diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2018-03-01 09:48:02 +0100 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2018-03-01 09:48:02 +0100 |
| commit | 4bd4606c76dfc152547e0f5899a98494a4290d33 (patch) | |
| tree | 36978d1bc83fcf56b1302181ce8367a60d6c156d /docs/reference | |
| parent | 3f82707cd1e974848185b1141c69734e2573594d (diff) | |
Rebuild static documentation with current pkdown
Diffstat (limited to 'docs/reference')
| -rw-r--r-- | docs/reference/chent-1.png | bin | 0 -> 34969 bytes | |||
| -rw-r--r-- | docs/reference/chent.html | 81 | ||||
| -rw-r--r-- | docs/reference/draw_svg.chent.html | 56 | ||||
| -rw-r--r-- | docs/reference/index.html | 122 | ||||
| -rw-r--r-- | docs/reference/pai.html | 38 | ||||
| -rw-r--r-- | docs/reference/plot.chent-1.png | bin | 0 -> 34969 bytes | |||
| -rw-r--r-- | docs/reference/plot.chent.html | 50 | ||||
| -rw-r--r-- | docs/reference/pp.html | 35 | ||||
| -rw-r--r-- | docs/reference/print.chent.html | 38 | ||||
| -rw-r--r-- | docs/reference/print.pai.html | 38 |
10 files changed, 313 insertions, 145 deletions
diff --git a/docs/reference/chent-1.png b/docs/reference/chent-1.png Binary files differnew file mode 100644 index 0000000..8731cf1 --- /dev/null +++ b/docs/reference/chent-1.png diff --git a/docs/reference/chent.html b/docs/reference/chent.html index 15c4d10..ef683ef 100644 --- a/docs/reference/chent.html +++ b/docs/reference/chent.html @@ -18,19 +18,30 @@ <!-- Font Awesome icons --> <link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> +<!-- clipboard.js --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> <script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> + + +<meta property="og:title" content="An R6 class for chemical entities with associated data — chent" /> +<meta property="og:description" content="The class is initialised with an identifier. Chemical information is retrieved from +the internet. Additionally, it can be generated using RDKit if RDKit and its +python bindings are installed and configured for use with PythonInR." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> -<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> +<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></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> @@ -49,6 +60,12 @@ <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> + <a href="../index.html"> + <span class="fa fa-home fa-lg"></span> + + </a> +</li> +<li> <a href="../reference/index.html">Reference</a> </li> </ul> @@ -75,7 +92,7 @@ the internet. Additionally, it can be generated using RDKit if RDKit and its python bindings are installed and configured for use with PythonInR.</p> - <pre><span class='no'>chent</span></pre> + <pre class="usage"><span class='no'>chent</span></pre> <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> @@ -83,52 +100,52 @@ python bindings are installed and configured for use with PythonInR.</p> <h2 class="hasAnchor" id="fields"><a class="anchor" href="#fields"></a>Fields</h2> - <p></p> - <p><dl class='dl-horizontal'> -<dt><code>identifier</code></dt><dd>The identifier that was used to initiate the object, with attribute 'source'</dd></p> - <p><dt><code>inchikey</code></dt><dd>InChI Key, with attribute 'source'</dd></p> - <p><dt><code>smiles</code></dt><dd>SMILES code, with attribute 'source'</dd></p> - <p><dt><code>mw</code></dt><dd>Molecular weight, with attribute 'source'</dd></p> - <p><dt><code>pubchem</code></dt><dd>List of information retreived from PubChem</dd></p> - <p><dt><code>rdkit</code></dt><dd>List of information obtained with RDKit, if installed and -configured for use with PythonInR</dd></p> - <p><dt><code>svg</code></dt><dd>SVG code</dd></p> - <p><dt><code>Picture</code></dt><dd>Graph as a <code>picture</code> object obtained using grImport</dd></p> - <p><dt><code>Pict_font_size</code></dt><dd>Font size as extracted from the intermediate PostScript file</dd></p> - <p><dt><code>pdf_height</code></dt><dd>Height of the MediaBox in the pdf after cropping</dd></p> - <p><dt><code>chyaml</code></dt><dd>List of information obtained from a YAML file</dd></p> - <p><dt><code>degradation</code></dt><dd>List of degradation endpoints</dd> -</dl></p> + + <dl class='dl-horizontal'> +<dt><code>identifier</code></dt><dd><p>The identifier that was used to initiate the object, with attribute 'source'</p></dd> + <dt><code>inchikey</code></dt><dd><p>InChI