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| author | Ranke Johannes <johannes.ranke@agroscope.admin.ch> | 2023-11-10 18:40:34 +0100 |
|---|---|---|
| committer | Ranke Johannes <johannes.ranke@agroscope.admin.ch> | 2023-11-10 19:21:11 +0100 |
| commit | 816de01ce642c1c3d633ffb1cbcf960036d27114 (patch) | |
| tree | cf732b6e18bcc0864b481f804a1cb0b16bdd7d4d /docs | |
| parent | 67384ac3c7c0b888d67d06473f81e46d520a7dd3 (diff) | |
Make an RStudio project and improve the docs
Diffstat (limited to 'docs')
| -rw-r--r-- | docs/404.html | 117 | ||||
| -rw-r--r-- | docs/authors.html | 139 | ||||
| -rw-r--r-- | docs/index.html | 73 | ||||
| -rw-r--r-- | docs/pkgdown.css | 83 | ||||
| -rw-r--r-- | docs/pkgdown.js | 4 | ||||
| -rw-r--r-- | docs/pkgdown.yml | 6 | ||||
| -rw-r--r-- | docs/reference/Rplot001.png | bin | 19923 -> 20712 bytes | |||
| -rw-r--r-- | docs/reference/chent-1.png | bin | 46431 -> 46730 bytes | |||
| -rw-r--r-- | docs/reference/chent.html | 807 | ||||
| -rw-r--r-- | docs/reference/draw_svg.chent.html | 173 | ||||
| -rw-r--r-- | docs/reference/index.html | 160 | ||||
| -rw-r--r-- | docs/reference/pai-1.png | bin | 33683 -> 34388 bytes | |||
| -rw-r--r-- | docs/reference/pai.html | 315 | ||||
| -rw-r--r-- | docs/reference/plot.chent-1.png | bin | 46149 -> 46142 bytes | |||
| -rw-r--r-- | docs/reference/plot.chent.html | 190 | ||||
| -rw-r--r-- | docs/reference/pp.html | 208 | ||||
| -rw-r--r-- | docs/reference/print.chent.html | 137 | ||||
| -rw-r--r-- | docs/reference/print.pai.html | 137 | ||||
| -rw-r--r-- | docs/sitemap.xml | 36 |
19 files changed, 1073 insertions, 1512 deletions
diff --git a/docs/404.html b/docs/404.html index 7bd3245..eb79a5d 100644 --- a/docs/404.html +++ b/docs/404.html @@ -1,66 +1,27 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> +<!-- 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>Page not found (404) • 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> - 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- - </head> - - <body data-spy="scroll" data-target="#toc"> <div class="container template-title-body"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <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"> @@ -71,40 +32,34 @@ </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="Released version">0.3.1</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.3.1</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> - <li> - <a href="index.html"> - <span class="fas fa-home fa-lg"></span> - - </a> -</li> <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/"> +<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 --> +</div> +<!--/.nav-collapse --> + </div> +<!--/.container --> +</div> +<!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="contents col-md-9"> <div class="page-header"> <h1>Page not found (404)</h1> @@ -115,31 +70,31 @@ Content not found. Please use links in the navbar. </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 id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> </nav> - </div> +</div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p> +<p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <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> +</div> + + </body> </html> - - diff --git a/docs/authors.html b/docs/authors.html index 327fe56..0c3b654 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -1,66 +1,12 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - <head> - <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>Authors • 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="Authors" /> - - - - -<!-- 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>Authors and Citation • 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="Authors and Citation"><!-- 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]--> - +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - - </head> - - <body data-spy="scroll" data-target="#toc"> - <div class="container template-authors"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container template-citation-authors"> + <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"> @@ -71,51 +17,58 @@ </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="Released version">0.3.1</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.3.1</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> - <a href="index.html"> - <span class="fas fa-home fa-lg"></span> - - </a> -</li> -<li> + <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/"> + </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 --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="contents col-md-9"> - <div class="page-header"> - <h1>Authors</h1> + <div class="section level2 authors-section"> + <div class="page-header"> + <h1>Authors</h1> + </div> + + + <ul class="list-unstyled"><li> + <p><strong>Johannes Ranke</strong>. Author, maintainer, copyright holder. + </p> + </li> + </ul></div> + <div class="section level2 citation-section"> + <div> + <h1 id="citation">Citation</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/chents/blob/HEAD/DESCRIPTION" class="external-link"><code>DESCRIPTION</code></a></small> + </div> </div> - <ul class="list-unstyled"> - <li> - <p><strong>Johannes Ranke</strong>. Author, maintainer, copyright holder. - </p> - </li> - </ul> + + <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>. +</p> + <pre>@Manual{, + title = {chents: Chemical Entities as R Objects}, + author = {Johannes Ranke}, + year = {2023}, + note = {R package version 0.3.1}, + url = {https://github.com/jranke/chents}, +}</pre> </div> @@ -123,22 +76,20 @@ - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <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> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/index.html b/docs/index.html index c4ad646..f241bb6 100644 --- a/docs/index.html +++ b/docs/index.html @@ -16,14 +16,15 @@ data as R objects. If Python and RDKit (> 2015.03) are installed and configured for use with reticulate, some basic chemoinformatics functions like the calculation of molecular weight and plotting of chemical - structures in R graphics are available. For plotting, you need - grConvert (https://sjp.co.nz/projects/grconvert) which is not on CRAN."> + structures in R graphics are 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]> <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-home"> <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> @@ -36,25 +37,19 @@ </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="Released version">0.3.1</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.3.1</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> - <a href="index.html"> - <span class="fas fa-home fa-lg"></span> - - </a> -</li> -<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/"> + <a href="https://github.com/jranke/chents/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> @@ -71,66 +66,72 @@ </header><div class="row"> <div class="contents col-md-9"> -<div id="chents" class="section level1"> -<div class="page-header"><h1 class="hasAnchor"> -<a href="#chents" class="anchor"></a>chents</h1></div> - +<div class="section level1"> +<div class="page-header"><h1 id="chents">chents<a class="anchor" aria-label="anchor" href="#chents"></a> +</h1></div> +<p><a href="https://app.travis-ci.com/github/jranke/chents" class="external-link"><img src="https://travis-ci.com/jranke/chents.svg?branch=main" alt="Build Status"></a> <a href="https://app.codecov.io/gh/jranke/chents" class="external-link"><img src="https://codecov.io/github/jranke/chents/branch/main/graphs/badge.svg" alt="codecov"></a></p> <p>The R package <strong>chents</strong> provides some utilities for working with chemical entities in R.</p> -<div id="features" class="section level2"> -<h2 class="hasAnchor"> -<a href="#features" class="anchor"></a>Features</h2> +<div class="section level2"> +<h2 id="features">Features<a class="anchor" aria-label="anchor" href="#features"></a> +</h2> <ul> <li>Some chemical information is retrieved from the PubChem website using the webchem package</li> <li>If Python and RDKit (> 2015.03) are installed and configured for use with ‘reticulate’, some basic chemoinformatics functions some additional chemical information is computed and a 2D graph can be plotted</li> <li>Additional information can be read from a local .yaml file</li> </ul> </div> -<div id="examples" class="section level2"> -<h2 class="hasAnchor"> -<a href="#examples" class="anchor"></a>Examples</h2> -<p>Some examples are available from the <a href="http://pkgdown.jrwb.de/chents/reference">reference on jrwb.de</a>.</p> +<div class="section level2"> +<h2 id="examples">Examples<a class="anchor" aria-label="anchor" href="#examples"></a> +</h2> +<p>Some examples are available from the <a href="https://pkgdown.jrwb.de/chents/reference" class="external-link">reference on jrwb.de</a>.</p> </div> </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> <div class="links"> -<h2>Links</h2> +<h2 data-toc-skip>Links</h2> <ul class="list-unstyled"> -<li>Browse source code at <br><a href="https://github.com/jranke/chents/">https://github.com/jranke/chents/</a> -</li> +<li><a href="https://github.com/jranke/chents/" class="external-link">Browse source code</a></li> </ul> </div> + <div class="license"> -<h2>License</h2> +<h2 data-toc-skip>License</h2> <ul class="list-unstyled"> <li>GPL</li> </ul> </div> -<div class="developers"> -<h2>Developers</h2> + + +<div class="citation"> +<h2 data-toc-skip>Citation</h2> <ul class="list-unstyled"> -<li>Johannes Ranke <br><small class="roles"> Author, maintainer, copyright holder </small> </li> +<li><a href="authors.html#citation">Citing chents</a></li> </ul> </div> - <div class="dev-status"> -<h2>Dev status</h2> +<div class="developers"> +<h2 data-toc-skip>Developers</h2> <ul class="list-unstyled"> -<li><a href="https://travis-ci.com/jranke/chents"><img src="https://travis-ci.com/jranke/chents.svg?branch=main" alt="Build Status"></a></li> -<li><a href="https://codecov.io/github/jranke/chents"><img src="https://codecov.io/github/jranke/chents/branch/main/graphs/badge.svg" alt="codecov"></a></li> +<li>Johannes Ranke <br><small class="roles"> Author, maintainer, copyright holder </small> </li> </ul> </div> -</div> + + + + </div> </div> <footer><div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <p></p> +<p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <p></p> +<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> </footer> @@ -139,5 +140,7 @@ + + </body> </html> diff --git a/docs/pkgdown.css b/docs/pkgdown.css index 1273238..80ea5b8 100644 --- a/docs/pkgdown.css +++ b/docs/pkgdown.css @@ -56,8 +56,10 @@ img.icon { float: right; } -img { +/* Ensure in-page images don't run outside their container */ +.contents img { max-width: 100%; + height: auto; } /* Fix bug in bootstrap (only seen in firefox) */ @@ -78,11 +80,10 @@ dd { /* Section anchors ---------------------------------*/ a.anchor { - margin-left: -30px; - display:inline-block; - width: 30px; - height: 30px; - visibility: hidden; + display: none; + margin-left: 5px; + width: 20px; + height: 20px; background-image: url(./link.svg); background-repeat: no-repeat; @@ -90,17 +91,15 @@ a.anchor { background-position: center center; } -.hasAnchor:hover a.anchor { - visibility: visible; -} - -@media (max-width: 767px) { - .hasAnchor:hover a.anchor { - visibility: hidden; - } +h1:hover .anchor, +h2:hover .anchor, +h3:hover .anchor, +h4:hover .anchor, +h5:hover .anchor, +h6:hover .anchor { + display: inline-block; } - /* Fixes for fixed navbar --------------------------*/ .contents h1, .contents h2, .contents h3, .contents h4 { @@ -264,31 +263,26 @@ table { /* Syntax highlighting ---------------------------------------------------- */ -pre { - word-wrap: normal; - word-break: normal; - border: 1px solid #eee; -} - -pre, code { +pre, code, pre code { background-color: #f8f8f8; color: #333; } +pre, pre code { + white-space: pre-wrap; + word-break: break-all; + overflow-wrap: break-word; +} -pre code { - overflow: auto; - word-wrap: normal; - white-space: pre; +pre { + border: 1px solid #eee; } -pre .img { +pre .img, pre .r-plt { margin: 5px 0; } -pre .img img { +pre .img img, pre .r-plt img { background-color: #fff; - display: block; - height: auto; } code a, pre a { @@ -305,9 +299,8 @@ a.sourceLine:hover { .kw {color: #264D66;} /* keyword */ .co {color: #888888;} /* comment */ -.message { color: black; font-weight: bolder;} -.error { color: orange; font-weight: bolder;} -.warning { color: #6A0366; font-weight: bolder;} +.error {font-weight: bolder;} +.warning {font-weight: bolder;} /* Clipboard --------------------------*/ @@ -365,3 +358,27 @@ mark { content: ""; } } + +/* Section anchors --------------------------------- + Added in pandoc 2.11: https://github.com/jgm/pandoc-templates/commit/9904bf71 +*/ + +div.csl-bib-body { } +div.csl-entry { + clear: both; +} +.hanging-indent div.csl-entry { + margin-left:2em; + text-indent:-2em; +} +div.csl-left-margin { + min-width:2em; + float:left; +} +div.csl-right-inline { + margin-left:2em; + padding-left:1em; +} +div.csl-indent { + margin-left: 2em; +} diff --git a/docs/pkgdown.js b/docs/pkgdown.js index 7e7048f..6f0eee4 100644 --- a/docs/pkgdown.js +++ b/docs/pkgdown.js @@ -80,7 +80,7 @@ $(document).ready(function() { var copyButton = "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-label='Copy to clipboard' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy'></i></button>"; - $(".examples, div.sourceCode").addClass("hasCopyButton"); + $("div.sourceCode").addClass("hasCopyButton"); // Insert copy buttons: $(copyButton).prependTo(".hasCopyButton"); @@ -91,7 +91,7 @@ // Initialize clipboard: var clipboardBtnCopies = new ClipboardJS('[data-clipboard-copy]', { text: function(trigger) { - return trigger.parentNode.textContent; + return trigger.parentNode.textContent.replace(/\n#>[^\n]*/g, ""); } }); diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 098ab97..dd7c4f0 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -1,6 +1,6 @@ -pandoc: 2.9.2.1 -pkgdown: 1.6.1 +pandoc: 3.1.1 +pkgdown: 2.0.7 pkgdown_sha: ~ articles: {} -last_built: 2021-11-26T15:14Z +last_built: 2023-11-10T17:41Z diff --git a/docs/reference/Rplot001.png b/docs/reference/Rplot001.png Binary files differindex 377b927..d92e93f 100644 --- a/docs/reference/Rplot001.png +++ b/docs/reference/Rplot001.png diff --git a/docs/reference/chent-1.png b/docs/reference/chent-1.png Binary files differindex 7229a66..acab3e6 100644 --- a/docs/reference/chent-1.png +++ b/docs/reference/chent-1.png diff --git a/docs/reference/chent.html b/docs/reference/chent.html index 941eabb..a6b8dde 100644 --- a/docs/reference/chent.html +++ b/docs/reference/chent.html @@ -1,69 +1,14 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - 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Chemical +information is retrieved from the internet. Additionally, it can be +generated using RDKit if RDKit and its python bindings are installed."><!-- 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> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <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"> @@ -74,361 +19,513 @@ python bindings are installed." /> </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="Released version">0.3.1</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.3.1</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> - <a href="../index.html"> - <span class="fas fa-home fa-lg"></span> - - </a> -</li> -<li> + <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/"> + </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 --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>An R6 class for chemical entities with associated data</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/chents/blob/master/R/chent.R'><code>R/chent.R</code></a></small> + <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>chent.Rd</code></div> </div> <div class="ref-description"> - <p>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.</p> + <p>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.</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>identifier</code></dt> +<dd><p>(<code>character(1)</code>)<br> +The identifier that was used to initiate the object, with attribute 'source'</p></dd> - <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> - <p>An <code>R6Class</code> generator object</p> - <h2 class="hasAnchor" id="public-fields"><a class="anchor" href="#public-fields"></a>Public fields</h2> +<dt><code>inchikey</code></dt> +<dd><p>(<code>character(1)</code>)<br> +InChI Key, with attribute 'source'</p></dd> + + +<dt><code>smiles</code></dt> +<dd><p>(<code><a href="https://rdrr.io/r/base/character.html" class="external-link">character()</a></code>)<br> +SMILES code(s), with attribute 'source'</p></dd> + + +<dt><code>mw</code></dt> +<dd><p>(<code>numeric(1)</code>)<br> +Molecular weight, with attribute 'source'</p></dd> + + +<dt><code>pubchem</code></dt> +<dd><p>(<code><a href="https://rdrr.io/r/base/list.html" class="external-link">list()</a></code>)<br> +List of information retrieved from PubChem</p></dd> + - <p><div class="r6-fields"></p><dl> -<dt><code>identifier</code></dt><dd><p>The identifier that was used to initiate the object, with attribute 'source'</p></dd> +<dt><code>rdkit</code></dt> +<dd><p>List of information obtained with RDKit</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>mol</code></dt> +<dd><p><rdkit.Chem.rdchem.Mol> object</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>svg</code></dt> +<dd><p>SVG code</p></dd> -<dt><code>rdkit</code></dt><dd><p>List of information obtained with RDKit</p></dd> -<dt><code>mol</code></dt><dd><p><rdkit.Chem.rdchem.Mol> object</p></dd> +<dt><code>Picture</code></dt> +<dd><p>Graph as a <code>picture</code> object obtained using grImport</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>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>pdf_height</code></dt> +<dd><p>Height of the MediaBox in the pdf after cropping</p></dd> -<dt><code>p0</code></dt><dd><p>Vapour pressure in Pa</p></dd> -<dt><code>cwsat</code></dt><dd><p>Water solubility in mg/L</p></dd> +<dt><code>p0</code></dt> +<dd><p>Vapour pressure in Pa</p></dd> -<dt><code>chyaml</code></dt><dd><p>List of information obtained from a YAML file</p></dd> -<dt><code>soil_degradation</code></dt><dd><p>Dataframe of modelling DT50 values</p></dd> +<dt><code>cwsat</code></dt> +<dd><p>Water solubility in mg/L</p></dd> -<dt><code>soil_ff</code></dt><dd><p>Dataframe of formation fractions</p></dd> -<dt><code>soil_sorption</code></dt><dd><p>Dataframe of soil sorption data</p></dd> +<dt><code>PUF</code></dt> +<dd><p>Plant uptake factor</p></dd> -<dt><code>PUF</code></dt><dd><p>Plant uptake factor</p></dd> -</dl><p></div></p> - <h2 class="hasAnchor" id="methods"><a class="anchor" href="#methods"></a>Methods</h2> +<dt><code>chyaml</code></dt> +<dd><p>List of information obtained from a YAML file</p></dd> + +<dt><code>TPs</code></dt> +<dd><p>List of transformation products as chent objects</p></dd> + + +<dt><code>transformations</code></dt> +<dd><p>Data frame of observed transformations</p></dd> + + +<dt><code>soil_degradation</code></dt> +<dd><p>Dataframe of modelling DT50 values</p></dd> + + +<dt><code>soil_ff</code></dt> +<dd><p>Dataframe of formation fractions</p></dd> + + +<dt><code>soil_sorption</code></dt> +<dd><p>Dataframe of soil sorption data</p></dd> + + +</dl><p></p></div> + </div> + <div id="methods"> + <h2>Methods</h2> -<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Public methods</h3> - -<ul> -<li><p><a href='#method-new'><code>chent$new()</code></a></p></li> -<li><p><a href='#method-try_pubchem'><code>chent$try_pubchem()</code></a></p></li> -<li><p><a href='#method-get_pubchem'><code>chent$get_pubchem()</code></a></p></li> -<li><p><a href='#method-get_rdkit'><code>chent$get_rdkit()</code></a></p></li> -<li><p><a href='#method-get_chyaml'><code>chent$get_chyaml()</code></a></p></li> -<li><p><a href='#method-add_p0'><code>chent$add_p0()</code></a></p></li> -<li><p><a href='#method-add_cwsat'><code>chent$add_cwsat()</code></a></p></li> -<li><p><a href='#method-add_PUF'><code>chent$add_PUF()</code></a></p></li> -<li><p><a href='#method-add_TP'><code>chent$add_TP()</code></a></p></li> -<li><p><a href='#method-add_transformation'><code>chent$add_transformation()</code></a></p></li> -<li><p><a href='#method-add_soil_degradation'><code>chent$add_soil_degradation()</code></a></p></li> -<li><p><a href='#method-add_soil_ff'><code>chent$add_soil_ff()</code></a></p></li> -<li><p><a href='#method-add_soil_sorption'><code>chent$add_soil_sorption()</code></a></p></li> -<li><p><a href='#method-pdf'><code>chent$pdf()</code></a></p></li> -<li><p><a href='#method-png'><code>chent$png()</code></a></p></li> -<li><p><a href='#method-emf'><code>chent$emf()</code></a></p></li> -<li><p><a href='#method-clone'><code>chent$clone()</code></a></p></li> -</ul> -<p><hr> -<a id="method-new"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>new()</code></h3> - -<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4> -<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</span><span class='fu'>new</span><span