Start new version, rename pp to ppp, more docs

8 files changed, 546 insertions, 24 deletions

diff --git a/docs/reference/chent.html b/docs/reference/chent.html
index a6b8dde..48ccf3f 100644
--- a/docs/reference/chent.html
+++ b/docs/reference/chent.html
@@ -19,7 +19,7 @@ generated using RDKit if RDKit and its python bindings are installed."><!-- math
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">chents</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.3.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.3.2</span>
       </span>
     </div>
 
@@ -126,15 +126,18 @@ List of information retrieved from PubChem</p></dd>
 
 
 <dt><code>TPs</code></dt>
-<dd><p>List of transformation products as chent objects</p></dd>
+<dd><p>List of transformation products as chent objects
+Add a transformation product to the internal list</p></dd>
 
 
 <dt><code>transformations</code></dt>
-<dd><p>Data frame of observed transformations</p></dd>
+<dd><p>Data frame of observed transformations
+Add a line in the internal dataframe holding observed transformations</p></dd>
 
 
 <dt><code>soil_degradation</code></dt>
-<dd><p>Dataframe of modelling DT50 values</p></dd>
+<dd><p>Dataframe of modelling DT50 values
+Add a line in the internal dataframe holding modelling DT50 values</p></dd>
 
 
 <dt><code>soil_ff</code></dt>
@@ -142,7 +145,8 @@ List of information retrieved from PubChem</p></dd>
 
 
 <dt><code>soil_sorption</code></dt>
-<dd><p>Dataframe of soil sorption data</p></dd>
+<dd><p>Dataframe of soil sorption data
+Add soil sorption data</p></dd>
 
 
 </dl><p></p></div>
@@ -262,7 +266,8 @@ Get chemical information from PubChem for a known PubChem CID</p></dd>
 <div class="section">
 <h4 id="arguments-2">Arguments<a class="anchor" aria-label="anchor" href="#arguments-2"></a></h4>
 <p></p><div class="arguments"><dl><dt><code>pubchem_cid</code></dt>
-<dd><p>CID</p></dd>
+<dd><p>CID
+Get chemical information from RDKit if available</p></dd>
 
 
 </dl><p></p></div>
@@ -276,6 +281,15 @@ Get chemical information from PubChem for a known PubChem CID</p></dd>
 <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">get_rdkit</span><span class="op">(</span>template <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span></span></code></pre></div><p></p></div>
 </div>
 
+<div class="section">
+<h4 id="arguments-3">Arguments<a class="anchor" aria-label="anchor" href="#arguments-3"></a></h4>
+<p></p><div class="arguments"><dl><dt><code>template</code></dt>
+<dd><p>Optional template specified as a SMILES code
+Obtain information from a YAML file</p></dd>
+
+
+</dl><p></p></div>
+</div>
 
 </div><p></p><hr><a id="method-chent-get_chyaml"></a><div class="section">
 <h3 id="method-get-chyaml-">Method <code>get_chyaml()</code><a class="anchor" aria-label="anchor" href="#method-get-chyaml-"></a></h3>
@@ -288,6 +302,21 @@ Get chemical information from PubChem for a known PubChem CID</p></dd>
 <span><span class="op">)</span></span></code></pre></div><p></p></div>
 </div>
 
+<div class="section">
+<h4 id="arguments-4">Arguments<a class="anchor" aria-label="anchor" href="#arguments-4"></a></h4>
+<p></p><div class="arguments"><dl><dt><code>repo</code></dt>
+<dd><p>Should the file be looked for in the current working
+directory, a local git repository under <code>~/git/chyaml</code>, or from
+the web (not implemented).</p></dd>
+
+
+<dt><code>chyaml</code></dt>
+<dd><p>The filename to be looked for
+Add a vapour pressure</p></dd>
+
+
+</dl><p></p></div>
+</div>
 
 </div><p></p><hr><a id="method-chent-add_p0"></a><div class="section">
 <h3 id="method-add-p-">Method <code>add_p0()</code><a class="anchor" aria-label="anchor" href="#method-add-p-"></a></h3>
@@ -297,6 +326,31 @@ Get chemical information from PubChem for a known PubChem CID</p></dd>
 <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">add_p0</span><span class="op">(</span><span class="va">p0</span>, T <span class="op">=</span> <span class="cn">NA</span>, source <span class="op">=</span> <span class="cn">NA</span>, page <span class="op">=</span> <span class="cn">NA</span>, remark <span class="op">=</span> <span class="st">""</span><span class="op">)</span></span></code></pre></div><p></p></div>
 </div>
 