Key, with attribute 'source'</p></dd> + <dt><code>smiles</code></dt><dd><p>SMILES code, with attribute 'source'</p></dd> + <dt><code>mw</code></dt><dd><p>Molecular weight, with attribute 'source'</p></dd> + <dt><code>pubchem</code></dt><dd><p>List of information retreived from PubChem</p></dd> + <dt><code>rdkit</code></dt><dd><p>List of information obtained with RDKit, if installed and +configured for use with PythonInR</p></dd> + <dt><code>svg</code></dt><dd><p>SVG code</p></dd> + <dt><code>Picture</code></dt><dd><p>Graph as a <code>picture</code> object obtained using grImport</p></dd> + <dt><code>Pict_font_size</code></dt><dd><p>Font size as extracted from the intermediate PostScript file</p></dd> + <dt><code>pdf_height</code></dt><dd><p>Height of the MediaBox in the pdf after cropping</p></dd> + <dt><code>chyaml</code></dt><dd><p>List of information obtained from a YAML file</p></dd> + <dt><code>degradation</code></dt><dd><p>List of degradation endpoints</p></dd> +</dl> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='no'>oct</span> <span class='kw'><-</span> <span class='no'>chent</span>$<span class='fu'>new</span>(<span class='st'>"1-octanol"</span>, <span class='kw'>smiles</span> <span class='kw'>=</span> <span class='st'>"CCCCCCCCO"</span>)</div><div class='output co'>#> <span class='message'>PubChem:</span></div><div class='output co'>#> <span class='message'>https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/cids/JSON</span></div><div class='output co'>#> <span class='message'>https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/property/MolecularFormula,MolecularWeight,CanonicalSMILES,IsomericSMILES,InChI,InChIKey,IUPACName,XLogP,TPSA,Complexity,Charge,HBondDonorCount,HBondAcceptorCount/JSON</span></div><div class='output co'>#> <span class='message'>https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/synonyms/JSON</span></div><div class='output co'>#> <span class='message'></span> -#> <span class='message'>Initialize Python Version 3.4.2 (default, Oct 8 2014, 10:47:48) </span> -#> <span class='message'>[GCC 4.9.1]</span></div><div class='output co'>#> <span class='message'>Trying to get chemical information from RDKit using user SMILES</span> -#> <span class='message'>CCCCCCCCO</span></div><div class='output co'>#> <span class='message'>Did not find chyaml file ./1-octanol.yaml</span></div><div class='input'><span class='fu'>print</span>(<span class='no'>oct</span>)</div><div class='output co'>#> <chent> +#> <span class='message'>Initialize Python Version 2.7.13 (default, Nov 24 2017, 17:33:09) </span> +#> <span class='message'>[GCC 6.3.0 20170516]</span></div><div class='output co'>#> <span class='message'>Trying to get chemical information from RDKit using user SMILES</span> +#> <span class='message'>CCCCCCCCO</span></div><div class='output co'>#> <span class='message'>Loading required namespace: grConvert</span></div><div class='output co'>#> <span class='message'>Did not find chyaml file ./1-octanol.yaml</span></div><div class='input'><span class='fu'>print</span>(<span class='no'>oct</span>)</div><div class='output co'>#> <chent> #> Identifier $identifier 1-octanol #> InChI Key $inchikey KBPLFHHGFOOTCA-UHFFFAOYSA-N #> SMILES string $smiles: #> user PubChem_Canonical -#> "CCCCCCCCO" "CCCCCCCCO" +#> "CCCCCCCCO" "CCCCCCCCO" #> Molecular weight $mw: 130.2 #> PubChem synonyms (up to 10): -#> [1] "957" "1-octanol" "Octan-1-ol" "octanol" -#> [5] "Octyl alcohol" "N-octanol" "Capryl alcohol" "n-Octyl alcohol" -#> [9] "111-87-5" "caprylic alcohol"</div><div class='input'><span class='fu'>plot</span>(<span class='no'>oct</span>)</div><div class='input'><span class='no'>caffeine</span> <span class='kw'><-</span> <span class='no'>chent</span>$<span class='fu'>new</span>(<span class='st'>"caffeine"</span>)</div><div class='output co'>#> <span class='message'>PubChem:</span></div><div class='output co'>#> <span class='message'>https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/cids/JSON</span></div><div class='output co'>#> <span class='message'>https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/property/MolecularFormula,MolecularWeight,CanonicalSMILES,IsomericSMILES,InChI,InChIKey,IUPACName,XLogP,TPSA,Complexity,Charge,HBondDonorCount,HBondAcceptorCount/JSON</span></div><div class='output co'>#> <span class='message'>https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/synonyms/JSON</span></div><div