class='op'>(</span> - <span class='va'>identifier</span>, - smiles <span class='op'>=</span> <span class='cn'>NULL</span>, - smiles_source <span class='op'>=</span> <span class='st'>"user"</span>, - inchikey <span class='op'>=</span> <span class='cn'>NULL</span>, - inchikey_source <span class='op'>=</span> <span class='st'>"user"</span>, - pubchem <span class='op'>=</span> <span class='cn'>TRUE</span>, - pubchem_from <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"name"</span>, <span class='st'>"smiles"</span>, <span class='st'>"inchikey"</span><span class='op'>)</span>, - rdkit <span class='op'>=</span> <span class='cn'>TRUE</span>, - template <span class='op'>=</span> <span class='cn'>NULL</span>, - chyaml <span class='op'>=</span> <span class='cn'>TRUE</span> -<span class='op'>)</span></pre><p></div></p> - -<p><hr> -<a id="method-try_pubchem"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>try_pubchem()</code></h3> - -<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4> -<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</span><span class='fu'>try_pubchem</span><span class='op'>(</span><span class='va'>query</span>, from <span class='op'>=</span> <span class='st'>"name"</span><span class='op'>)</span></pre><p></div></p> - -<p><hr> -<a id="method-get_pubchem"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>get_pubchem()</code></h3> - -<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4> -<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</span><span class='fu'>get_pubchem</span><span class='op'>(</span><span class='va'>pubchem_cid</span><span class='op'>)</span></pre><p></div></p> - -<p><hr> -<a id="method-get_rdkit"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>get_rdkit()</code></h3> - -<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4> -<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</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></pre><p></div></p> - -<p><hr> -<a id="method-get_chyaml"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>get_chyaml()</code></h3> - -<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4> -<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</span><span class='fu'>get_chyaml</span><span class='op'>(</span> - repo <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"wd"</span>, <span class='st'>"local"</span>, <span class='st'>"web"</span><span class='op'>)</span>, - chyaml <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/utils/URLencode.html'>URLencode</a></span><span class='op'>(</span><span class='va'>self</span><span class='op'>$</span><span class='va'>identifier</span><span class='op'>)</span>, <span class='st'>".yaml"</span><span class='op'>)</span> -<span class='op'>)</span></pre><p></div></p> - -<p><hr> -<a id="method-add_p0"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>add_p0()</code></h3> - -<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4> -<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</span><span class='fu'>add_p0</span><span class='op'>(</span><span class='va'>p0</span>, T <span class='op'>=</span> <span class='cn'>NA</span>, source <span class='op'>=</span> <span class='cn'>NA</span>, page <span class='op'>=</span> <span class='cn'>NA</span>, remark <span class='op'>=</span> <span class='st'>""</span><span class='op'>)</span></pre><p></div></p> - -<p><hr> -<a id="method-add_cwsat"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>add_cwsat()</code></h3> - -<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4> -<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</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></pre><p></div></p> - -<p><hr> -<a id="method-add_PUF"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>add_PUF()</code></h3> - -<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4> -<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</span><span class='fu'>add_PUF</span><span class='op'>(</span> - PUF <span class='op'>=</span> <span class='fl'>0</span>, - source <span class='op'>=</span> <span class='st'>"focus_generic_gw_2014"</span>, - page <span class='op'>=</span> <span class='fl'>41</span>, - remark <span class='op'>=</span> <span class='st'>"Conservative default value"</span> -<span class='op'>)</span></pre><p></div></p> - -<p><hr> -<a id="method-add_TP"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>add_TP()</code></h3> - -<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4> -<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</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></pre><p></div></p> - -<p><hr> -<a id="method-add_transformation"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>add_transformation()</code></h3> - -<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4> -<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</span><span class='fu'>add_transformation</span><span class='op'>(</span> - <span class='va'>study_type</span>, - <span class='va'>TP_identifier</span>, - <span class='va'>max_occurrence</span>, - remark <span class='op'>=</span> <span class='st'>""</span>, - source <span class='op'>=</span> <span class='cn'>NA</span>, - pages <span class='op'>=</span> <span class='cn'>NA</span> -<span class='op'>)</span></pre><p></div></p> - -<p><hr> -<a id="method-add_soil_degradation"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>add_soil_degradation()</code></h3> - -<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4> -<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</span><span class='fu'>add_soil_degradation</span><span class='op'>(</span> - <span class='va'>soils</span>, - <span class='va'>DT50_mod</span>, - <span class='va'>DT50_mod_ref</span>, - type <span class='op'>=</span> <span class='cn'>NA</span>, - country <span class='op'>=</span> <span class='cn'>NA</span>, - pH_orig <span class='op'>=</span> <span class='cn'>NA</span>, - pH_medium <span class='op'>=</span> <span class='cn'>NA</span>, - pH_H2O <span class='op'>=</span> <span class='cn'>NA</span>, - perc_OC <span class='op'>=</span> <span class='cn'>NA</span>, - temperature <span class='op'>=</span> <span class='cn'>NA</span>, - moisture <span class='op'>=</span> <span class='cn'>NA</span>, - category <span class='op'>=</span> <span class='st'>"lab"</span>, - formulation <span class='op'>=</span> <span class='cn'>NA</span>, - model <span class='op'>=</span> <span class='cn'>NA</span>, - chi2 <span class='op'>=</span> <span class='cn'>NA</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></pre><p></div></p> - -<p><hr> -<a id="method-add_soil_ff"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>add_soil_ff()</code></h3> - -<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4> -<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</span><span class='fu'>add_soil_ff</span><span class='op'>(</span><span class='va'>target</span>, <span class='va'>soils</span>, ff <span class='op'>=</span> <span class='fl'>1</span>, remark <span class='op'>=</span> <span class='st'>""</span>, <span class='va'>source</span>, page <span class='op'>=</span> <span class='cn'>NA</span><span class='op'>)</span></pre><p></div></p> - -<p><hr> -<a id="method-add_soil_sorption"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>add_soil_sorption()</code></h3> - -<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4> -<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</span><span class='fu'>add_soil_sorption</span><span class='op'>(</span> - <span class='va'>soils</span>, - <span class='va'>Kf</span>, - <span class='va'>Kfoc</span>, - <span class='va'>N</span>, - type <span class='op'>=</span> <span class='cn'>NA</span>, - pH_orig <span class='op'>=</span> <span class='cn'>NA</span>, - pH_medium <span class='op'>=</span> <span class='cn'>NA</span>, - pH_H2O <span class='op'>=</span> <span class='cn'>NA</span>, - perc_OC <span class='op'>=</span> <span class='cn'>NA</span>, - perc_clay <span class='op'>=</span> <span class='cn'>NA</span>, - CEC <span class='op'>=</span> <span class='cn'>NA</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></pre><p></div></p> - -<p><hr> -<a id="method-pdf"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code><a href='https://rdrr.io/r/grDevices/pdf.html'>pdf()</a></code></h3> - -<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4> -<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</span><span class='fu'>pdf</span><span class='op'>(</span> - file <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span><span class='op'>(</span><span class='va'>self</span><span class='op'>$</span><span class='va'>identifier</span>, <span class='st'>".pdf"</span><span class='op'>)</span>, - dir <span class='op'>=</span> <span class='st'>"structures/pdf"</span>, - template <span class='op'>=</span> <span class='cn'>NULL</span> -<span class='op'>)</span></pre><p></div></p> - -<p><hr> -<a id="method-png"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code><a href='https://rdrr.io/r/grDevices/png.html'>png()</a></code></h3> - -<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4> -<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</span><span class='fu'>png</span><span class='op'>(</span> - file <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span><span class='op'>(</span><span class='va'>self</span><span class='op'>$</span><span class='va'>identifier</span>, <span class='st'>".png"</span><span class='op'>)</span>, - dir <span class='op'>=</span> <span class='st'>"structures/png"</span>, - antialias <span class='op'>=</span> <span class='st'>"gray"</span> -<span class='op'>)</span></pre><p></div></p> - -<p><hr> -<a id="method-emf"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>emf()</code></h3> - -<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4> -<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</span><span class='fu'>emf</span><span class='op'>(</span>file <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span><span class='op'>(</span><span class='va'>self</span><span class='op'>$</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></pre><p></div></p> - -<p><hr> -<a id="method-clone"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>clone()</code></h3> -<p>The objects of this class are cloneable with this method.</p><h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4> -<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</span><span class='fu'>clone</span><span class='op'>(</span>deep <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span></pre><p></div></p> - -<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Arguments</h4> -<p><div class="arguments"></p><dl> -<dt><code>deep</code></dt><dd><p>Whether to make a deep clone.