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<div style="font-size:12.8px;text-decoration-style:initial;text-decoration-color:initial"><font color="#000000">Hi,</font></div><div style="font-size:12.8px;text-decoration-style:initial;text-decoration-color:initial"><font color="#000000"><br></font></div><div style="font-size:12.8px;text-decoration-style:initial;text-decoration-color:initial"><font color="#000000">My name is Hugh and
<span style="background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline">I'm hoping to download all records for several hundred trees species.</span></font></div><div style="font-size:12.8px;text-decoration-style:initial;text-decoration-color:initial"><font color="#000000"><br></font></div><div style="font-size:12.8px;text-decoration-style:initial;text-decoration-color:initial">
<div dir="auto" style="background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial"><font color="#000000">I've been speaking to Scott Chamberlain, and I'm trying to determine if<span> </span><i><span class="" id=":yr.55" tabindex="-1" style="">occ</span>_data</i><span> can be used to </span>return all records identified as all synonyms for a given <span class="" id=":yr.56" tabindex="-1" style="">taxa</span>, if you search using either the scientific name, or the <span class="" id=":yr.57" tabindex="-1" style="">taxon</span> key?</font></div><div dir="auto" style="background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial"><font color="#000000"><br></font></div><div dir="auto" style="background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial"><font color="#000000">It seems that for some <span class="" id=":yr.58" tabindex="-1" style="">taxa</span> with unresolved synonyms, we could be missing records, depending on which synonym we use, and thus underestimating the range. Ideally we' like to get all <span style="font-size:12.8px">records for a <span class="" id=":yr.59" tabindex="-1" style="">taxa</span> in one go, regardless of which synonym we search. </span></font></div><div style="background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial"><font color="#000000"><br></font></div><div style="background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial"><font color="#000000">However, both different synonyms, and different numbers of records, are returned for these species:</font></div><div style="background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial"><font color="#000000"><br></font></div><div style="background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial">
<div style="text-decoration-style:initial;text-decoration-color:initial"><font color="#0000ff">## Create keys</font></div><div style="text-decoration-style:initial;text-decoration-color:initial"><div><font color="#0000ff"><span id="gmail-m_1652888918331982635:2cz.45"><span class="" id=":yr.60" tabindex="-1" style="">palustris</span></span>.key <- name_backbone(name = 'Quercus palustris', rank = 'species')$<span id="gmail-m_1652888918331982635:2cz.46"><span class="" id=":yr.61" tabindex="-1" style="">usageKey</span></span></font></div><div><font color="#0000ff"><span id="gmail-m_1652888918331982635:2cz.47" style=""><span class="" id=":yr.62" tabindex="-1" style="">coccinea</span></span>.key <- name_backbone(name = 'Quercus coccinea', rank = 'species')$<span id="gmail-m_1652888918331982635:2cz.48" style=""><span class="" id=":yr.63" tabindex="-1" style="">usageKey</span></span></font></div><div><font color="#000000"><br></font></div><div><font color="#000000"><br></font></div><div><font color="#0000ff">## Search data</font></div><div><font color="#0000ff"><span id="gmail-m_1652888918331982635:2cz.49"><span class="" id=":yr.64" tabindex="-1" style="">palustris</span></span>.<span id="gmail-m_1652888918331982635:2cz.50"><span class="" id=":yr.65" tabindex="-1" style="">occ</span></span><span> </span>=<span> </span><span id="gmail-m_1652888918331982635:2cz.51"><span class="" id=":yr.66" tabindex="-1" style="">occ</span></span>_data(<span id="gmail-m_1652888918331982635:2cz.52"><span class="" id=":yr.67" tabindex="-1" style="">taxonKey</span></span><span> </span>=<span> </span><span id="gmail-m_1652888918331982635:2cz.53"><span class="" id=":yr.68" tabindex="-1" style="">palustris</span></span>.key, limit = 200000) ## equivalent to<span> </span><span id="gmail-m_1652888918331982635:2cz.54"><span class="" id=":yr.69" tabindex="-1" style="">gbif</span></span>(<span> </span><span style="font-size:small;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline">'Quercus palustris'</span><span> </span>, download = TRUE) </font></div><div><font color="#0000ff"><span id="gmail-m_1652888918331982635:2cz.55" style=""><span class="" id=":yr.70" tabindex="-1" style="">coccinea</span></span>.