class='output co'>#> <span class='message'>Trying to get chemical information from RDKit using PubChem_Canonical SMILES</span> +#> [1] "957" "1-octanol" "Octan-1-ol" "octanol" +#> [5] "Octyl alcohol" "N-octanol" "111-87-5" "Capryl alcohol" +#> [9] "caprylic alcohol" "n-Octyl alcohol" </div><div class='input'><span class='fu'>plot</span>(<span class='no'>oct</span>)</div><div class='input'><span class='no'>caffeine</span> <span class='kw'><-</span> <span class='no'>chent</span>$<span class='fu'>new</span>(<span class='st'>"caffeine"</span>)</div><div class='output co'>#> <span class='message'>PubChem:</span></div><div class='output co'>#> <span class='message'>https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/cids/JSON</span></div><div class='output co'>#> <span class='message'>https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/property/MolecularFormula,MolecularWeight,CanonicalSMILES,IsomericSMILES,InChI,InChIKey,IUPACName,XLogP,TPSA,Complexity,Charge,HBondDonorCount,HBondAcceptorCount/JSON</span></div><div class='output co'>#> <span class='message'>https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/synonyms/JSON</span></div><div class='output co'>#> <span class='message'>Trying to get chemical information from RDKit using PubChem_Canonical SMILES</span> #> <span class='message'>CN1C=NC2=C1C(=O)N(C(=O)N2C)C</span></div><div class='output co'>#> <span class='message'>Did not find chyaml file ./caffeine.yaml</span></div><div class='input'><span class='fu'>print</span>(<span class='no'>caffeine</span>)</div><div class='output co'>#> <chent> #> Identifier $identifier caffeine #> InChI Key $inchikey RYYVLZVUVIJVGH-UHFFFAOYSA-N #> SMILES string $smiles: #> PubChem_Canonical -#> "CN1C=NC2=C1C(=O)N(C(=O)N2C)C" +#> "CN1C=NC2=C1C(=O)N(C(=O)N2C)C" #> Molecular weight $mw: 194.2 #> PubChem synonyms (up to 10): -#> [1] "2519" "caffeine" -#> [3] "Guaranine" "1,3,7-Trimethylxanthine" -#> [5] "Methyltheobromine" "Cafeina" -#> [7] "Thein" "Koffein" -#> [9] "Mateina" "Theine" </div><div class='input'><span class='fu'>plot</span>(<span class='no'>caffeine</span>)</div><img src='chent-22.png' alt='' width='540' height='400' /></pre> +#> [1] "2519" "caffeine" +#> [3] "1,3,7-Trimethylxanthine" "58-08-2" +#> [5] "Guaranine" "Thein" +#> [7] "Cafeina" "Methyltheobromine" +#> [9] "Koffein" "Mateina" </div><div class='input'><span class='fu'>plot</span>(<span class='no'>caffeine</span>)</div><div class='img'><img src='chent-1.png' alt='' width='700' height='432.632880098887' /></div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> @@ -150,7 +167,7 @@ configured for use with PythonInR</dd></p> </div> <div class="pkgdown"> - <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> + <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p> </div> </footer> diff --git a/docs/reference/draw_svg.chent.html b/docs/reference/draw_svg.chent.html index 2cc3804..5342eca 100644 --- a/docs/reference/draw_svg.chent.html +++ b/docs/reference/draw_svg.chent.html @@ -18,19 +18,28 @@ <!-- Font Awesome icons --> <link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> +<!-- clipboard.js --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> <script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> + + +<meta property="og:title" content="Draw SVG graph from a chent object using RDKit — draw_svg.chent" /> +<meta property="og:description" content="Draw SVG graph from a chent object using RDKit" /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> -<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> +<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></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> @@ -49,6 +58,12 @@ <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> + <a href="../index.html"> + <span class="fa fa-home fa-lg"></span> + + </a> +</li> +<li> <a href="../reference/index.html">Reference</a> </li> </ul> @@ -73,22 +88,33 @@ <p>Draw SVG graph from a chent object using RDKit</p> - <pre><span class='fu'>draw_svg.chent</span>(<span class='no'>x</span>, <span class='kw'>width</span> <span class='kw'>=</span> <span class='fl'>300</span>, <span class='kw'>height</span> <span class='kw'>=</span> <span class='fl'>150</span>, + <pre class="usage"><span class='fu'>draw_svg.chent</span>(<span class='no'>x</span>, <span class='kw'>width</span> <span class='kw'>=</span> <span class='fl'>300</span>, <span