+<div class="section">
+<h4 id="arguments-5">Arguments<a class="anchor" aria-label="anchor" href="#arguments-5"></a></h4>
+<p></p><div class="arguments"><dl><dt><code>p0</code></dt>
+<dd><p>The vapour pressure in Pa</p></dd>
+
+
+<dt><code>T</code></dt>
+<dd><p>Temperature</p></dd>
+
+
+<dt><code>source</code></dt>
+<dd><p>An acronym specifying the source of the information</p></dd>
+
+
+<dt><code>page</code></dt>
+<dd><p>The page from which the information was taken</p></dd>
+
+
+<dt><code>remark</code></dt>
+<dd><p>A remark
+Add a water solubility</p></dd>
+
+
+</dl><p></p></div>
+</div>
 
 </div><p></p><hr><a id="method-chent-add_cwsat"></a><div class="section">
 <h3 id="method-add-cwsat-">Method <code>add_cwsat()</code><a class="anchor" aria-label="anchor" href="#method-add-cwsat-"></a></h3>
@@ -306,6 +360,35 @@ Get chemical information from PubChem for a known PubChem CID</p></dd>
 <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">add_cwsat</span><span class="op">(</span><span class="va">cwsat</span>, T <span class="op">=</span> <span class="cn">NA</span>, pH <span class="op">=</span> <span class="cn">NA</span>, source <span class="op">=</span> <span class="cn">NA</span>, page <span class="op">=</span> <span class="cn">NA</span>, remark <span class="op">=</span> <span class="st">""</span><span class="op">)</span></span></code></pre></div><p></p></div>
 </div>
 
+<div class="section">
+<h4 id="arguments-6">Arguments<a class="anchor" aria-label="anchor" href="#arguments-6"></a></h4>
+<p></p><div class="arguments"><dl><dt><code>cwsat</code></dt>
+<dd><p>The water solubility in mg/L</p></dd>
+
+
+<dt><code>T</code></dt>
+<dd><p>Temperature</p></dd>
+
+
+<dt><code>pH</code></dt>
+<dd><p>The pH value</p></dd>
+
+
+<dt><code>source</code></dt>
+<dd><p>An acronym specifying the source of the information</p></dd>
+
+
+<dt><code>page</code></dt>
+<dd><p>The page from which the information was taken</p></dd>
+
+
+<dt><code>remark</code></dt>
+<dd><p>A remark
+Add a plant uptake factor</p></dd>
+
+
+</dl><p></p></div>
+</div>
 
 </div><p></p><hr><a id="method-chent-add_PUF"></a><div class="section">
 <h3 id="method-add-puf-">Method <code>add_PUF()</code><a class="anchor" aria-label="anchor" href="#method-add-puf-"></a></h3>
@@ -320,6 +403,26 @@ Get chemical information from PubChem for a known PubChem CID</p></dd>
 <span><span class="op">)</span></span></code></pre></div><p></p></div>
 </div>
 
+<div class="section">
+<h4 id="arguments-7">Arguments<a class="anchor" aria-label="anchor" href="#arguments-7"></a></h4>
+<p></p><div class="arguments"><dl><dt><code>PUF</code></dt>
+<dd><p>The plant uptake factor, a number between 0 and 1</p></dd>
+
+
+<dt><code>source</code></dt>
+<dd><p>An acronym specifying the source of the information</p></dd>
+
+
+<dt><code>page</code></dt>
+<dd><p>The page from which the information was taken</p></dd>
+
+
+<dt><code>remark</code></dt>
+<dd><p>A remark</p></dd>
+
+
+</dl><p></p></div>
+</div>
 
 </div><p></p><hr><a id="method-chent-add_TP"></a><div class="section">
 <h3 id="method-add-tp-">Method <code>add_TP()</code><a class="anchor" aria-label="anchor" href="#method-add-tp-"></a></h3>
@@ -329,6 +432,22 @@ Get chemical information from PubChem for a known PubChem CID</p></dd>
 <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">add_TP</span><span class="op">(</span><span class="va">x</span>, smiles <span class="op">=</span> <span class="cn">NULL</span>, pubchem <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div><p></p></div>
 </div>
 
