website update

2025-07-09 04:02:19 +02:00 · 2018-12-31 14:30:06 +01:00
parent 154fec27dd
commit 4255707cb7
28 changed files with 64036 additions and 613 deletions
--- a/docs/reference/mo_property.html
+++ b/docs/reference/mo_property.html
@ -270,87 +270,67 @@ This package contains the <strong>complete microbial taxonomic data</strong> (wi
    

    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
-<span class='co'># All properties of Escherichia coli</span>
+    <pre class="examples"><div class='input'><span class='co'># All properties of Escherichia coli</span>
 <span class='co'>## taxonomic properties</span>
-<span class='fu'>mo_kingdom</span>(<span class='st'>"E. coli"</span>)         <span class='co'># "Bacteria"</span>
-<span class='fu'>mo_subkingdom</span>(<span class='st'>"E. coli"</span>)      <span class='co'># "Negibacteria"</span>
-<span class='fu'>mo_phylum</span>(<span class='st'>"E. coli"</span>)          <span class='co'># "Proteobacteria"</span>
-<span class='fu'>mo_class</span>(<span class='st'>"E. coli"</span>)           <span class='co'># "Gammaproteobacteria"</span>
-<span class='fu'>mo_order</span>(<span class='st'>"E. coli"</span>)           <span class='co'># "Enterobacteriales"</span>
-<span class='fu'>mo_family</span>(<span class='st'>"E. coli"</span>)          <span class='co'># "Enterobacteriaceae"</span>
-<span class='fu'>mo_genus</span>(<span class='st'>"E. coli"</span>)           <span class='co'># "Escherichia"</span>
-<span class='fu'>mo_species</span>(<span class='st'>"E. coli"</span>)         <span class='co'># "coli"</span>
-<span class='fu'>mo_subspecies</span>(<span class='st'>"E. coli"</span>)      <span class='co'># NA</span>
-<span class='fu'>mo_TSN</span>(<span class='st'>"E. coli"</span>)             <span class='co'># 285 (Taxonomic Serial Number)</span>
-
+<span class='fu'>mo_kingdom</span>(<span class='st'>"E. coli"</span>)         <span class='co'># "Bacteria"</span></div><div class='output co'>#&gt; [1] "Bacteria"</div><div class='input'><span class='fu'>mo_subkingdom</span>(<span class='st'>"E. coli"</span>)      <span class='co'># "Negibacteria"</span></div><div class='output co'>#&gt; [1] "Negibacteria"</div><div class='input'><span class='fu'>mo_phylum</span>(<span class='st'>"E. coli"</span>)          <span class='co'># "Proteobacteria"</span></div><div class='output co'>#&gt; [1] "Proteobacteria"</div><div class='input'><span class='fu'>mo_class</span>(<span class='st'>"E. coli"</span>)           <span class='co'># "Gammaproteobacteria"</span></div><div class='output co'>#&gt; [1] "Gammaproteobacteria"</div><div class='input'><span class='fu'>mo_order</span>(<span class='st'>"E. coli"</span>)           <span class='co'># "Enterobacteriales"</span></div><div class='output co'>#&gt; [1] "Enterobacteriales"</div><div class='input'><span class='fu'>mo_family</span>(<span class='st'>"E. coli"</span>)          <span class='co'># "Enterobacteriaceae"</span></div><div class='output co'>#&gt; [1] "Enterobacteriaceae"</div><div class='input'><span class='fu'>mo_genus</span>(<span class='st'>"E. coli"</span>)           <span class='co'># "Escherichia"</span></div><div class='output co'>#&gt; [1] "Escherichia"</div><div class='input'><span class='fu'>mo_species</span>(<span class='st'>"E. coli"</span>)         <span class='co'># "coli"</span></div><div class='output co'>#&gt; [1] "coli"</div><div class='input'><span class='fu'>mo_subspecies</span>(<span class='st'>"E. coli"</span>)      <span class='co'># NA</span></div><div class='output co'>#&gt; [1] NA</div><div class='input'><span class='fu'>mo_TSN</span>(<span class='st'>"E. coli"</span>)             <span class='co'># 285 (Taxonomic Serial Number)</span></div><div class='output co'>#&gt; [1] 285</div><div class='input'>
