diff options
author | Ranke Johannes <johannes.ranke@agroscope.admin.ch> | 2023-11-11 08:23:28 +0100 |
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committer | Ranke Johannes <johannes.ranke@agroscope.admin.ch> | 2023-11-11 08:23:28 +0100 |
commit | bf535e05f09864d5a88591d55bb8993b0619e57a (patch) | |
tree | 2a0c086315cb7747fe3e7d5867a602b18f871931 /docs | |
parent | 816de01ce642c1c3d633ffb1cbcf960036d27114 (diff) |
Start new version, rename pp to ppp, more docs
Diffstat (limited to 'docs')
-rw-r--r-- | docs/404.html | 2 | ||||
-rw-r--r-- | docs/authors.html | 6 | ||||
-rw-r--r-- | docs/index.html | 2 | ||||
-rw-r--r-- | docs/pkgdown.yml | 2 | ||||
-rw-r--r-- | docs/reference/chent.html | 319 | ||||
-rw-r--r-- | docs/reference/draw_svg.chent.html | 2 | ||||
-rw-r--r-- | docs/reference/index.html | 6 | ||||
-rw-r--r-- | docs/reference/pai.html | 43 | ||||
-rw-r--r-- | docs/reference/plot.chent.html | 2 | ||||
-rw-r--r-- | docs/reference/ppp.html | 194 | ||||
-rw-r--r-- | docs/reference/print.chent.html | 2 | ||||
-rw-r--r-- | docs/reference/print.pai.html | 2 | ||||
-rw-r--r-- | docs/sitemap.xml | 3 |
13 files changed, 555 insertions, 30 deletions
diff --git a/docs/404.html b/docs/404.html index eb79a5d..26a509c 100644 --- a/docs/404.html +++ b/docs/404.html @@ -32,7 +32,7 @@ </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/authors.html b/docs/authors.html index 0c3b654..1e764a7 100644 --- a/docs/authors.html +++ b/docs/authors.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> @@ -60,13 +60,13 @@ <p>Ranke J (2023). <em>chents: Chemical Entities as R Objects</em>. -R package version 0.3.1, <a href="https://github.com/jranke/chents" class="external-link">https://github.com/jranke/chents</a>. +R package version 0.3.2, <a href="https://github.com/jranke/chents" class="external-link">https://github.com/jranke/chents</a>. </p> <pre>@Manual{, title = {chents: Chemical Entities as R Objects}, author = {Johannes Ranke}, year = {2023}, - note = {R package version 0.3.1}, + note = {R package version 0.3.2}, url = {https://github.com/jranke/chents}, }</pre> diff --git a/docs/index.html b/docs/index.html index f241bb6..313ff06 100644 --- a/docs/index.html +++ b/docs/index.html @@ -37,7 +37,7 @@ </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/pkgdown.yml b/docs/pkgdown.yml index dd7c4f0..eb77ea1 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -2,5 +2,5 @@ pandoc: 3.1.1 pkgdown: 2.0.7 pkgdown_sha: ~ articles: {} -last_built: 2023-11-10T17:41Z +last_built: 2023-11-11T07:23Z 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> 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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> -> <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 <pesticidecompendium.bcpc.org> +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> diff --git a/docs/sitemap.xml b/docs/sitemap.xml index 986ccf3..63ab18d 100644 --- a/docs/sitemap.xml +++ b/docs/sitemap.xml @@ -28,6 +28,9 @@ <loc>/reference/pp.html</loc> </url> <url> + <loc>/reference/ppp.html</loc> + </url> + <url> <loc>/reference/print.chent.html</loc> </url> <url> |