</p></dd> - -</dl><p></div></p> - - - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='va'>oct</span> <span class='op'><-</span> <span class='va'>chent</span><span class='op'>$</span><span class='fu'>new</span><span class='op'>(</span><span class='st'>"1-octanol"</span>, smiles <span class='op'>=</span> <span class='st'>"CCCCCCCCO"</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>PubChem:</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'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>oct</span><span class='op'>)</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" -#> Molecular weight $mw: 130.2 -#> PubChem synonyms (up to 10): -#> [1] "1-octanol" "Octan-1-ol" "octanol" "111-87-5" -#> [5] "N-octanol" "Octyl alcohol" "Capryl alcohol" "caprylic alcohol" -#> [9] "n-Octyl alcohol" "Heptyl carbinol" </div><div class='input'><span class='kw'>if</span> <span class='op'>(</span><span class='op'>!</span><span class='fu'><a href='https://rdrr.io/r/base/NULL.html'>is.null</a></span><span class='op'>(</span><span class='va'>oct</span><span class='op'>$</span><span class='va'>Picture</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span> - <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>oct</span><span class='op'>)</span> -<span class='op'>}</span> -</div><div class='input'> -<span class='va'>caffeine</span> <span class='op'><-</span> <span class='va'>chent</span><span class='op'>$</span><span class='fu'>new</span><span class='op'>(</span><span class='st'>"caffeine"</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>PubChem:</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'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>caffeine</span><span class='op'>)</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" -#> Molecular weight $mw: 194.2 -#> PubChem synonyms (up to 10): -#> [1] "caffeine" "58-08-2" -#> [3] "1,3,7-Trimethylxanthine" "Guaranine" -#> [5] "Thein" "Methyltheobromine" -#> [7] "Cafeina" "Theine" -#> [9] "Koffein" "Mateina" </div><div class='input'><span class='kw'>if</span> <span class='op'>(</span><span class='op'>!</span><span class='fu'><a href='https://rdrr.io/r/base/NULL.html'>is.null</a></span><span class='op'>(</span><span class='va'>caffeine</span><span class='op'>$</span><span class='va'>Picture</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span> - <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>caffeine</span><span class='op'>)</span> -<span class='op'>}</span> -</div><div class='img'><img src='chent-1.png' alt='' width='700' height='433' /></div></pre> +<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-chent-new"><code>chent$new()</code></a></p></li> +<li><p><a href="#method-chent-try_pubchem"><code>chent$try_pubchem()</code></a></p></li> +<li><p><a href="#method-chent-get_pubchem"><code>chent$get_pubchem()</code></a></p></li> +<li><p><a href="#method-chent-get_rdkit"><code>chent$get_rdkit()</code></a></p></li> +<li><p><a href="#method-chent-get_chyaml"><code>chent$get_chyaml()</code></a></p></li> +<li><p><a href="#method-chent-add_p0"><code>chent$add_p0()</code></a></p></li> +<li><p><a href="#method-chent-add_cwsat"><code>chent$add_cwsat()</code></a></p></li> +<li><p><a href="#method-chent-add_PUF"><code>chent$add_PUF()</code></a></p></li> +<li><p><a href="#method-chent-add_TP"><code>chent$add_TP()</code></a></p></li> +<li><p><a href="#method-chent-add_transformation"><code>chent$add_transformation()</code></a></p></li> +<li><p><a href="#method-chent-add_soil_degradation"><code>chent$add_soil_degradation()</code></a></p></li> +<li><p><a href="#method-chent-add_soil_ff"><code>chent$add_soil_ff()</code></a></p></li> +<li><p><a href="#method-chent-add_soil_sorption"><code>chent$add_soil_sorption()</code></a></p></li> +<li><p><a href="#method-chent-pdf"><code>chent$pdf()</code></a></p></li> +<li><p><a href="#method-chent-png"><code>chent$png()</code></a></p></li> +<li><p><a href="#method-chent-emf"><code>chent$emf()</code></a></p></li> +<li><p><a href="#method-chent-clone"><code>chent$clone()</code></a></p></li> +</ul></div><p></p><hr><a id="method-chent-new"></a><div class="section"> +<h3 id="method-new-">Method <code>new()</code><a class="anchor" aria-label="anchor" href="#method-new-"></a></h3> +<p>Creates a new instance of this <a href="https://r6.r-lib.org/reference/R6Class.html" class="external-link">R6</a> class.</p><div class="section"> +<h4 id="usage">Usage<a class="anchor" aria-label="anchor" href="#usage"></a></h4> +<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va"><a href="../reference/chent.html">chent</a></span><span class="op">$</span><span class="fu">new</span><span class="op">(</span></span> +<span> <span class="va">identifier</span>,</span> +<span> smiles <span class="op">=</span> <span class="cn">NULL</span>,</span> +<span> inchikey <span class="op">=</span> <span class="cn">NULL</span>,</span> +<span> pubchem <span class="op">=</span> <span class="cn">TRUE</span>,</span> +<span> pubchem_from <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"name"</span>, <span class="st">"smiles"</span>, <span class="st">"inchikey"</span><span class="op">)</span>,</span> +<span> rdkit <span class="op">=</span> <span class="cn">TRUE</span>,</span> +<span> template <span class="op">=</span> <span class="cn">NULL</span>,</span> +<span> chyaml <span class="op">=</span> <span class="cn">TRUE</span></span> +<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>identifier</code></dt> +<dd><p>Identifier to be stored in the object</p></dd> + + +<dt><code>smiles</code></dt> +<dd><p>Optional user provided SMILES code</p></dd> + + +<dt><code>inchikey</code></dt> +<dd><p>Optional user provided InChI Key</p></dd> + + +<dt><code>pubchem</code></dt> +<dd><p>Should an attempt be made to retrieve chemical +information from PubChem via the webchem package?</p></dd> + + +<dt><code>pubchem_from</code></dt> +<dd><p>Possibility to select the argument +that is used to query pubchem</p></dd> + + +<dt><code>rdkit</code></dt> +<dd><p>Should an attempt be made to retrieve chemical +information from a local rdkit installation via python +and the reticulate package?</p></dd> + + +<dt><code>template</code></dt> +<dd><p>An optional SMILES code to be used as template for RDKit</p></dd> + + +<dt><code>chyaml</code></dt> +<dd><p>Should we look for a identifier.yaml file in the working +directory? +Try to get chemical information from PubChem</p></dd> + + +</dl><p></p></div> +</div> + +</div><p></p><hr><a id="method-chent-try_pubchem"></a><div class="section"> +<h3 id="method-try-pubchem-">Method <code>try_pubchem()</code><a class="anchor" aria-label="anchor" href="#method-try-pubchem-"></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">chent</span><span class="op">$</span><span class="fu">try_pubchem</span><span class="op">(</span><span class="va">query</span>, from <span class="op">=</span> <span class="st">"name"</span><span class="op">)</span></span></code></pre></div><p></p></div> +</div> + +<div class="section"> +<h4 id="arguments-1">Arguments<a class="anchor" aria-label="anchor" href="#arguments-1"></a></h4> +<p></p><div class="arguments"><dl><dt><code>query</code></dt> +<dd><p>Query string to be passed to <a href="https://docs.ropensci.org/webchem/reference/get_cid.html" class="external-link">get_cid</a></p></dd> + + +<dt><code>from</code></dt> +<dd><p>Passed to <a href="https://docs.ropensci.org/webchem/reference/get_cid.html" class="external-link">get_cid</a> +Get chemical information from PubChem for a known PubChem CID</p></dd> + + +</dl><p></p></div> +</div> + +</div><p></p><hr><a id="method-chent-get_pubchem"></a><div class="section"> +<h3 id="method-get-pubchem-">Method <code>get_pubchem()</code><a class="anchor" aria-label="anchor" href="#method-get-pubchem-"></a></h3> + +<div class="section"> +<h4 id="usage-2">Usage<a class="anchor" aria-label="anchor" href="#usage-2"></a></h4> +<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">get_pubchem</span><span class="op">(</span><span class="va">pubchem_cid</span><span class="op">)</span></span></code></pre></div><p></p></div> +</div> + +<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> + + +</dl><p></p></div> +</div> + +</div><p></p><hr><a id="method-chent-get_rdkit"></a><div class="section"> +<h3 id="method-get-rdkit-">Method <code>get_rdkit()</code><a class="anchor" aria-label="anchor" href="#method-get-rdkit-"></a></h3> + +<div class="section"> +<h4 id="usage-3">Usage<a class="anchor" aria-label="anchor" href="#usage-3"></a></h4> +<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">get_rdkit</span><span class="op">(</span>template <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span></span></code></pre></div><p></p></div> +</div> + + +</div><p></p><hr><a id="method-chent-get_chyaml"></a><div class="section"> +<h3 id="method-get-chyaml-">Method <code>get_chyaml()</code><a class="anchor" aria-label="anchor" href="#method-get-chyaml-"></a></h3> + +<div class="section"> +<h4 id="usage-4">Usage<a class="anchor" aria-label="anchor" href="#usage-4"></a></h4> +<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">get_chyaml</span><span class="op">(</span></span> +<span> repo <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"wd"</span>, <span class="st">"local"</span>, <span class="st">"web"</span><span class="op">)</span>,</span> +<span> chyaml <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="fu"><a href="https://rdrr.io/r/utils/URLencode.html" class="external-link">URLencode</a></span><span class="op">(</span><span class="va">self</span><span class="op">$</span><span class="va">identifier</span><span class="op">)</span>, <span class="st">".yaml"</span><span class="op">)</span></span> +<span><span class="op">)</span></span></code></pre></div><p></p></div> +</div> + + +</div><p></p><hr><a id="method-chent-add_p0"></a><div class="section"> +<h3 id="method-add-p-">Method <code>add_p0()</code><a class="anchor" aria-label="anchor" href="#method-add-p-"></a></h3> + +<div class="section"> +<h4 id="usage-5">Usage<a class="anchor" aria-label="anchor" href="#usage-5"></a></h4> +<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</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><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> + +<div class="section"> +<h4 id="usage-6">Usage<a class="anchor" aria-label="anchor" href="#usage-6"></a></h4> +<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">add_cwsat</span><span class="op">(</span><span class="va">cwsat</span>, T <span class="op">=</span> <span