 <span class='co'>## colloquial properties</span>
-<span class='fu'>mo_fullname</span>(<span class='st'>"E. coli"</span>)        <span class='co'># "Escherichia coli"</span>
-<span class='fu'>mo_shortname</span>(<span class='st'>"E. coli"</span>)       <span class='co'># "E. coli"</span>
-
+<span class='fu'>mo_fullname</span>(<span class='st'>"E. coli"</span>)        <span class='co'># "Escherichia coli"</span></div><div class='output co'>#&gt; [1] "Escherichia coli"</div><div class='input'><span class='fu'>mo_shortname</span>(<span class='st'>"E. coli"</span>)       <span class='co'># "E. coli"</span></div><div class='output co'>#&gt; [1] "E. coli"</div><div class='input'>
 <span class='co'>## other properties</span>
-<span class='fu'>mo_gramstain</span>(<span class='st'>"E. coli"</span>)       <span class='co'># "Gram negative"</span>
-<span class='fu'>mo_type</span>(<span class='st'>"E. coli"</span>)            <span class='co'># "Bacteria" (equal to kingdom)</span>
-
+<span class='fu'>mo_gramstain</span>(<span class='st'>"E. coli"</span>)       <span class='co'># "Gram negative"</span></div><div class='output co'>#&gt; [1] "Gram-negatief"</div><div class='input'><span class='fu'>mo_type</span>(<span class='st'>"E. coli"</span>)            <span class='co'># "Bacteria" (equal to kingdom)</span></div><div class='output co'>#&gt; [1] "Bacteriën"</div><div class='input'>
 <span class='co'>## scientific reference</span>
-<span class='fu'>mo_ref</span>(<span class='st'>"E. coli"</span>)             <span class='co'># "Castellani and Chalmers, 1919"</span>
-<span class='fu'>mo_authors</span>(<span class='st'>"E. coli"</span>)         <span class='co'># "Castellani and Chalmers"</span>
-<span class='fu'>mo_year</span>(<span class='st'>"E. coli"</span>)            <span class='co'># 1919</span>
-
+<span class='fu'>mo_ref</span>(<span class='st'>"E. coli"</span>)             <span class='co'># "Castellani and Chalmers, 1919"</span></div><div class='output co'>#&gt; [1] "Castellani and Chalmers, 1919"</div><div class='input'><span class='fu'>mo_authors</span>(<span class='st'>"E. coli"</span>)         <span class='co'># "Castellani and Chalmers"</span></div><div class='output co'>#&gt; [1] "Castellani and Chalmers"</div><div class='input'><span class='fu'>mo_year</span>(<span class='st'>"E. coli"</span>)            <span class='co'># 1919</span></div><div class='output co'>#&gt; [1] 1919</div><div class='input'>

 <span class='co'># Abbreviations known in the field</span>
-<span class='fu'>mo_genus</span>(<span class='st'>"MRSA"</span>)              <span class='co'># "Staphylococcus"</span>
-<span class='fu'>mo_species</span>(<span class='st'>"MRSA"</span>)            <span class='co'># "aureus"</span>
-<span class='fu'>mo_shortname</span>(<span class='st'>"MRSA"</span>)          <span class='co'># "S. aureus"</span>
-<span class='fu'>mo_gramstain</span>(<span class='st'>"MRSA"</span>)          <span class='co'># "Gram positive"</span>
-
-<span class='fu'>mo_genus</span>(<span class='st'>"VISA"</span>)              <span class='co'># "Staphylococcus"</span>
-<span class='fu'>mo_species</span>(<span class='st'>"VISA"</span>)            <span class='co'># "aureus"</span>
-
+<span class='fu'>mo_genus</span>(<span class='st'>"MRSA"</span>)              <span class='co'># "Staphylococcus"</span></div><div class='output co'>#&gt; [1] "Staphylococcus"</div><div class='input'><span class='fu'>mo_species</span>(<span class='st'>"MRSA"</span>)            <span class='co'># "aureus"</span></div><div class='output co'>#&gt; [1] "aureus"</div><div class='input'><span class='fu'>mo_shortname</span>(<span class='st'>"MRSA"</span>)          <span class='co'># "S. aureus"</span></div><div class='output co'>#&gt; [1] "S. aureus"</div><div class='input'><span class='fu'>mo_gramstain</span>(<span class='st'>"MRSA"</span>)          <span class='co'># "Gram positive"</span></div><div class='output co'>#&gt; [1] "Gram-positief"</div><div class='input'>
