span class="keyword">,</span> <span class="formalargs">site2</span><span class="keyword">)</span> <span class="keyword">{</span>
<span id="sym149" class="symbol" onmouseover='showVariable("d", symIdentifiers);' onmouseout='hideVariable("d", symIdentifiers);'>d</span> <span class="assignement"><-</span> <span id="sym150" class="symbol" onmouseover='showVariable("adata", symIdentifiers);' onmouseout='hideVariable("adata", symIdentifiers);'>adata</span><span class="keyword">[</span><span class="keyword">,</span> <span class="keyword">,</span> <span id="sym151" class="symbol" onmouseover='showVariable("site1", symIdentifiers);' onmouseout='hideVariable("site1", symIdentifiers);'>site1</span><span class="keyword">]</span> <span class="keyword">-</span> <span id="sym152" class="symbol" onmouseover='showVariable("adata", symIdentifiers);' onmouseout='hideVariable("adata", symIdentifiers);'>adata</span><span class="keyword">[</span><span class="keyword">,</span> <span class="keyword">,</span> <span id="sym153" class="symbol" onmouseover='showVariable("site2", symIdentifiers);' onmouseout='hideVariable("site2", symIdentifiers);'>site2</span><span class="keyword">]</span>
<a href="base/sum.html">sum</a><span class="keyword">(</span><a href="stats/complete.cases.html">complete.cases</a><span class="keyword">(</span><span id="sym154" class="symbol" onmouseover='showVariable("d", symIdentifiers);' onmouseout='hideVariable("d", symIdentifiers);'>d</span><span class="keyword">)</span><span class="keyword">)</span>
<span class="keyword">}</span><span class="keyword">,</span> <span id="sym155" class="symbol" onmouseover='showVariable("sitepairs", symIdentifiers);' onmouseout='hideVariable("sitepairs", symIdentifiers);'>sitepairs</span><span class="keyword">[</span><span class="keyword">,</span> <span class="number">1</span><span class="keyword">]</span><span class="keyword">,</span> <span id="sym156" class="symbol" onmouseover='showVariable("sitepairs", symIdentifiers);' onmouseout='hideVariable("sitepairs", symIdentifiers);'>sitepairs</span><span class="keyword">[</span><span class="keyword">,</span> <span class="number">2</span><span class="keyword">]</span><span class="keyword">,</span> <span class="argument">USE.NAMES</span> <span class="argument">=</span> <span class="number">FALSE</span><span class="keyword">)</span>
<a href="base/rownames.html">rownames</a><span class="keyword">(</span><span id="sym157" class="symbol" onmouseover='showVariable("vars", symIdentifiers);' onmouseout='hideVariable("vars", symIdentifiers);'>vars</span><span class="keyword">)</span> <span class="assignement"><-</span> NULL
<a href="base/rownames.html">rownames</a><span class="keyword">(</span><span id="sym158" class="symbol" onmouseover='showVariable("means", symIdentifiers);' onmouseout='hideVariable("means", symIdentifiers);'>means</span><span class="keyword">)</span> <span class="assignement"><-</span> NULL
<a href="base/rownames.html">rownames</a><span class="keyword">(</span><span id="sym159" class="symbol" onmouseover='showVariable("covs", symIdentifiers);' onmouseout='hideVariable("covs", symIdentifiers);'>covs</span><span class="keyword">)</span> <span class="assignement"><-</span> NULL
<a href="base/rownames.html">rownames</a><span class="keyword">(</span><span id="sym160" class="symbol" onmouseover='showVariable("cors", symIdentifiers);' onmouseout='hideVariable("cors", symIdentifiers);'>cors</span><span class="keyword">)</span> <span class="assignement"><-</span> NULL