class="cn">NA</span>, pH <span class="op">=</span> <span class="cn">NA</span>, source <span class="op">=</span> <span class="cn">NA</span>, page <span class="op">=</span> <span class="cn">NA</span>, remark <span class="op">=</span> <span class="st">""</span><span class="op">)</span></span></code></pre></div><p></p></div> +</div> + + +</div><p></p><hr><a id="method-chent-add_PUF"></a><div class="section"> +<h3 id="method-add-puf-">Method <code>add_PUF()</code><a class="anchor" aria-label="anchor" href="#method-add-puf-"></a></h3> + +<div class="section"> +<h4 id="usage-7">Usage<a class="anchor" aria-label="anchor" href="#usage-7"></a></h4> +<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">add_PUF</span><span class="op">(</span></span> +<span> PUF <span class="op">=</span> <span class="fl">0</span>,</span> +<span> source <span class="op">=</span> <span class="st">"focus_generic_gw_2014"</span>,</span> +<span> page <span class="op">=</span> <span class="fl">41</span>,</span> +<span> remark <span class="op">=</span> <span class="st">"Conservative default value"</span></span> +<span><span class="op">)</span></span></code></pre></div><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> + +<div class="section"> +<h4 id="usage-8">Usage<a class="anchor" aria-label="anchor" href="#usage-8"></a></h4> +<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">add_TP</span><span class="op">(</span><span class="va">x</span>, smiles <span class="op">=</span> <span class="cn">NULL</span>, pubchem <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div><p></p></div> +</div> + + +</div><p></p><hr><a id="method-chent-add_transformation"></a><div class="section"> +<h3 id="method-add-transformation-">Method <code>add_transformation()</code><a class="anchor" aria-label="anchor" href="#method-add-transformation-"></a></h3> + +<div class="section"> +<h4 id="usage-9">Usage<a class="anchor" aria-label="anchor" href="#usage-9"></a></h4> +<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">add_transformation</span><span class="op">(</span></span> +<span> <span class="va">study_type</span>,</span> +<span> <span class="va">TP_identifier</span>,</span> +<span> <span class="va">max_occurrence</span>,</span> +<span> remark <span class="op">=</span> <span class="st">""</span>,</span> +<span> source <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> pages <span class="op">=</span> <span class="cn">NA</span></span> +<span><span class="op">)</span></span></code></pre></div><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> + +<div class="section"> +<h4 id="usage-10">Usage<a class="anchor" aria-label="anchor" href="#usage-10"></a></h4> +<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">add_soil_degradation</span><span class="op">(</span></span> +<span> <span class="va">soils</span>,</span> +<span> <span class="va">DT50_mod</span>,</span> +<span> <span class="va">DT50_mod_ref</span>,</span> +<span> type <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> country <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> pH_orig <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> pH_medium <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> pH_H2O <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> perc_OC <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> temperature <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> moisture <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> category <span class="op">=</span> <span class="st">"lab"</span>,</span> +<span> formulation <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> model <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> chi2 <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> remark <span class="op">=</span> <span class="st">""</span>,</span> +<span> <span class="va">source</span>,</span> +<span> page <span class="op">=</span> <span class="cn">NA</span></span> +<span><span class="op">)</span></span></code></pre></div><p></p></div> +</div> + + +</div><p></p><hr><a id="method-chent-add_soil_ff"></a><div class="section"> +<h3 id="method-add-soil-ff-">Method <code>add_soil_ff()</code><a class="anchor" aria-label="anchor" href="#method-add-soil-ff-"></a></h3> + +<div class="section"> +<h4 id="usage-11">Usage<a class="anchor" aria-label="anchor" href="#usage-11"></a></h4> +<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</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><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> + +<div class="section"> +<h4 id="usage-12">Usage<a class="anchor" aria-label="anchor" href="#usage-12"></a></h4> +<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">add_soil_sorption</span><span class="op">(</span></span> +<span> <span class="va">soils</span>,</span> +<span> <span class="va">Kf</span>,</span> +<span> <span class="va">Kfoc</span>,</span> +<span> <span class="va">N</span>,</span> +<span> type <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> pH_orig <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> pH_medium <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> pH_H2O <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> perc_OC <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> perc_clay <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> CEC <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> remark <span class="op">=</span> <span class="st">""</span>,</span> +<span> <span class="va">source</span>,</span> +<span> page <span class="op">=</span> <span class="cn">NA</span></span> +<span><span class="op">)</span></span></code></pre></div><p></p></div> +</div> + + +</div><p></p><hr><a id="method-chent-pdf"></a><div class="section"> +<h3 id="method-pdf-">Method <code><a href="https://rdrr.io/r/grDevices/pdf.html" class="external-link">pdf()</a></code><a class="anchor" aria-label="anchor" href="#method-pdf-"></a></h3> + +<div class="section"> +<h4 id="usage-13">Usage<a class="anchor" aria-label="anchor" href="#usage-13"></a></h4> +<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">pdf</span><span class="op">(</span></span> +<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">$</span><span class="va">identifier</span>, <span class="st">".pdf"</span><span class="op">)</span>,</span> +<span> dir <span class="op">=</span> <span class="st">"structures/pdf"</span>,</span> +<span> template <span class="op">=</span> <span class="cn">NULL</span></span> +<span><span class="op">)</span></span></code></pre></div><p></p></div> +</div> + + +</div><p></p><hr><a id="method-chent-png"></a><div class="section"> +<h3 id="method-png-">Method <code><a href="https://rdrr.io/r/grDevices/png.html" class="external-link">png()</a></code><a class="anchor" aria-label="anchor" href="#method-png-"></a></h3> + +<div class="section"> +<h4 id="usage-14">Usage<a class="anchor" aria-label="anchor" href="#usage-14"></a></h4> +<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">png</span><span class="op">(</span></span> +<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">$</span><span class="va">identifier</span>, <span class="st">".png"</span><span class="op">)</span>,</span> +<span> dir <span class="op">=</span> <span class="st">"structures/png"</span>,</span> +<span> antialias <span class="op">=</span> <span class="st">"gray"</span></span> +<span><span class="op">)</span></span></code></pre></div><p></p></div> +</div> + + +</div><p></p><hr><a id="method-chent-emf"></a><div class="section"> +<h3 id="method-emf-">Method <code>emf()</code><a class="anchor" aria-label="anchor" href="#method-emf-"></a></h3> + +<div class="section"> +<h4 id="usage-15">Usage<a class="anchor" aria-label="anchor" href="#usage-15"></a></h4> +<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</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">$</span><span class="va">identifier</span>, <span class="st">".emf"</span><span class="op">)</span>, dir <span class="op">=</span> <span class="st">"structures/emf"</span><span class="op">)</span></span></code></pre></div><p></p></div> +</div> + + +</div><p></p><hr><a id="method-chent-clone"></a><div class="section"> +<h3 id="method-clone-">Method <code>clone()</code><a class="anchor" aria-label="anchor" href="#method-clone-"></a></h3> +<p>The objects of this class are cloneable with this method.</p><div class="section"> +<h4 id="usage-16">Usage<a class="anchor" aria-label="anchor" href="#usage-16"></a></h4> +<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</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-3">Arguments<a class="anchor" aria-label="anchor" href="#arguments-3"></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 id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">oct</span> <span class="op"><-</span> <span class="va">chent</span><span class="op">$</span><span class="fu">new</span><span class="op">(</span><span class="st">"1-octanol"</span>, smiles <span class="op">=</span> <span class="st">"CCCCCCCCO"</span>, pubchem <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Trying to get chemical information from RDKit using user SMILES</span> +<span class="r-msg co"><span class="r-pr">#></span> CCCCCCCCO</span> +<span class="r-msg co"><span class="r-pr">#></span> Did not find chyaml file ./1-octanol.yaml</span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">oct</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> <chent></span> +<span class="r-out co"><span class="r-pr">#></span> Identifier $identifier 1-octanol </span> +<span class="r-out co"><span class="r-pr">#></span> InChI Key $inchikey </span> +<span class="r-out co"><span class="r-pr">#></span> SMILES string $smiles:</span> +<span class="r-out co"><span class="r-pr">#></span> user </span> +<span class="r-out co"><span class="r-pr">#></span> "CCCCCCCCO" </span> +<span class="r-out co"><span class="r-pr">#></span> Molecular weight $mw: 130.2 </span> +<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NULL.html" class="external-link">is.null</a></span><span class="op">(</span><span class="va">oct</span><span class="op">$</span><span class="va">Picture</span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">oct</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="op">}</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">caffeine</span> <span class="op"><-</span> <span class="va">chent</span><span class="op">$</span><span class="fu">new</span><span class="op">(</span><span class="st">"caffeine"</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> PubChem:</span> +<span class="r-msg co"><span class="r-pr">#></span> Trying to get chemical information