class='kw'>height</span> <span class='kw'>=</span> <span class='fl'>150</span>, <span class='kw'>filename</span> <span class='kw'>=</span> <span class='fu'>paste0</span>(<span class='fu'>names</span>(<span class='no'>x</span>$<span class='no'>identifier</span>), <span class='st'>".svg"</span>), <span class='kw'>subdir</span> <span class='kw'>=</span> <span class='st'>"svg"</span>)</pre> <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> - <dl class="dl-horizontal"> - <dt>x</dt> - <dd>The chent object to be plotted</dd> - <dt>width</dt> - <dd>The desired width in pixels</dd> - <dt>height</dt> - <dd>The desired height in pixels</dd> - <dt>filename</dt> - <dd>The filename</dd> - <dt>subdir</dt> - <dd>The path to which the file should be written</dd> - </dl> + <table class="ref-arguments"> + <colgroup><col class="name" /><col class="desc" /></colgroup> + <tr> + <th>x</th> + <td><p>The chent object to be plotted</p></td> + </tr> + <tr> + <th>width</th> + <td><p>The desired width in pixels</p></td> + </tr> + <tr> + <th>height</th> + <td><p>The desired height in pixels</p></td> + </tr> + <tr> + <th>filename</th> + <td><p>The filename</p></td> + </tr> + <tr> + <th>subdir</th> + <td><p>The path to which the file should be written</p></td> + </tr> + </table> </div> @@ -107,7 +133,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> + <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p> </div> </footer> diff --git a/docs/reference/index.html b/docs/reference/index.html index 52967a5..29771c9 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -18,19 +18,25 @@ <!-- Font Awesome icons --> <link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> +<!-- clipboard.js --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> <script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> - + + +<meta property="og:title" content="Function reference" /> <!-- mathjax --> -<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> +<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></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> @@ -49,6 +55,12 @@ <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> + <a href="../index.html"> + <span class="fa fa-home fa-lg"></span> + + </a> +</li> +<li> <a href="../reference/index.html">Reference</a> </li> </ul> @@ -66,50 +78,72 @@ <div class="row"> <div class="col-md-9"> <div class="page-header"> - <h1>Function reference</h1> - <h4>version 0.2-6</h4> + <h1> + Reference + <small>version 0.2-6</small> + </h1> </div> <div class="contents"> - <h2 id="section-r-class-definitions-and-methods" class="hasAnchor"><a href="#section-r-class-definitions-and-methods" class="anchor"></a>R6 Class definitions and methods</h2> - <p class="section-desc"></p> - - - <p><a href="chent.html">An R6 class for chemical entities with associated data</a></p> - <ul> - <li><code><a href="chent.html">chent</a></code></li> - </ul> - - <p><a href="draw_svg.chent.html">Draw SVG graph from a chent object using RDKit</a></p> - <ul> - <li><code><a href="draw_svg.chent.html">draw_svg.chent</a></code></li> - </ul> - - <p><a href="plot.chent.html">Plot method for chent objects</a></p> - <ul> - <li><code><a href="plot.chent.html">plot.chent</a></code></li> - </ul> - - <p><a href="print.chent.html">Printing method for chent objects</a></p> - <ul> - <li><code><a href="print.chent.html">print.chent</a></code></li> - </ul> - - <p><a href="pai.html">An R6 class for pesticidal active ingredients and associated data</a></p> - <ul> - <li><code><a href="pai.html">pai</a></code></li> - </ul> - - <p><a href="print.pai.html">Printing method for pai objects (pesticidal active ingredients)</a></p> - <ul> - <li><code><a href="print.pai.html">print.pai</a></code></li> - </ul> - - <p><a href="pp.html">R6 class for holding a product with at least one active ingredient</a></p> - <ul> - <li><code><a href="pp.html">pp</a></code></li> - </ul> - + <table class="ref-index"> + + <colgroup> + <col class="alias" /> + <col class="title" /> + </colgroup> + + <tbody> + <tr> + <th colspan="2"> + <h2 id="section-r-class-definitions-and-methods" class="hasAnchor"><a href="#section-r-class-definitions-and-methods" class="anchor"></a>R6 Class definitions and methods</h2> + <p class="section-desc"></p> + </th> + </tr> + <tr> + <!-- --> + <td> + <p><code><a href="chent.html">chent</a></code> </p> + </td> + <td><p>An R6 class for chemical entities with associated data</p></td> + </tr><tr> + <!