<span id="sym161" class="symbol" onmouseover='showVariable("sitepairs", symIdentifiers);' onmouseout='hideVariable("sitepairs", symIdentifiers);'>sitepairs</span> <span class="assignement"><-</span> <a href="base/data.frame.html">data.frame</a><span class="keyword">(</span><span id="sym162" class="symbol" onmouseover='showVariable("sitepairs", symIdentifiers);' onmouseout='hideVariable("sitepairs", symIdentifiers);'>sitepairs</span><span class="keyword">,</span> <span id="sym163" class="symbol" onmouseover='showVariable("vars", symIdentifiers);' onmouseout='hideVariable("vars", symIdentifiers);'>vars</span><span class="keyword">,</span> <span id="sym164" class="symbol" onmouseover='showVariable("means", symIdentifiers);' onmouseout='hideVariable("means", symIdentifiers);'>means</span><span class="keyword">,</span> <span id="sym165" class="symbol" onmouseover='showVariable("covs", symIdentifiers);' onmouseout='hideVariable("covs", symIdentifiers);'>covs</span><span class="keyword">,</span> <span id="sym166" class="symbol" onmouseover='showVariable("cors", symIdentifiers);' onmouseout='hideVariable("cors", symIdentifiers);'>cors</span><span class="keyword">)</span>
<span id="sym167" class="symbol" onmouseover='showVariable("sitepairs", symIdentifiers);' onmouseout='hideVariable("sitepairs", symIdentifiers);'>sitepairs</span><span class="keyword">$</span><span id="sym168" class="symbol" onmouseover='showVariable("nobs", symIdentifiers);' onmouseout='hideVariable("nobs", symIdentifiers);'>nobs</span> <span class="assignement"><-</span> <span id="sym169" class="symbol" onmouseover='showVariable("nobs", symIdentifiers);' onmouseout='hideVariable("nobs", symIdentifiers);'>nobs</span>
<span id="sym170" class="symbol" onmouseover='showVariable("use", symIdentifiers);' onmouseout='hideVariable("use", symIdentifiers);'>use</span> <span class="assignement"><-</span> <a href="stats/complete.cases.html">complete.cases</a><span class="keyword">(</span><span id="sym171" class="symbol" onmouseover='showVariable("sitepairs", symIdentifiers);' onmouseout='hideVariable("sitepairs", symIdentifiers);'>sitepairs</span><span class="keyword">)</span>
<span id="sym172" class="symbol" onmouseover='showVariable("sitepairs", symIdentifiers);' onmouseout='hideVariable("sitepairs", symIdentifiers);'>sitepairs</span> <span class="assignement"><-</span> <span id="sym173" class="symbol" onmouseover='showVariable("sitepairs", symIdentifiers);' onmouseout='hideVariable("sitepairs", symIdentifiers);'>sitepairs</span><span class="keyword">[</span><span id="sym174" class="symbol" onmouseover='showVariable("use", symIdentifiers);' onmouseout='hideVariable("use", symIdentifiers);'>use</span><span class="keyword">,</span> <span class="keyword">]</span>
<span id="sym175" class="symbol" onmouseover='showVariable("keep", symIdentifiers);' onmouseout='hideVariable("keep", symIdentifiers);'>keep</span> <span class="assignement"><-</span> <span id="sym176" class="symbol" onmouseover='showVariable("sitepairs", symIdentifiers);' onmouseout='hideVariable("sitepairs", symIdentifiers);'>sitepairs</span><span class="keyword">$</span><span id="sym177" class="symbol" onmouseover='showVariable("nobs", symIdentifiers);' onmouseout='hideVariable("nobs", symIdentifiers);'>nobs</span> <span class="keyword">></span> <span class="number">0</span>
<span id="sym178" class="symbol" onmouseover='showVariable("sitepairs", symIdentifiers);' onmouseout='hideVariable("sitepairs", symIdentifiers);'>sitepairs</span> <span class="assignement"><-</span> <span id="sym179" class="symbol" onmouseover='showVariable("sitepairs", symIdentifiers);' onmouseout='hideVariable("sitepairs", symIdentifiers);'>sitepairs</span><span class="keyword">[</span><span id="sym180" class="symbol" onmouseover='showVariable("keep", symIdentifiers);' onmouseout='hideVariable("keep", symIdentifiers);'>keep</span><span class="keyword">,</span> <span class="keyword">]</span>
<a href="base/.saveRDS.html">.saveRDS</a><span class="keyword">(</span><span id="sym181" class="symbol" onmouseover='showVariable("sitepairs", symIdentifiers);' onmouseout='hideVariable("sitepairs", symIdentifiers);'>sitepairs</span><span class="keyword">,</span> <span class="argument">file</span> <span class="argument">=</span> <span class="string">"sitepairs.rds"</span><span class="keyword">)</span>
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