from RDKit using PubChem_Canonical SMILES</span> +<span class="r-msg co"><span class="r-pr">#></span> CN1C=NC2=C1C(=O)N(C(=O)N2C)C</span> +<span class="r-msg co"><span class="r-pr">#></span> Did not find chyaml file ./caffeine.yaml</span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">caffeine</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> <chent></span> +<span class="r-out co"><span class="r-pr">#></span> Identifier $identifier caffeine </span> +<span class="r-out co"><span class="r-pr">#></span> InChI Key $inchikey RYYVLZVUVIJVGH-UHFFFAOYSA-N </span> +<span class="r-out co"><span class="r-pr">#></span> SMILES string $smiles:</span> +<span class="r-out co"><span class="r-pr">#></span> PubChem_Canonical </span> +<span class="r-out co"><span class="r-pr">#></span> "CN1C=NC2=C1C(=O)N(C(=O)N2C)C" </span> +<span class="r-out co"><span class="r-pr">#></span> Molecular weight $mw: 194.2 </span> +<span class="r-out co"><span class="r-pr">#></span> PubChem synonyms (up to 10):</span> +<span class="r-out co"><span class="r-pr">#></span> [1] "caffeine" "58-08-2" </span> +<span class="r-out co"><span class="r-pr">#></span> [3] "Guaranine" "1,3,7-Trimethylxanthine"</span> +<span class="r-out co"><span class="r-pr">#></span> [5] "Methyltheobromine" "Theine" </span> +<span class="r-out co"><span class="r-pr">#></span> [7] "Thein" "Cafeina" </span> +<span class="r-out co"><span class="r-pr">#></span> [9] "Koffein" "Mateina" </span> +<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NULL.html" class="external-link">is.null</a></span><span class="op">(</span><span class="va">caffeine</span><span class="op">$</span><span class="va">Picture</span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">caffeine</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="op">}</span></span></span> +<span class="r-plt img"><img src="chent-1.png" alt="" width="700" height="433"></span> +</code></pre></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> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <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> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/reference/draw_svg.chent.html b/docs/reference/draw_svg.chent.html index 1805ff1..cae8c0b 100644 --- a/docs/reference/draw_svg.chent.html +++ b/docs/reference/draw_svg.chent.html @@ -1,67 +1,12 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html 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href="../pkgdown.css" rel="stylesheet"><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"><!-- 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]--> - +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - - </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"> + <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"> @@ -72,44 +17,31 @@ </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="Released version">0.3.1</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.3.1</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> - <a href="../index.html"> - <span class="fas fa-home fa-lg"></span> - - </a> -</li> -<li> + <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/"> + </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 --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Draw SVG graph from a chent object using RDKit</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/chents/blob/master/R/chent.R'><code>R/chent.R</code></a></small> + <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>draw_svg.chent.Rd</code></div> </div> @@ -117,65 +49,60 @@ <p>Draw SVG graph from a chent object using RDKit</p> </div> - <pre class="usage"><span class='fu'>draw_svg.chent</span><span class='op'>(</span> - <span class='va'>x</span>, - width <span class='op'>=</span> <span class='fl'>300</span>, - height <span class='op'>=</span> <span class='fl'>150</span>, - filename <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</span><span class='va'>identifier</span><span class='op'>)</span>, <span class='st'>".svg"</span><span class='op'>)</span>, - subdir <span class='op'>=</span> <span class='st'>"svg"</span> -<span class='op'>)</span></pre> - - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>x</th> - <td><p>The chent object to be plotted</p></td> - </tr> - <tr> - <th>width</th> - <td><p>The desired width in pixels</p></td> - </tr> - <tr> - <th>height</th> - <td><p>The desired height in pixels</p></td> - </tr> - <tr> - <th>filename</th> - <td><p>The filename</p></td> - </tr> - <tr> - <th>subdir</th> - <td><p>The path to which the file should be written</p></td> - </tr> - </table> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">draw_svg.chent</span><span class="op">(</span></span> +<span> <span class="va">x</span>,</span> +<span> width <span class="op">=</span> <span class="fl">300</span>,</span> +<span> height <span class="op">=</span> <span class="fl">150</span>,</span> +<span> filename <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">x</span><span class="op">$</span><span class="va">identifier</span><span class="op">)</span>, <span class="st">".svg"</span><span class="op">)</span>,</span> +<span> subdir <span class="op">=</span> <span class="st">"svg"</span></span> +<span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>x</dt> +<dd><p>The chent object to be plotted</p></dd> + +<dt>width</dt> +<dd><p>The desired width in pixels</p></dd> + + +<dt>height</dt> +<dd><p>The desired height in pixels</p></dd> + + +<dt>filename</dt> +<dd><p>The filename</p></dd> + + +<dt>subdir</dt> +<dd><p>The path to which the file should be written</p></dd> + +</dl></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> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <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> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/reference/index.html b/docs/reference/index.html index 9de4a87..d9eb797 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -1,66 +1,12 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - <head> - <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>Function reference • chents</title> - - -<!-- jquery --> -<script 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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]--> - - +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - </head> - - <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-index"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <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"> @@ -71,136 +17,86 @@ </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="Released version">0.3.1</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.3.1</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> - <a href="../index.html"> - <span class="fas fa-home fa-lg"></span> - - </a> -</li> -<li> + <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/"> + </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 --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="contents col-md-9"> <div class="page-header"> <h1>Reference</h1> </div> - <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> + <table class="ref-index"><colgroup><col class="alias"><col class="title"></colgroup><tbody><tr><th colspan="2"> + <h2 id="r-class-definitions-and-methods">R6 Class definitions and methods <a href="#r-class-definitions-and-methods" class="anchor" aria-hidden="true"></a></h2> <p class="section-desc"></p> </th> - </tr> - - - </tbody><tbody> - - - <tr> - - <td> + </tr></tbody><tbody><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> + </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> + </tr><tr><td> <p><code><a href="plot.chent.html">plot(<i><chent></i>)</a></code> </p> </td> <td><p>Plot method for chent objects</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="print.chent.html">print(<i><chent></i>)</a></code> </p> </td> <td><p>Printing method for chent objects</p></td> - </tr><tr> - - <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> + </tr><tr><td> <p><code><a href="print.pai.html">print(<i><pai></i>)</a></code> </p> </td> <td><p>Printing method for pai objects (pesticidal active ingredients)</p></td> - </tr><tr> - - <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> + </tr></tbody></table></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> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <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> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/reference/pai-1.png b/docs/reference/pai-1.png Binary files differindex c235304..802fd50 100644 --- a/docs/reference/pai-1.png +++ b/docs/reference/pai-1.png diff --git a/docs/reference/pai.html b/docs/reference/pai.html index 0bb3399..636007f 100644 --- a/docs/reference/pai.html +++ b/docs/reference/pai.html @@ -1,68 +1,13 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - <head> - <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 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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> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <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"> @@ -73,44 +18,31 @@ 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="Released version">0.3.1</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.3.1</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> - <a href="../index.html"> - <span class="fas fa-home fa-lg"></span> - - </a> -</li> -<li> + <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/"> + </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 --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>An R6 class for pesticidal active ingredients and associated data</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/chents/blob/master/R/chent.R'><code>R/chent.R</code></a></small> + <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>pai.Rd</code></div> </div> @@ -120,132 +52,143 @@ Additional chemical information is retrieved from the internet if available.