+<div class="section">
+<h4 id="arguments-8">Arguments<a class="anchor" aria-label="anchor" href="#arguments-8"></a></h4>
+<p></p><div class="arguments"><dl><dt><code>x</code></dt>
+<dd><p>A chent object, or an identifier to generate a chent object</p></dd>
+
+
+<dt><code>smiles</code></dt>
+<dd><p>A SMILES code for defining a chent object</p></dd>
+
+
+<dt><code>pubchem</code></dt>
+<dd><p>Should chemical information be obtained from PubChem?</p></dd>
+
+
+</dl><p></p></div>
+</div>
 
 </div><p></p><hr><a id="method-chent-add_transformation"></a><div class="section">
 <h3 id="method-add-transformation-">Method <code>add_transformation()</code><a class="anchor" aria-label="anchor" href="#method-add-transformation-"></a></h3>
@@ -345,6 +464,37 @@ Get chemical information from PubChem for a known PubChem CID</p></dd>
 <span><span class="op">)</span></span></code></pre></div><p></p></div>
 </div>
 
+<div class="section">
+<h4 id="arguments-9">Arguments<a class="anchor" aria-label="anchor" href="#arguments-9"></a></h4>
+<p></p><div class="arguments"><dl><dt><code>study_type</code></dt>
+<dd><p>A characterisation of the study type</p></dd>
+
+
+<dt><code>TP_identifier</code></dt>
+<dd><p>An identifier of one of the transformation products
+in <code>self$TPs</code></p></dd>
+
+
+<dt><code>max_occurrence</code></dt>
+<dd><p>The maximum observed occurrence of the
+transformation product, expressed as a fraction of the amount that would
+result from stochiometric transformation</p></dd>
+
+
+<dt><code>remark</code></dt>
+<dd><p>A remark</p></dd>
+
+
+<dt><code>source</code></dt>
+<dd><p>An acronym specifying the source of the information</p></dd>
+
+
+<dt><code>pages</code></dt>
+<dd><p>The page from which the information was taken</p></dd>
+
+
+</dl><p></p></div>
+</div>
 
 </div><p></p><hr><a id="method-chent-add_soil_degradation"></a><div class="section">
 <h3 id="method-add-soil-degradation-">Method <code>add_soil_degradation()</code><a class="anchor" aria-label="anchor" href="#method-add-soil-degradation-"></a></h3>
@@ -373,6 +523,85 @@ Get chemical information from PubChem for a known PubChem CID</p></dd>
 <span><span class="op">)</span></span></code></pre></div><p></p></div>
 </div>
 
+<div class="section">
+<h4 id="arguments-10">Arguments<a class="anchor" aria-label="anchor" href="#arguments-10"></a></h4>
+<p></p><div class="arguments"><dl><dt><code>soils</code></dt>
+<dd><p>Names of the soils</p></dd>
+
+
+<dt><code>DT50_mod</code></dt>
+<dd><p>The modelling DT50 in the sense of regulatory pesticide
+fate modelling</p></dd>
+
+
+<dt><code>DT50_mod_ref</code></dt>
+<dd><p>The normalised modelling DT50 in the sense of
+regulatory pesticide fate modelling</p></dd>
+
+
+<dt><code>type</code></dt>
+<dd><p>The soil type</p></dd>
+
+
+<dt><code>country</code></dt>
+<dd><p>The country (mainly for field studies)</p></dd>
+
+
+<dt><code>pH_orig</code></dt>
+<dd><p>The pH stated in the study</p></dd>
+
+
+<dt><code>pH_medium</code></dt>
+<dd><p>The medium in which this pH was measured</p></dd>
+
+
+<dt><code>pH_H2O</code></dt>
+<dd><p>The pH extrapolated to pure water</p></dd>
+
+
+<dt><code>perc_OC</code></dt>
+<dd><p>The percentage of organic carbon in the soil</p></dd>
+
+
+<dt><code>temperature</code></dt>
+<dd><p>The temperature during the study in degrees Celsius</p></dd>
+
+
+<dt><code>moisture</code></dt>
+<dd><p>The moisture during the study</p></dd>
+
+
+<dt><code>category</code></dt>
+<dd><p>Is it a laboratory ('lab') or field study ('field')</p></dd>
+
+
+<dt><code>formulation</code></dt>
+<dd><p>Name of the formulation applied, if it was not
+the technical active ingredient</p></dd>
+
+
+<dt><code>model</code></dt>
+<dd><p>The degradation model used for deriving <code>DT50_mod</code></p></dd>
+
+
+<dt><code>chi2</code></dt>
+<dd><p>The relative error as defined in FOCUS kinetics</p></dd>
+
+
+<dt><code>remark</code></dt>
+<dd><p>A remark</p></dd>
+
+
+<dt><code>source</code></dt>
+<dd><p>An acronym specifying the source of the information</p></dd>
+
+
+<dt><code>page</code></dt>
+<dd><p>The page from which the information was taken</p></dd>
+
+
+</dl><p></p></div>
+</div>
 