+<span class='fu'>mo_genus</span>(<span class='st'>"VISA"</span>)              <span class='co'># "Staphylococcus"</span></div><div class='output co'>#&gt; [1] "Staphylococcus"</div><div class='input'><span class='fu'>mo_species</span>(<span class='st'>"VISA"</span>)            <span class='co'># "aureus"</span></div><div class='output co'>#&gt; [1] "aureus"</div><div class='input'>

 <span class='co'># Known subspecies</span>
-<span class='fu'>mo_genus</span>(<span class='st'>"doylei"</span>)            <span class='co'># "Campylobacter"</span>
-<span class='fu'>mo_species</span>(<span class='st'>"doylei"</span>)          <span class='co'># "jejuni"</span>
-<span class='fu'>mo_fullname</span>(<span class='st'>"doylei"</span>)         <span class='co'># "Campylobacter jejuni doylei"</span>
-
-<span class='fu'>mo_fullname</span>(<span class='st'>"K. pneu rh"</span>)     <span class='co'># "Klebsiella pneumoniae rhinoscleromatis"</span>
-<span class='fu'>mo_shortname</span>(<span class='st'>"K. pneu rh"</span>)    <span class='co'># "K. pneumoniae"</span>
-
+<span class='fu'>mo_genus</span>(<span class='st'>"doylei"</span>)            <span class='co'># "Campylobacter"</span></div><div class='output co'>#&gt; <span class='warning'>Warning: <span style='color: #BB0000;'>These 1 values could not be coerced to a valid MO code: "doylei". See mo_failures() to review them.</span><span></span></div><div class='output co'>#&gt; [1] NA</div><div class='input'><span class='fu'>mo_species</span>(<span class='st'>"doylei"</span>)          <span class='co'># "jejuni"</span></div><div class='output co'>#&gt; <span class='warning'>Warning: </span><span style='color: #BB0000;'>These 1 values could not be coerced to a valid MO code: "doylei". See mo_failures() to review them.</span><span></span></div><div class='output co'>#&gt; [1] NA</div><div class='input'><span class='fu'>mo_fullname</span>(<span class='st'>"doylei"</span>)         <span class='co'># "Campylobacter jejuni doylei"</span></div><div class='output co'>#&gt; <span class='warning'>Warning: </span><span style='color: #BB0000;'>These 1 values could not be coerced to a valid MO code: "doylei". See mo_failures() to review them.</span><span></span></div><div class='output co'>#&gt; [1] NA</div><div class='input'>
+<span class='fu'>mo_fullname</span>(<span class='st'>"K. pneu rh"</span>)     <span class='co'># "Klebsiella pneumoniae rhinoscleromatis"</span></div><div class='output co'>#&gt; [1] "Klebsiella pneumoniae rhinoscleromatis"</div><div class='input'><span class='fu'>mo_shortname</span>(<span class='st'>"K. pneu rh"</span>)    <span class='co'># "K. pneumoniae"</span></div><div class='output co'>#&gt; [1] "K. pneumoniae"</div><div class='input'>

 <span class='co'># Becker classification, see ?as.mo</span>
-<span class='fu'>mo_fullname</span>(<span class='st'>"S. epi"</span>)                     <span class='co'># "Staphylococcus epidermidis"</span>
-<span class='fu'>mo_fullname</span>(<span class='st'>"S. epi"</span>, <span class='kw'>Becker</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)      <span class='co'># "Coagulase Negative Staphylococcus (CoNS)"</span>
-<span class='fu'>mo_shortname</span>(<span class='st'>"S. epi"</span>)                    <span class='co'># "S. epidermidis"</span>
-<span class='fu'>mo_shortname</span>(<span class='st'>"S. epi"</span>, <span class='kw'>Becker</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)     <span class='co'># "CoNS"</span>