<span id="gmail-m_1652888918331982635:2cz.56" style=""><span class="" id=":yr.71" tabindex="-1" style="">occ</span></span> = <span id="gmail-m_1652888918331982635:2cz.57" style=""><span class="" id=":yr.72" tabindex="-1" style="">occ</span></span>_data(<span id="gmail-m_1652888918331982635:2cz.58" style=""><span class="" id=":yr.73" tabindex="-1" style="">taxonKey</span></span> = <span id="gmail-m_1652888918331982635:2cz.59" style=""><span class="" id=":yr.74" tabindex="-1" style="">coccinea</span></span>.key, limit = 200000)</font></div></div><font color="#000000"><br></font><div><font color="#0000ff">> unique(<span class="" id=":yr.75" tabindex="-1" style="">palustris</span>.<span class="" id=":yr.76" tabindex="-1" style="">occ</span>$data$<span class="" id=":yr.77" tabindex="-1" style="">scie</span><wbr><span class="" id=":yr.78" tabindex="-1" style="">ntificName</span>)</font><br><br></div><div><font color="#0000ff">[1] "<span class="" id=":yr.79" tabindex="-1" style="">Quercus</span> <span class="" id=":yr.80" tabindex="-1" style="">palustris</span> <span class="" id=":yr.81" tabindex="-1" style="">Münchh</span>."</font><br><br></div><div><font color="#0000ff">> unique(<span class="" id=":yr.82" tabindex="-1" style="">coccinea</span>.<span class="" id=":yr.83" tabindex="-1" style="">occ</span>$data$<span class="" id=":yr.84" tabindex="-1" style="">scien</span><wbr><span class="" id=":yr.85" tabindex="-1" style="">tificName</span>)</font><br><br></div><div><font color="#0000ff">[1] "<span class="" id=":yr.86" tabindex="-1" style="">Quercus</span> <span class="" id=":yr.87" tabindex="-1" style="">coccinea</span> <span class="" id=":yr.88" tabindex="-1" style="">Münchh</span>." "<span class="" id=":yr.89" tabindex="-1" style="">Quercus</span> <span class="" id=":yr.90" tabindex="-1" style="">palustris</span> <span class="" id=":yr.91" tabindex="-1" style="">Regel</span> ex A.DC." "<span class="" id=":yr.92" tabindex="-1" style="">Quercus</span> <span class="" id=":yr.93" tabindex="-1" style="">coccinea</span> var. <span class="" id=":yr.94" tabindex="-1" style="">tuberculata</span> <span class="" id=":yr.95" tabindex="-1" style="">Sarg</span>." </font></div><div><font color="#0000ff">[4] "<span class="" id=":yr.96" tabindex="-1" style="">Quercus</span> <span class="" id=":yr.97" tabindex="-1" style="">coccinea</span> <span class="" id=":yr.98" tabindex="-1" style="">subsp</span>. <span class="" id=":yr.99" tabindex="-1" style="">microcarpa</span> Torrey" "<span class="" id=":yr.100" tabindex="-1" style="">Quercus</span> <span class="" id=":yr.101" tabindex="-1" style="">coccinea</span> var. <span class="" id=":yr.102" tabindex="-1" style="">coccinea</span></font></div></div>
<font color="#000000"><br></font></div><div style="font-size:12.8px;text-decoration-style:initial;text-decoration-color:initial"><font color="#000000">Scott suggested an alternative approach ::</font></div><div style="font-size:12.8px;text-decoration-style:initial;text-decoration-color:initial"><font color="#000000"><br></font></div><div style="font-size:12.8px;text-decoration-style:initial;text-decoration-color:initial"><font color="#0000ff">x = name_<span class="" id=":yr.103" tabindex="-1" style="">lookup</span>('Quercus palustris')</font></div><div style="font-size:12.8px;text-decoration-style:initial;text-decoration-color:initial"><font color="#0000ff">keys = x$data$key</font></div><div style="font-size:12.8px;text-decoration-style:initial;text-decoration-color:initial"><font color="#0000ff">out = <span class="" id=":yr.104" tabindex="-1" style="">occ</span>_data(<span class="" id=":yr.105" tabindex="-1" style="">taxonKey</span> = keys, limit = 200000)</font><br></div><div style="font-size:12.8px;text-decoration-style:initial;text-decoration-color:initial"><font color="#000000"><br></font></div>
<div><font color="#000000">However, using this approach on another species (e.g. Acacia <span class="" id=":yr.106" tabindex="-1" style="">baileyana</span>) returns names for other organisms (e.g. invertebrates!).<br></font></div><div><font color="#000000"><br></font></div><div><font color="#000000">So it sounds like using
<span id="gmail-m_1652888918331982635:2cz.51" style="font-size:12.8px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial"><span class="" id=":yr.107" tabindex="-1" style="">occ</span></span><span style="font-size:12.8px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline">_data on the <span class="" id=":yr.108" tabindex="-1" style="">taxon</span> key, then searching all synonyms separately might be the safest approach?<br><br>Thanks very much,</span></font></div><div><font color="#000000"><br></font></div><font color="#000000">-- <br></font><div class="gmail_signature"><font color="#000000">Hugh</font></div>
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