 </div><p></p><hr><a id="method-chent-add_soil_ff"></a><div class="section">
 <h3 id="method-add-soil-ff-">Method <code>add_soil_ff()</code><a class="anchor" aria-label="anchor" href="#method-add-soil-ff-"></a></h3>
@@ -382,6 +611,22 @@ Get chemical information from PubChem for a known PubChem CID</p></dd>
 <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">add_soil_ff</span><span class="op">(</span><span class="va">target</span>, <span class="va">soils</span>, ff <span class="op">=</span> <span class="fl">1</span>, remark <span class="op">=</span> <span class="st">""</span>, <span class="va">source</span>, page <span class="op">=</span> <span class="cn">NA</span><span class="op">)</span></span></code></pre></div><p></p></div>
 </div>
 
+<div class="section">
+<h4 id="arguments-11">Arguments<a class="anchor" aria-label="anchor" href="#arguments-11"></a></h4>
+<p></p><div class="arguments"><dl><dt><code>target</code></dt>
+<dd><p>The identifier(s) of the transformation product</p></dd>
+
+
+<dt><code>soils</code></dt>
+<dd><p>The soil name(s) in which the transformation was observed</p></dd>
+
+
+<dt><code>ff</code></dt>
+<dd><p>The formation fraction(s)</p></dd>
+
+
+</dl><p></p></div>
+</div>
 
 </div><p></p><hr><a id="method-chent-add_soil_sorption"></a><div class="section">
 <h3 id="method-add-soil-sorption-">Method <code>add_soil_sorption()</code><a class="anchor" aria-label="anchor" href="#method-add-soil-sorption-"></a></h3>
@@ -406,6 +651,32 @@ Get chemical information from PubChem for a known PubChem CID</p></dd>
 <span><span class="op">)</span></span></code></pre></div><p></p></div>
 </div>
 
+<div class="section">
+<h4 id="arguments-12">Arguments<a class="anchor" aria-label="anchor" href="#arguments-12"></a></h4>
+<p></p><div class="arguments"><dl><dt><code>Kf</code></dt>
+<dd><p>The sorption constant in L/kg, either linear (then <code>N</code> is 1)
+or according to Freundlich</p></dd>
+
+
+<dt><code>Kfoc</code></dt>
+<dd><p>The constant from above, normalised to soil organic carbon</p></dd>
+
+
+<dt><code>N</code></dt>
+<dd><p>The Freundlich exponent</p></dd>
+
+
+<dt><code>perc_clay</code></dt>
+<dd><p>The percentage of clay in the soil</p></dd>
+
+
+<dt><code>CEC</code></dt>
+<dd><p>The cation exchange capacity
+Write a PDF image of the structure</p></dd>
+
+
+</dl><p></p></div>
+</div>
 
 </div><p></p><hr><a id="method-chent-pdf"></a><div class="section">
 <h3 id="method-pdf-">Method <code><a href="https://rdrr.io/r/grDevices/pdf.html" class="external-link">pdf()</a></code><a class="anchor" aria-label="anchor" href="#method-pdf-"></a></h3>
@@ -419,6 +690,23 @@ Get chemical information from PubChem for a known PubChem CID</p></dd>
 <span><span class="op">)</span></span></code></pre></div><p></p></div>
 </div>
 
+<div class="section">
+<h4 id="arguments-13">Arguments<a class="anchor" aria-label="anchor" href="#arguments-13"></a></h4>
+<p></p><div class="arguments"><dl><dt><code>file</code></dt>
+<dd><p>The file to write to</p></dd>
+
+
+<dt><code>dir</code></dt>
+<dd><p>The directory to write the file to</p></dd>
+
+
+<dt><code>template</code></dt>
+<dd><p>A template expressed as SMILES to use in RDKit
+Write a PNG image of the structure</p></dd>
+
+
+</dl><p></p></div>
+</div>
 