-
+<span class='fu'>mo_fullname</span>(<span class='st'>"S. epi"</span>)                     <span class='co'># "Staphylococcus epidermidis"</span></div><div class='output co'>#&gt; [1] "Staphylococcus epidermidis"</div><div class='input'><span class='fu'>mo_fullname</span>(<span class='st'>"S. epi"</span>, <span class='kw'>Becker</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)      <span class='co'># "Coagulase Negative Staphylococcus (CoNS)"</span></div><div class='output co'>#&gt; [1] "Coagulase-negatieve Staphylococcus (CNS)"</div><div class='input'><span class='fu'>mo_shortname</span>(<span class='st'>"S. epi"</span>)                    <span class='co'># "S. epidermidis"</span></div><div class='output co'>#&gt; [1] "S. epidermidis"</div><div class='input'><span class='fu'>mo_shortname</span>(<span class='st'>"S. epi"</span>, <span class='kw'>Becker</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)     <span class='co'># "CoNS"</span></div><div class='output co'>#&gt; [1] "CNS"</div><div class='input'>
 <span class='co'># Lancefield classification, see ?as.mo</span>
-<span class='fu'>mo_fullname</span>(<span class='st'>"S. pyo"</span>)                     <span class='co'># "Streptococcus pyogenes"</span>
-<span class='fu'>mo_fullname</span>(<span class='st'>"S. pyo"</span>, <span class='kw'>Lancefield</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)  <span class='co'># "Streptococcus group A"</span>
-<span class='fu'>mo_shortname</span>(<span class='st'>"S. pyo"</span>)                    <span class='co'># "S. pyogenes"</span>
-<span class='fu'>mo_shortname</span>(<span class='st'>"S. pyo"</span>, <span class='kw'>Lancefield</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='co'># "GAS" ('Group A streptococci')</span>
-
+<span class='fu'>mo_fullname</span>(<span class='st'>"S. pyo"</span>)                     <span class='co'># "Streptococcus pyogenes"</span></div><div class='output co'>#&gt; [1] "Streptococcus pyogenes"</div><div class='input'><span class='fu'>mo_fullname</span>(<span class='st'>"S. pyo"</span>, <span class='kw'>Lancefield</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)  <span class='co'># "Streptococcus group A"</span></div><div class='output co'>#&gt; [1] "Streptococcus groep A"</div><div class='input'><span class='fu'>mo_shortname</span>(<span class='st'>"S. pyo"</span>)                    <span class='co'># "S. pyogenes"</span></div><div class='output co'>#&gt; [1] "S. pyogenes"</div><div class='input'><span class='fu'>mo_shortname</span>(<span class='st'>"S. pyo"</span>, <span class='kw'>Lancefield</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='co'># "GAS" ('Group A streptococci')</span></div><div class='output co'>#&gt; [1] "GAS"</div><div class='input'>

 <span class='co'># Language support for German, Dutch, Spanish, Portuguese, Italian and French</span>
-<span class='fu'>mo_gramstain</span>(<span class='st'>"E. coli"</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='st'>"de"</span>)  <span class='co'># "Gramnegativ"</span>
-<span class='fu'>mo_gramstain</span>(<span class='st'>"E. coli"</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='st'>"nl"</span>)  <span class='co'># "Gram-negatief"</span>
-<span class='fu'>mo_gramstain</span>(<span class='st'>"E. coli"</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='st'>"es"</span>)  <span class='co'># "Gram negativo"</span>
-