-- --> + <td> + <p><code><a href="draw_svg.chent.html">draw_svg.chent</a></code> </p> + </td> + <td><p>Draw SVG graph from a chent object using RDKit</p></td> + </tr><tr> + <!-- --> + <td> + <p><code><a href="plot.chent.html">plot</a></code> </p> + </td> + <td><p>Plot method for chent objects</p></td> + </tr><tr> + <!-- --> + <td> + <p><code><a href="print.chent.html">print</a></code> </p> + </td> + <td><p>Printing method for chent objects</p></td> + </tr><tr> + <!-- --> + <td> + <p><code><a href="pai.html">pai</a></code> </p> + </td> + <td><p>An R6 class for pesticidal active ingredients and associated data</p></td> + </tr><tr> + <!-- --> + <td> + <p><code><a href="print.pai.html">print</a></code> </p> + </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> + </td> + <td><p>R6 class for holding a product with at least one active ingredient</p></td> + </tr> + </tbody> + </table> </div> </div> @@ -127,7 +161,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> + <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p> </div> </footer> diff --git a/docs/reference/pai.html b/docs/reference/pai.html index 4c143a1..30a5b77 100644 --- a/docs/reference/pai.html +++ b/docs/reference/pai.html @@ -18,19 +18,29 @@ <!-- Font Awesome icons --> <link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> +<!-- clipboard.js --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> <script src="../jquery.sticky-kit.min.js"></script> <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." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> -<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> +<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></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> @@ -49,6 +59,12 @@ <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> + <a href="../index.html"> + <span class="fa fa-home fa-lg"></span> + + </a> +</li> +<li> <a href="../reference/index.html">Reference</a> </li> </ul> @@ -74,7 +90,7 @@ Additional chemical information is retrieved from the internet if available.</p> - <pre><span class='no'>pai</span></pre> + <pre class="usage"><span class='no'>pai</span></pre> <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> @@ -82,11 +98,11 @@ Additional chemical information is retrieved from the internet if available.</p> <h2 class="hasAnchor" id="fields"><a class="anchor" href="#fields"></a>Fields</h2> - <p></p> - <p><dl class='dl-horizontal'> -<dt><code>iso</code></dt><dd>ISO common name according to ISO 1750 as retreived from www.alanwood.net/pesticides</dd></p> - <p><dt><code>alanwood</code></dt><dd>List of information retreived from www.alanwood.net/pesticides</dd> -</dl></p> + + <dl class='dl-horizontal'> +<dt><code>iso</code></dt><dd><p>ISO common name according to ISO 1750 as retreived from www.alanwood.net/pesticides</p></dd> + <dt><code>alanwood</code></dt><dd><p>List of information retreived from www.alanwood.net/pesticides</p></dd> +</dl> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> @@ -97,11 +113,11 @@ Additional chemical information is retrieved from the internet if available.</p> #> InChI Key $inchikey MXWJVTOOROXGIU-UHFFFAOYSA-N #> SMILES string $smiles: #> PubChem_Canonical -#> "CCNC1=NC(=NC(=N1)Cl)NC(C)C" +#> "CCNC1=NC(=NC(=N1)Cl)NC(C)C" #> Molecular weight $mw: 215.7 #> PubChem synonyms (up to 10): -#> [1] "2256" "atrazine" "1912-24-9" "Atranex" "Fenatrol" -#> [6] "Atred" "Oleogesaprim" "Atazinax" "Atrasine" "Chromozin" </div></pre> +#> [1] "2256" "atrazine" "1912-24-9" "Gesaprim" "Chromozin" +#> [6] "Oleogesaprim" "Aktikon" "Argezin" "Atazinax" "Atranex" </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> @@ -123,7 +139,7 @@ Additional chemical information is retrieved from the internet if available.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> + <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p> </div> </footer> diff --git a/docs/reference/plot.chent-1.png b/docs/reference/plot.chent-1.png Binary files differnew file mode 100644 index 0000000..8731cf1 --- /dev/null +++ b/docs/reference/plot.chent-1.png diff --git a/docs/reference/plot.chent.html b/docs/reference/plot.chent.html index 3cc23d9..cc3b96b 100644 --- a/docs/reference/plot.chent.html +++ b/docs/reference/plot.chent.html @@ -18,19 +18,28 @@ <!-- Font Awesome icons --> <link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> +<!