 </div><p></p><hr><a id="method-chent-png"></a><div class="section">
 <h3 id="method-png-">Method <code><a href="https://rdrr.io/r/grDevices/png.html" class="external-link">png()</a></code><a class="anchor" aria-label="anchor" href="#method-png-"></a></h3>
@@ -432,6 +720,15 @@ Get chemical information from PubChem for a known PubChem CID</p></dd>
 <span><span class="op">)</span></span></code></pre></div><p></p></div>
 </div>
 
+<div class="section">
+<h4 id="arguments-14">Arguments<a class="anchor" aria-label="anchor" href="#arguments-14"></a></h4>
+<p></p><div class="arguments"><dl><dt><code>antialias</code></dt>
+<dd><p>Passed to <a href="https://rdrr.io/r/grDevices/png.html" class="external-link">png</a>
+Write an EMF image of the structure using <a href="https://rdrr.io/pkg/devEMF/man/emf.html" class="external-link">emf</a></p></dd>
+
+
+</dl><p></p></div>
+</div>
 
 </div><p></p><hr><a id="method-chent-emf"></a><div class="section">
 <h3 id="method-emf-">Method <code>emf()</code><a class="anchor" aria-label="anchor" href="#method-emf-"></a></h3>
@@ -441,6 +738,14 @@ Get chemical information from PubChem for a known PubChem CID</p></dd>
 <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">emf</span><span class="op">(</span>file <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="va">self</span><span class="op">$</span><span class="va">identifier</span>, <span class="st">".emf"</span><span class="op">)</span>, dir <span class="op">=</span> <span class="st">"structures/emf"</span><span class="op">)</span></span></code></pre></div><p></p></div>
 </div>
 
+<div class="section">
+<h4 id="arguments-15">Arguments<a class="anchor" aria-label="anchor" href="#arguments-15"></a></h4>
+<p></p><div class="arguments"><dl><dt><code>file</code></dt>
+<dd><p>The file to write to</p></dd>
+
+
+</dl><p></p></div>
+</div>
 
 </div><p></p><hr><a id="method-chent-clone"></a><div class="section">
 <h3 id="method-clone-">Method <code>clone()</code><a class="anchor" aria-label="anchor" href="#method-clone-"></a></h3>
@@ -450,7 +755,7 @@ Get chemical information from PubChem for a known PubChem CID</p></dd>
 </div>
 
 <div class="section">
-<h4 id="arguments-3">Arguments<a class="anchor" aria-label="anchor" href="#arguments-3"></a></h4>
+<h4 id="arguments-16">Arguments<a class="anchor" aria-label="anchor" href="#arguments-16"></a></h4>
 <p></p><div class="arguments"><dl><dt><code>deep</code></dt>
 <dd><p>Whether to make a deep clone.</p></dd>
 
diff --git a/docs/reference/draw_svg.chent.html b/docs/reference/draw_svg.chent.html
index cae8c0b..a95748e 100644
--- a/docs/reference/draw_svg.chent.html
+++ b/docs/reference/draw_svg.chent.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">chents</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.3.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.3.2</span>
       </span>
     </div>
 
diff --git a/docs/reference/index.html b/docs/reference/index.html
index d9eb797..6bc6df8 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">chents</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.3.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.3.2</span>
       </span>
     </div>
 
@@ -72,9 +72,9 @@
         </td>
         <td><p>Printing method for pai objects (pesticidal active ingredients)</p></td>
       </tr><tr><td>
-          <p><code><a href="pp.html">pp</a></code> </p>
+          <p><code><a href="ppp.html">ppp</a></code> </p>
         </td>
-        <td><p>R6 class for holding a product with at least one active ingredient</p></td>
+        <td><p>R6 class for a plant protection product with at least one active ingredient</p></td>
       </tr></tbody></table></div>
 