</p> </div> + <div id="format"> + <h2>Format</h2> + <p>An <code>R6Class</code> generator object</p> + </div> + <div id="super-class"> + <h2>Super class</h2> + <p><code><a href="chent.html">chents::chent</a></code> -> <code>pai</code></p> + </div> + <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> + + +<dt><code>bcpc</code></dt> +<dd><p>List of information retrieved from pesticidecompendium.bcpc.org</p></dd> - <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> - <p>An <code>R6Class</code> generator object</p> - <h2 class="hasAnchor" id="super-class"><a class="anchor" href="#super-class"></a>Super class</h2> +</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-pai-new"><code>pai$new()</code></a></p></li> +<li><p><a href="#method-pai-clone"><code>pai$clone()</code></a></p></li> +</ul></div><p><details><summary>Inherited methods</summary><ul><li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_PUF"><a href="chent.html#method-add_PUF"><code>chents::chent$add_PUF()</code></a></span></li> +<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_TP"><a href="chent.html#method-add_TP"><code>chents::chent$add_TP()</code></a></span></li> +<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_cwsat"><a href="chent.html#method-add_cwsat"><code>chents::chent$add_cwsat()</code></a></span></li> +<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_p0"><a href="chent.html#method-add_p0"><code>chents::chent$add_p0()</code></a></span></li> +<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_soil_degradation"><a href="chent.html#method-add_soil_degradation"><code>chents::chent$add_soil_degradation()</code></a></span></li> +<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_soil_ff"><a href="chent.html#method-add_soil_ff"><code>chents::chent$add_soil_ff()</code></a></span></li> +<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_soil_sorption"><a href="chent.html#method-add_soil_sorption"><code>chents::chent$add_soil_sorption()</code></a></span></li> +<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_transformation"><a href="chent.html#method-add_transformation"><code>chents::chent$add_transformation()</code></a></span></li> +<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="emf"><a href="chent.html#method-emf"><code>chents::chent$emf()</code></a></span></li> +<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="get_chyaml"><a href="chent.html#method-get_chyaml"><code>chents::chent$get_chyaml()</code></a></span></li> +<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="get_pubchem"><a href="chent.html#method-get_pubchem"><code>chents::chent$get_pubchem()</code></a></span></li> +<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="get_rdkit"><a href="chent.html#method-get_rdkit"><code>chents::chent$get_rdkit()</code></a></span></li> +<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="pdf"><a href="chent.html#method-pdf"><code>chents::chent$pdf()</code></a></span></li> +<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="png"><a href="chent.html#method-png"><code>chents::chent$png()</code></a></span></li> +<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$try_pubchem()</code></a></span></li> +</ul></details></p><hr><a id="method-pai-new"></a><div class="section"> +<h3 id="method-new-">Method <code>new()</code><a class="anchor" aria-label="anchor" href="#method-new-"></a></h3> + +<div class="section"> +<h4 id="usage">Usage<a class="anchor" aria-label="anchor" href="#usage"></a></h4> +<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va"><a href="../reference/pai.html">pai</a></span><span class="op">$</span><span class="fu">new</span><span class="op">(</span></span> +<span> <span class="va">iso</span>,</span> +<span> identifier <span class="op">=</span> <span class="va">iso</span>,</span> +<span> smiles <span class="op">=</span> <span class="cn">NULL</span>,</span> +<span> inchikey <span class="op">=</span> <span class="cn">NULL</span>,</span> +<span> bcpc <span class="op">=</span> <span class="cn">TRUE</span>,</span> +<span> pubchem <span class="op">=</span> <span class="cn">TRUE</span>,</span> +<span> pubchem_from <span class="op">=</span> <span class="st">"auto"</span>,</span> +<span> rdkit <span class="op">=</span> <span class="cn">TRUE</span>,</span> +<span> template <span class="op">=</span> <span class="cn">NULL</span>,</span> +<span> chyaml <span class="op">=</span> <span class="cn">TRUE</span></span> +<span><span class="op">)</span></span></code></pre></div><p></p></div> +</div> - <p><code><a href='chent.html'>chents::chent</a></code> -> <code>pai</code></p> - <h2 class="hasAnchor" id="public-fields"><a class="anchor" href="#public-fields"></a>Public fields</h2> - <p><div class="r6-fields"></p><dl> -<dt><code>iso</code></dt><dd><p>ISO common name according to ISO 1750 as retreived from pesticidecompendium.bcpc.org</p></dd> +</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> +<p>The objects of this class are cloneable with this method.</p><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">pai</span><span class="op">$</span><span class="fu">clone</span><span class="op">(</span>deep <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div><p></p></div> +</div> -<dt><code>bcpc</code></dt><dd><p>List of information retrieved from pesticidecompendium.bcpc.org</p></dd> +<div class="section"> +<h4 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h4> +<p></p><div class="arguments"><dl><dt><code>deep</code></dt> +<dd><p>Whether to make a deep clone.</p></dd> -</dl><p></div></p> - <h2 class="hasAnchor" id="methods"><a class="anchor" href="#methods"></a>Methods</h2> - -<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Public methods</h3> - -<ul> -<li><p><a href='#method-new'><code>pai$new()</code></a></p></li> -<li><p><a href='#method-clone'><code>pai$clone()</code></a></p></li> -</ul> -<p><details ><summary>Inherited methods</summary> -<ul> -<li><p><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_PUF"><a href='../../chents/html/chent.html#method-add_PUF'><code>chents::chent$add_PUF()</code></a></span></p></li> -<li><p><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_TP"><a href='../../chents/html/chent.html#method-add_TP'><code>chents::chent$add_TP()</code></a></span></p></li> -<li><p><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_cwsat"><a href='../../chents/html/chent.html#method-add_cwsat'><code>chents::chent$add_cwsat()</code></a></span></p></li> -<li><p><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_p0"><a href='../../chents/html/chent.html#method-add_p0'><code>chents::chent$add_p0()</code></a></span></p></li> -<li><p><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_soil_degradation"><a href='../../chents/html/chent.html#method-add_soil_degradation'><code>chents::chent$add_soil_degradation()</code></a></span></p></li> -<li><p><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_soil_ff"><a href='../../chents/html/chent.html#method-add_soil_ff'><code>chents::chent$add_soil_ff()</code></a></span></p></li> -<li><p><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_soil_sorption"><a href='../../chents/html/chent.html#method-add_soil_sorption'><code>chents::chent$add_soil_sorption()</code></a></span></p></li> -<li><p><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_transformation"><a href='../../chents/html/chent.html#method-add_transformation'><code>chents::chent$add_transformation()</code></a></span></p></li> -<li><p><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="emf"><a href='../../chents/html/chent.html#method-emf'><code>chents::chent$emf()</code></a></span></p></li> -<li><p><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="get_chyaml"><a href='../../chents/html/chent.html#method-get_chyaml'><code>chents::chent$get_chyaml()</code></a></span></p></li> -<li><p><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="get_pubchem"><a href='../../chents/html/chent.html#method-get_pubchem'><code>chents::chent$get_pubchem()</code></a></span></p></li> -<li><p><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="get_rdkit"><a href='../../chents/html/chent.html#method-get_rdkit'><code>chents::chent$get_rdkit()</code></a></span></p></li> -<li><p><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="pdf"><a href='../../chents/html/chent.html#method-pdf'><code>chents::chent$pdf()</code></a></span></p></li> -<li><p><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="png"><a href='../../chents/html/chent.html#method-png'><code>chents::chent$png()</code></a></span></p></li> -<li><p><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="try_pubchem"><a href='../../chents/html/chent.html#method-try_pubchem'><code>chents::chent$try_pubchem()</code></a></span></p></li> -</ul> -</details> - -<hr> -<a id="method-new"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>new()</code></h3> - -<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4> -<p><div class="r"></p><pre><span class='va'>pai</span><span class='op'>$</span><span class='fu'>new</span><span class='op'>(</span> - <span class='va'>iso</span>, - identifier <span class='op'>=</span> <span class='va'>iso</span>, - smiles <span class='op'>=</span> <span class='cn'>NULL</span>, - smiles_source <span class='op'>=</span> <span class='st'>"user"</span>, - inchikey <span class='op'>=</span> <span class='cn'>NULL</span>, - inchikey_source <span class='op'>=</span> <span class='st'>"user"</span>, - bcpc <span class='op'>=</span> <span class='cn'>TRUE</span>, - pubchem <span class='op'>=</span> <span class='cn'>TRUE</span>, - pubchem_from <span class='op'>=</span> <span class='st'>"auto"</span>, - rdkit <span class='op'>=</span> <span class='cn'>TRUE</span>, - template <span class='op'>=</span> <span class='cn'>NULL</span>, - chyaml <span class='op'>=</span> <span class='cn'>TRUE</span> -<span class='op'>)</span></pre><p></div></p> - -<p><hr> -<a id="method-clone"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>clone()</code></h3> -<p>The objects of this class are cloneable with this method.</p><h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4> -<p><div class="r"></p><pre><span class='va'>pai</span><span class='op'>$</span><span class='fu'>clone</span><span class='op'>(</span>deep <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span></pre><p></div></p> - -<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Arguments</h4> -<p><div class="arguments"></p><dl> -<dt><code>deep</code></dt><dd><p>Whether to make a deep clone.</p></dd> - -</dl><p></div></p> - - - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='co'># On Travis, we get a certificate validation error,</span> -<span class='co'># likely because the system (xenial) is so old,</span> -<span class='co'># therefore don't run this example on Travis</span> -<span class='kw'>if</span> <span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/Sys.getenv.html'>Sys.getenv</a></span><span class='op'>(</span><span class='st'>"TRAVIS"</span><span class='op'>)</span> <span class='op'>==</span> <span class='st'>""</span><span class='op'>)</span> <span class='op'>{</span> - -<span class='va'>atr</span> <span class='op'><-</span> <span class='va'>pai</span><span class='op'>$</span><span class='fu'>new</span><span class='op'>(</span><span class='st'>"atrazine"</span><span class='op'>)</span> -<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>atr</span><span class='op'>)</span> -<span class='kw'>if</span> <span class='op'>(</span><span class='op'>!