-- clipboard.js --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> <script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> + + +<meta property="og:title" content="Plot method for chent objects — plot.chent" /> +<meta property="og:description" content="Plot method for chent objects" /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> -<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> +<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></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> @@ -49,6 +58,12 @@ <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> + <a href="../index.html"> + <span class="fa fa-home fa-lg"></span> + + </a> +</li> +<li> <a href="../reference/index.html">Reference</a> </li> </ul> @@ -73,16 +88,21 @@ <p>Plot method for chent objects</p> - <pre><span class='co'># S3 method for chent</span> + <pre class="usage"><span class='co'># S3 method for chent</span> <span class='fu'>plot</span>(<span class='no'>x</span>, <span class='no'>...</span>)</pre> <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> - <dl class="dl-horizontal"> - <dt>x</dt> - <dd>The chent object to be plotted</dd> - <dt>...</dt> - <dd>Further arguments passed to <code>grid.picture</code></dd> - </dl> + <table class="ref-arguments"> + <colgroup><col class="name" /><col class="desc" /></colgroup> + <tr> + <th>x</th> + <td><p>The chent object to be plotted</p></td> + </tr> + <tr> + <th>...</th> + <td><p>Further arguments passed to <code>grid.picture</code></p></td> + </tr> + </table> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> @@ -92,14 +112,14 @@ #> InChI Key $inchikey RYYVLZVUVIJVGH-UHFFFAOYSA-N #> SMILES string $smiles: #> PubChem_Canonical -#> "CN1C=NC2=C1C(=O)N(C(=O)N2C)C" +#> "CN1C=NC2=C1C(=O)N(C(=O)N2C)C" #> Molecular weight $mw: 194.2 #> PubChem synonyms (up to 10): -#> [1] "2519" "caffeine" -#> [3] "Guaranine" "1,3,7-Trimethylxanthine" -#> [5] "Methyltheobromine" "Cafeina" -#> [7] "Thein" "Koffein" -#> [9] "Mateina" "Theine" </div><div class='input'><span class='fu'>plot</span>(<span class='no'>caffeine</span>)</div><img src='plot.chent-11.png' alt='' width='540' height='400' /></pre> +#> [1] "2519" "caffeine" +#> [3] "1,3,7-Trimethylxanthine" "58-08-2" +#> [5] "Guaranine" "Thein" +#> [7] "Cafeina" "Methyltheobromine" +#> [9] "Koffein" "Mateina" </div><div class='input'><span class='fu'>plot</span>(<span class='no'>caffeine</span>)</div><div class='img'><img src='plot.chent-1.png' alt='' width='700' height='432.632880098887' /></div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> @@ -118,7 +138,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> + <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p> </div> </footer> diff --git a/docs/reference/pp.html b/docs/reference/pp.html index 4569a6f..538b885 100644 --- a/docs/reference/pp.html +++ b/docs/reference/pp.html @@ -18,19 +18,28 @@ <!-- Font Awesome icons --> <link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> +<!-- clipboard.js --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> <script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> + + +<meta property="og:title" content="R6 class for holding a product with at least one active ingredient — pp" /> +<meta property="og:description" content="An R6 class for holding information about a product with at least one active ingredient" /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> -<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> +<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></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> @@ -49,6 +58,12 @@ <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> + <a href="../index.html"> + <span class="fa fa-home fa-lg"></span> + + </a> +</li> +<li> <a href="../reference/index.html">Reference</a> </li> </ul> @@ -73,7 +88,7 @@ <p>An R6 class for holding information about a product with at least one active ingredient</p> - <pre><span class='no'>pp</span></pre> + <pre class="usage"><span class='no'>pp</span></pre> <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> @@ -81,13 +96,13 @@ <h2 class="hasAnchor" id="fields"><a class="anchor" href="#fields"></a>Fields</h2> - <p></p> - <p><dl class='dl-horizontal'> -<dt><code>name</code></dt><dd>The name of the product</dd></p> - <p><dt><code>ais</code></dt><dd>A list of active ingredients</dd></p> - <p><dt><code>concentrations</code></dt><dd>The concentration of the ais</dd></p> - <p><dt><code>concentration_units</code></dt><dd>Defaults to g/L</dd> -</dl></p> + + <dl class='dl-horizontal'> +<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> +</dl> </div> @@ -109,7 +124,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> + <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p> </div> </footer> diff --git a/docs/reference/print.chent.html b/docs/reference/print.chent.html index 29b215a..81fde0d 100644 --- a/docs/reference/print.chent.html +++ b/docs/reference/print.chent.html @@ -18,19 +18,28 @@ <!