+<span class='fu'>mo_gramstain</span>(<span class='st'>"E. coli"</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='st'>"de"</span>)  <span class='co'># "Gramnegativ"</span></div><div class='output co'>#&gt; [1] "Gramnegativ"</div><div class='input'><span class='fu'>mo_gramstain</span>(<span class='st'>"E. coli"</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='st'>"nl"</span>)  <span class='co'># "Gram-negatief"</span></div><div class='output co'>#&gt; [1] "Gram-negatief"</div><div class='input'><span class='fu'>mo_gramstain</span>(<span class='st'>"E. coli"</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='st'>"es"</span>)  <span class='co'># "Gram negativo"</span></div><div class='output co'>#&gt; [1] "Gram negativo"</div><div class='input'>
 <span class='co'># mo_type is equal to mo_kingdom, but mo_kingdom will remain official</span>
-<span class='fu'>mo_kingdom</span>(<span class='st'>"E. coli"</span>)                     <span class='co'># "Bacteria" on a German system</span>
-<span class='fu'>mo_type</span>(<span class='st'>"E. coli"</span>)                        <span class='co'># "Bakterien" on a German system</span>
-<span class='fu'>mo_type</span>(<span class='st'>"E. coli"</span>)                        <span class='co'># "Bacteria" on an English system</span>
-
+<span class='fu'>mo_kingdom</span>(<span class='st'>"E. coli"</span>)                     <span class='co'># "Bacteria" on a German system</span></div><div class='output co'>#&gt; [1] "Bacteria"</div><div class='input'><span class='fu'>mo_type</span>(<span class='st'>"E. coli"</span>)                        <span class='co'># "Bakterien" on a German system</span></div><div class='output co'>#&gt; [1] "Bacteriën"</div><div class='input'><span class='fu'>mo_type</span>(<span class='st'>"E. coli"</span>)                        <span class='co'># "Bacteria" on an English system</span></div><div class='output co'>#&gt; [1] "Bacteriën"</div><div class='input'>
 <span class='fu'>mo_fullname</span>(<span class='st'>"S. pyogenes"</span>,
            <span class='kw'>Lancefield</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
-            <span class='kw'>language</span> <span class='kw'>=</span> <span class='st'>"de"</span>)              <span class='co'># "Streptococcus Gruppe A"</span>
-<span class='fu'>mo_fullname</span>(<span class='st'>"S. pyogenes"</span>,
+            <span class='kw'>language</span> <span class='kw'>=</span> <span class='st'>"de"</span>)              <span class='co'># "Streptococcus Gruppe A"</span></div><div class='output co'>#&gt; [1] "Streptococcus Gruppe A"</div><div class='input'><span class='fu'>mo_fullname</span>(<span class='st'>"S. pyogenes"</span>,
            <span class='kw'>Lancefield</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
-            <span class='kw'>language</span> <span class='kw'>=</span> <span class='st'>"nl"</span>)              <span class='co'># "Streptococcus groep A"</span>
-
+            <span class='kw'>language</span> <span class='kw'>=</span> <span class='st'>"nl"</span>)              <span class='co'># "Streptococcus groep A"</span></div><div class='output co'>#&gt; [1] "Streptococcus groep A"</div><div class='input'>

 <span class='co'># Get a list with the complete taxonomy (subkingdom to subspecies)</span>
-<span class='fu'>mo_taxonomy</span>(<span class='st'>"E. coli"</span>)
-<span class='co'># }</span></pre>
+<span class='fu'>mo_taxonomy</span>(<span class='st'>"E. coli"</span>)</div><div class='output co'>#&gt; $kingdom
+#&gt; [1] "Bacteria"
+#&gt; 
+#&gt; $subkingdom
+#&gt; [1] "Negibacteria"
+#&gt; 
+#&gt; $phylum
+#&gt; [1] "Proteobacteria"
+#&gt; 
+#&gt; $class
+#&gt; [1] "Gammaproteobacteria"
+#&gt; 
+#&gt; $order
+#&gt; [1] "Enterobacteriales"
+#&gt; 
+#&gt; $family
+#&gt; [1] "Enterobacteriaceae"
+#&gt; 
+#&gt; $genus
+#&gt; [1] "Escherichia"
+#&gt; 
+#&gt; $species
+#&gt; [1] "coli"
+#&gt; 
+#&gt; $subspecies
+#&gt; [1] NA
+#&gt; </div></span></pre>
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