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
diff --git a/docs/reference/pai.html b/docs/reference/pai.html
index 636007f..d8811d0 100644
--- a/docs/reference/pai.html
+++ b/docs/reference/pai.html
@@ -1,6 +1,6 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>An R6 class for pesticidal active ingredients and associated data — pai • chents</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="An R6 class for pesticidal active ingredients and associated data — pai"><meta property="og:description" content="The class is initialised with an identifier which is generally an ISO common name.
-Additional chemical information is retrieved from the internet if available."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>An R6 class for pesticidal active ingredients and associated data — pai • chents</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="An R6 class for pesticidal active ingredients and associated data — pai"><meta property="og:description" content="An R6 class for pesticidal active ingredients and associated data
+An R6 class for pesticidal active ingredients and associated data"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body data-spy="scroll" data-target="#toc">
@@ -18,7 +18,7 @@ Additional chemical information is retrieved from the internet if available."><!
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">chents</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.3.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.3.2</span>
       </span>
     </div>
 
@@ -47,8 +47,8 @@ Additional chemical information is retrieved from the internet if available."><!
     </div>
 
     <div class="ref-description">
-    <p>The class is initialised with an identifier which is generally an ISO common name.
-Additional chemical information is retrieved from the internet if available.</p>
+    <p>An R6 class for pesticidal active ingredients and associated data</p>
+<p>An R6 class for pesticidal active ingredients and associated data</p>
     </div>
 
 
@@ -56,6 +56,11 @@ Additional chemical information is retrieved from the internet if available.</p>
     <h2>Format</h2>
     <p>An <code>R6Class</code> generator object</p>
     </div>
+    <div id="details">
+    <h2>Details</h2>
+    <p>The class is initialised with an identifier which is generally an ISO common name.
+Additional chemical information is retrieved from the internet if available.</p>
+    </div>
     <div id="super-class">
     <h2>Super class</h2>
     <p><code><a href="chent.html">chents::chent</a></code> -&gt; <code>pai</code></p>
@@ -63,11 +68,13 @@ Additional chemical information is retrieved from the internet if available.</p>
     <div id="public-fields">
     <h2>Public fields</h2>
     <p></p><div class="r6-fields"><dl><dt><code>iso</code></dt>
-<dd><p>ISO common name according to ISO 1750 as retreived from pesticidecompendium.bcpc.org</p></dd>
+<dd><p>ISO common name of the active ingredient according to ISO 1750</p></dd>
 
 
 <dt><code>bcpc</code></dt>
-<dd><p>List of information retrieved from pesticidecompendium.bcpc.org</p></dd>
+<dd><p>Information retrieved from the BCPC compendium available online
+at &lt;pesticidecompendium.bcpc.org&gt;
+Creates a new instance of this <a href="https://r6.r-lib.org/reference/R6Class.html" class="external-link">R6</a> class.</p></dd>
 
 
 </dl><p></p></div>
@@ -97,8 +104,11 @@ Additional chemical information is retrieved from the internet if available.</p>
 <li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="try_pubchem"><a href="chent.html#method-try_pubchem"><code>chents::chent$try_pubchem()</code></a></span></li>
 </ul></details></p><hr><a id="method-pai-new"></a><div class="section">
 <h3 id="method-new-">Method <code>new()</code><a class="anchor" aria-label="anchor" href="#method-new-"></a></h3>
-
-<div class="section">
+<p>This class is derived from <a href="chent.html">chent</a>. It makes it easy
+to create a <a href="chent.html">chent</a> from the ISO common name of a pesticide active
+ingredient, and additionally stores the ISO name as well as
+the complete result of querying the BCPC compendium using
+<a href="https://docs.ropensci.org/webchem/reference/bcpc_query.html" class="external-link">bcpc_query</a>.</p><div class="section">
 <h4 id="usage">Usage<a class="anchor" aria-label="anchor" href="#usage"></a></h4>
 <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va"><a href="../reference/pai.html">pai</a></span><span class="op">$</span><span class="fu">new</span><span class="op">(</span></span>
 <span>  <span class="va">iso</span>,</span>
@@ -114,6 +124,19 @@ Additional chemical information is retrieved from the internet if available.</p>
 <span><span class="op">)</span></span></code></pre></div><p></p></div>
 </div>
 
+<div class="section">
+<h4 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h4>
+<p></p><div class="arguments"><dl><dt><code>iso</code></dt>
+<dd><p>The ISO common name to be used in the query of the
+BCPC compendium</p></dd>
+
+
+<dt><code>identifier</code></dt>
+<dd><p>Alternative identifier used for querying pubchem</p></dd>
+
+
+</dl><p></p></div>
+</div>
 