-- Font Awesome icons --> <link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> +<!-- clipboard.js --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> <script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> + + +<meta property="og:title" content="Printing method for chent objects — print.chent" /> +<meta property="og:description" content="Printing method for chent objects" /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> -<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> +<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></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> @@ -49,6 +58,12 @@ <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> + <a href="../index.html"> + <span class="fa fa-home fa-lg"></span> + + </a> +</li> +<li> <a href="../reference/index.html">Reference</a> </li> </ul> @@ -73,16 +88,21 @@ <p>Printing method for chent objects</p> - <pre><span class='co'># S3 method for chent</span> + <pre class="usage"><span class='co'># S3 method for chent</span> <span class='fu'>print</span>(<span class='no'>x</span>, <span class='no'>...</span>)</pre> <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> - <dl class="dl-horizontal"> - <dt>x</dt> - <dd>The chent object to be printed</dd> - <dt>...</dt> - <dd>Further arguments for compatibility with the S3 method</dd> - </dl> + <table class="ref-arguments"> + <colgroup><col class="name" /><col class="desc" /></colgroup> + <tr> + <th>x</th> + <td><p>The chent object to be printed</p></td> + </tr> + <tr> + <th>...</th> + <td><p>Further arguments for compatibility with the S3 method</p></td> + </tr> + </table> </div> @@ -101,7 +121,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> + <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p> </div> </footer> diff --git a/docs/reference/print.pai.html b/docs/reference/print.pai.html index d2da6b8..08966de 100644 --- a/docs/reference/print.pai.html +++ b/docs/reference/print.pai.html @@ -18,19 +18,28 @@ <!-- Font Awesome icons --> <link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> +<!-- clipboard.js --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> <script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> + + +<meta property="og:title" content="Printing method for pai objects (pesticidal active ingredients) — print.pai" /> +<meta property="og:description" content="Printing method for pai objects (pesticidal active ingredients)" /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> -<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> +<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></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> @@ -49,6 +58,12 @@ <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> + <a href="../index.html"> + <span class="fa fa-home fa-lg"></span> + + </a> +</li> +<li> <a href="../reference/index.html">Reference</a> </li> </ul> @@ -73,16 +88,21 @@ <p>Printing method for pai objects (pesticidal active ingredients)</p> - <pre><span class='co'># S3 method for pai</span> + <pre class="usage"><span class='co'># S3 method for pai</span> <span class='fu'>print</span>(<span class='no'>x</span>, <span class='no'>...</span>)</pre> <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> - <dl class="dl-horizontal"> - <dt>x</dt> - <dd>The chent object to be printed</dd> - <dt>...</dt> - <dd>Further arguments for compatibility with the S3 method</dd> - </dl> + <table class="ref-arguments"> + <colgroup><col class="name" /><col class="desc" /></colgroup> + <tr> + <th>x</th> + <td><p>The chent object to be printed</p></td> + </tr> + <tr> + <th>...</th> + <td><p>Further arguments for compatibility with the S3 method</p></td> + </tr> + </table> </div> @@ -101,7 +121,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> + <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p> </div> </footer> |