 </div><p></p><hr><a id="method-pai-clone"></a><div class="section">
 <h3 id="method-clone-">Method <code>clone()</code><a class="anchor" aria-label="anchor" href="#method-clone-"></a></h3>
@@ -123,7 +146,7 @@ Additional chemical information is retrieved from the internet if available.</p>
 </div>
 
 <div class="section">
-<h4 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h4>
+<h4 id="arguments-1">Arguments<a class="anchor" aria-label="anchor" href="#arguments-1"></a></h4>
 <p></p><div class="arguments"><dl><dt><code>deep</code></dt>
 <dd><p>Whether to make a deep clone.</p></dd>
 
diff --git a/docs/reference/plot.chent.html b/docs/reference/plot.chent.html
index 470ce79..26d8445 100644
--- a/docs/reference/plot.chent.html
+++ b/docs/reference/plot.chent.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">chents</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.3.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.3.2</span>
       </span>
     </div>
 
diff --git a/docs/reference/ppp.html b/docs/reference/ppp.html
new file mode 100644
index 0000000..7a9b861
--- /dev/null
+++ b/docs/reference/ppp.html
@@ -0,0 +1,194 @@
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>R6 class for a plant protection product with at least one active ingredient — ppp • chents</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="R6 class for a plant protection product with at least one active ingredient — ppp"><meta property="og:description" content="Contains basic information about the active ingredients in the
+product"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]--></head><body data-spy="scroll" data-target="#toc">
+    
+
+    <div class="container template-reference-topic">
+      <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
+  <div class="container">
+    <div class="navbar-header">
+      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+        <span class="sr-only">Toggle navigation</span>
+        <span class="icon-bar"></span>
+        <span class="icon-bar"></span>
+        <span class="icon-bar"></span>
+      </button>
+      <span class="navbar-brand">
+        <a class="navbar-link" href="../index.html">chents</a>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.3.2</span>
+      </span>
+    </div>
+
+    <div id="navbar" class="navbar-collapse collapse">
+      <ul class="nav navbar-nav"><li>
+  <a href="../reference/index.html">Reference</a>
+</li>
+      </ul><ul class="nav navbar-nav navbar-right"><li>
+  <a href="https://github.com/jranke/chents/" class="external-link">
+    <span class="fab fa-github fa-lg"></span>
+     
+  </a>
+</li>
+      </ul></div><!--/.nav-collapse -->
+  </div><!--/.container -->
+</div><!--/.navbar -->
+
+      
+
+      </header><div class="row">
+  <div class="col-md-9 contents">
+    <div class="page-header">
+    <h1>R6 class for a plant protection product with at least one active ingredient</h1>
+    <small class="dont-index">Source: <a href="https://github.com/jranke/chents/blob/HEAD/R/chent.R" class="external-link"><code>R/chent.R</code></a></small>
+    <div class="hidden name"><code>ppp.Rd</code></div>
+    </div>
+
+    <div class="ref-description">
+    <p>Contains basic information about the active ingredients in the
+product</p>
+    </div>
+
+
+    <div id="format">
+    <h2>Format</h2>
+    <p>An <code>R6Class</code> generator object.</p>
+    </div>
+    <div id="public-fields">
+    <h2>Public fields</h2>
+    <p></p><div class="r6-fields"><dl><dt><code>name</code></dt>
+<dd><p>The name of the product</p></dd>
+
+
+<dt><code>ais</code></dt>
+<dd><p>A list of active ingredients</p></dd>
+
+
+<dt><code>concentrations</code></dt>
+<dd><p>The concentration of the ais</p></dd>
+
+
+<dt><code>concentration_units</code></dt>
+<dd><p>Defaults to g/L</p></dd>
+
+
+<dt><code>density</code></dt>
+<dd><p>The density of the product</p></dd>
+
+
+<dt><code>density_units</code></dt>
+<dd><p>Defaults to g/L
+Creates a new instance of this <a href="https://r6.r-lib.org/reference/R6Class.html" class="external-link">R6</a> class.</p></dd>
+
+
+<dt><code>...</code></dt>
+<dd><p>Identifiers of the active ingredients</p></dd>
+
+
+<dt><code>concentrations</code></dt>
+<dd><p>Concentrations of the active ingredients</p></dd>
+
+
+<dt><code>concentration_units</code></dt>
+<dd><p>Defaults to g/L</p></dd>
+
+
+<dt><code>density</code></dt>
+<dd><p>The density</p></dd>
+
+
+<dt><code>density_units</code></dt>
+<dd><p>Defaults to g/L
+Printing method</p></dd>
+
+
+</dl><p></p></div>
+    </div>
+    <div id="active-bindings">
+    <h2>Active bindings</h2>
+    <p></p><div class="r6-active-bindings"><dl><dt><code>...</code></dt>
+<dd><p>Identifiers of the active ingredients</p></dd>
+
+
+</dl><p></p></div>
+    </div>
+    <div id="methods">
+    <h2>Methods</h2>
+    
+<div class="section">
+<h3 id="public-methods">Public methods<a class="anchor" aria-label="anchor" href="#public-methods"></a></h3>
+
+<ul><li><p><a href="#method-ppp-new"><code>ppp$new()</code></a></p></li>
+<li><p><a href="#method-ppp-print"><code>ppp$print()</code></a></p></li>
+<li><p><a href="#method-ppp-clone"><code>ppp$clone()</code></a></p></li>
+</ul></div><p></p><hr><a id="method-ppp-new"></a><div class="section">
+<h3 id="method-new-">Method <code>new()</code><a class="anchor" aria-label="anchor" href="#method-new-"></a></h3>
+
+<div class="section">
+<h4 id="usage">Usage<a class="anchor" aria-label="anchor" href="#usage"></a></h4>
+<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va"><a href="../reference/ppp.html">ppp</a></span><span class="op">$</span><span class="fu">new</span><span class="op">(</span></span>
+<span>  <span class="va">name</span>,</span>
+<span>  <span class="va">...</span>,</span>
+<span>  <span class="va">concentrations</span>,</span>
+<span>  concentration_units <span class="op">=</span> <span class="st">"g/L"</span>,</span>
+<span>  density <span class="op">=</span> <span class="fl">1000</span>,</span>
+<span>  density_units <span class="op">=</span> <span class="st">"g/L"</span></span>
+<span><span class="op">)</span></span></code></pre></div><p></p></div>
+</div>
+
+
+</div><p></p><hr><a id="method-ppp-print"></a><div class="section">
+<h3 id="method-print-">Method <code><a href="https://rdrr.io/r/base/print.html" class="external-link">print()</a></code><a class="anchor" aria-label="anchor" href="#method-print-"></a></h3>
+
+<div class="section">
+<h4 id="usage-1">Usage<a class="anchor" aria-label="anchor" href="#usage-1"></a></h4>
+<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">ppp</span><span class="op">$</span><span class="fu">print</span><span class="op">(</span><span class="op">)</span></span></code></pre></div><p></p></div>
+</div>
+
+
+</div><p></p><hr><a id="method-ppp-clone"></a><div class="section">
+<h3 id="method-clone-">Method <code>clone()</code><a class="anchor" aria-label="anchor" href="#method-clone-"></a></h3>
+<p>The objects of this class are cloneable with this method.</p><div class="section">
+<h4 id="usage-2">Usage<a class="anchor" aria-label="anchor" href="#usage-2"></a></h4>
+<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">ppp</span><span class="op">$</span><span class="fu">clone</span><span class="op">(</span>deep <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div><p></p></div>
+</div>
+
+<div class="section">
+<h4 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h4>
+<p></p><div class="arguments"><dl><dt><code>deep</code></dt>
+<dd><p>Whether to make a deep clone.</p></dd>
+
+
+</dl><p></p></div>
+</div>
+
+</div>
+
+    </div>
+
+  </div>
+  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
+    <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2>
+    </nav></div>
+</div>
+
+
+      <footer><div class="copyright">
+  <p></p><p>Developed by Johannes Ranke.</p>
+</div>
+
+<div class="pkgdown">
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+</div>
+
+      </footer></div>
+
+  
+
+
+  
+
+  </body></html>
+
diff --git a/docs/reference/print.chent.html b/docs/reference/print.chent.html
index 08497dd..da3ba4f 100644
--- a/docs/reference/print.chent.html
+++ b/docs/reference/print.chent.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">chents</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.3.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.3.2</span>
       </span>
     </div>
 
diff --git a/docs/reference/print.pai.html b/docs/reference/print.pai.html
index 3faa5f7..5a08066 100644
--- a/docs/reference/print.pai.html
+++ b/docs/reference/print.pai.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">chents</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.3.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.3.2</span>
       </span>
     </div>