</span><span class='fu'><a href='https://rdrr.io/r/base/NULL.html'>is.null</a></span><span class='op'>(</span><span class='va'>atr</span><span class='op'>$</span><span class='va'>Picture</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span> - <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>atr</span><span class='op'>)</span> -<span class='op'>}</span> - -<span class='op'>}</span> -</div><div class='output co'>#> <span class='message'>BCPC:</span></div><div class='output co'>#> <span class='message'>PubChem:</span></div><div class='output co'>#> <span class='message'>Trying to get chemical information from RDKit using PubChem_Canonical SMILES</span> -#> <span class='message'>CCNC1=NC(=NC(=N1)Cl)NC(C)C</span></div><div class='output co'>#> <span class='message'>Did not find chyaml file ./atrazine.yaml</span></div><div class='img'><img src='pai-1.png' alt='' width='700' height='433' /></div><div class='output co'>#> <pai> with ISO common name $iso atrazine -#> <chent> -#> Identifier $identifier atrazine -#> InChI Key $inchikey MXWJVTOOROXGIU-UHFFFAOYSA-N -#> SMILES string $smiles: -#> PubChem_Canonical -#> "CCNC1=NC(=NC(=N1)Cl)NC(C)C" -#> Molecular weight $mw: 215.7 -#> PubChem synonyms (up to 10): -#> [1] "atrazine" "1912-24-9" "Gesaprim" "Oleogesaprim" "Chromozin" -#> [6] "Aktikon" "Atrazin" "Argezin" "Atazinax" "Atranex" </div></pre> +</dl><p></p></div> +</div> + +</div> + + </div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># On Travis, we get a certificate validation error,</span></span></span> +<span class="r-in"><span><span class="co"># likely because the system (xenial) is so old,</span></span></span> +<span class="r-in"><span><span class="co"># therefore don't run this example on Travis</span></span></span> +<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Sys.getenv.html" class="external-link">Sys.getenv</a></span><span class="op">(</span><span class="st">"TRAVIS"</span><span class="op">)</span> <span class="op">==</span> <span class="st">""</span><span class="op">)</span> <span class="op">{</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">atr</span> <span class="op"><-</span> <span class="va">pai</span><span class="op">$</span><span class="fu">new</span><span class="op">(</span><span class="st">"atrazine"</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">atr</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NULL.html" class="external-link">is.null</a></span><span class="op">(</span><span class="va">atr</span><span class="op">$</span><span class="va">Picture</span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">atr</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="op">}</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="op">}</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> BCPC:</span> +<span class="r-msg co"><span class="r-pr">#></span> PubChem:</span> +<span class="r-msg co"><span class="r-pr">#></span> Trying to get chemical information from RDKit using PubChem_Canonical SMILES</span> +<span class="r-msg co"><span class="r-pr">#></span> CCNC1=NC(=NC(=N1)Cl)NC(C)C</span> +<span class="r-msg co"><span class="r-pr">#></span> Did not find chyaml file ./atrazine.yaml</span> +<span class="r-plt img"><img src="pai-1.png" alt="" width="700" height="433"></span> +<span class="r-out co"><span class="r-pr">#></span> <pai> with ISO common name $iso atrazine </span> +<span class="r-out co"><span class="r-pr">#></span> <chent></span> +<span class="r-out co"><span class="r-pr">#></span> Identifier $identifier atrazine </span> +<span class="r-out co"><span class="r-pr">#></span> InChI Key $inchikey MXWJVTOOROXGIU-UHFFFAOYSA-N </span> +<span class="r-out co"><span class="r-pr">#></span> SMILES string $smiles:</span> +<span class="r-out co"><span class="r-pr">#></span> PubChem_Canonical </span> +<span class="r-out co"><span class="r-pr">#></span> "CCNC1=NC(=NC(=N1)Cl)NC(C)C" </span> +<span class="r-out co"><span class="r-pr">#></span> Molecular weight $mw: 215.7 </span> +<span class="r-out co"><span class="r-pr">#></span> PubChem synonyms (up to 10):</span> +<span class="r-out co"><span class="r-pr">#></span> [1] "atrazine" "1912-24-9" "Gesaprim" "Oleogesaprim" "Aktikon" </span> +<span class="r-out co"><span class="r-pr">#></span> [6] "Atranex" "Chromozin" "Atazinax" "Atrasine" "Gesoprim" </span> +</code></pre></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> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + 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<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -72,44 +17,31 @@ </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="Released version">0.3.1</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.3.1</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> - <a href="../index.html"> - <span class="fas fa-home fa-lg"></span> - - </a> -</li> -<li> + <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/"> + </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 --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Plot method for chent objects</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/chents/blob/master/R/chent.R'><code>R/chent.R</code></a></small> + <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>plot.chent.Rd</code></div> </div> @@ -117,68 +49,70 @@ <p>Plot method for chent objects</p> </div> - <pre class="usage"><span class='co'># S3 method for chent</span> -<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>...</span><span class='op'>)</span></pre> - - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <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> - <pre class="examples"><div class='input'><span class='va'>caffeine</span> <span class='op'><-</span> <span class='va'><a href='chent.html'>chent</a></span><span class='op'>$</span><span class='fu'>new</span><span class='op'>(</span><span class='st'>"caffeine"</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>PubChem:</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'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>caffeine</span><span class='op'>)</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" -#> Molecular weight $mw: 194.2 -#> PubChem synonyms (up to 10): -#> [1] "caffeine" "58-08-2" -#> [3] "1,3,7-Trimethylxanthine" "Guaranine" -#> [5] "Thein" "Methyltheobromine" -#> [7] "Cafeina" "Theine" -#> [9] "Koffein" "Mateina" </div><div class='input'><span class='kw'>if</span> <span class='op'>(</span><span class='op'>!</span><span class='fu'><a href='https://rdrr.io/r/base/NULL.html'>is.null</a></span><span class='op'>(</span><span class='va'>caffeine</span><span class='op'>$</span><span class='va'>Picture</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span> - <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>caffeine</span><span class='op'>)</span> -<span class='op'>}</span> -</div><div class='img'><img src='plot.chent-1.png' alt='' width='700' height='433' /></div></pre> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for chent</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>x</dt> +<dd><p>The chent object to be plotted</p></dd> + + +<dt>...</dt> +<dd><p>Further arguments passed to <code>grid.picture</code></p></dd> + +</dl></div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">caffeine</span> <span class="op"><-</span> <span class="va"><a href="chent.html">chent</a></span><span class="op">$</span><span class="fu">new</span><span class="op">(</span><span class="st">"caffeine"</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> PubChem:</span> +<span class="r-msg co"><span class="r-pr">#></span> Trying to get chemical information from RDKit using PubChem_Canonical SMILES</span> +<span class="r-msg co"><span class="r-pr">#></span> CN1C=NC2=C1C(=O)N(C(=O)N2C)C</span> +<span class="r-msg co"><span class="r-pr">#></span> Did not find chyaml file ./caffeine.yaml</span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">caffeine</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> <chent></span> +<span class="r-out co"><span class="r-pr">#></span> Identifier $identifier caffeine </span> +<span class="r-out co"><span class="r-pr">#></span> InChI Key $inchikey RYYVLZVUVIJVGH-UHFFFAOYSA-N </span> +<span class="r-out co"><span class="r-pr">#></span> SMILES string $smiles:</span> +<span class="r-out co"><span class="r-pr">#></span> PubChem_Canonical </span> +<span class="r-out co"><span class="r-pr">#></span> "CN1C=NC2=C1C(=O)N(C(=O)N2C)C" </span> +<span class="r-out co"><span class="r-pr">#></span> Molecular weight $mw: 194.2 </span> +<span class="r-out co"><span class="r-pr">#></span> PubChem synonyms (up to 10):</span> +<span class="r-out co"><span class="r-pr">#></span> [1] "caffeine" "58-08-2" </span> +<span class="r-out co"><span class="r-pr">#></span> [3] "Guaranine" "1,3,7-Trimethylxanthine"</span> +<span class="r-out co"><span class="r-pr">#></span> [5] "Methyltheobromine" "Theine" </span> +<span class="r-out co"><span class="r-pr">#></span> [7] "Thein" "Cafeina" </span> +<span class="r-out co"><span class="r-pr">#></span> [9] "Koffein" "Mateina" </span> +<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NULL.html" class="external-link">is.null</a></span><span class="op">(</span><span class="va">caffeine</span><span class="op">$</span><span class="va">Picture</span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">caffeine</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="op">}</span></span></span> +<span class="r-plt img"><img src="plot.chent-1.png" alt="" width="700" height="433"></span> +</code></pre></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> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <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> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/reference/pp.html b/docs/reference/pp.html index c4e4a01..2607035 100644 --- a/docs/reference/pp.html +++ 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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> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <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"> @@ -72,44 +17,31 @@ </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="Released version">0.3.1</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.3.1</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> - <a href="../index.html"> - <span class="fas fa-home fa-lg"></span> - - </a> -</li> -<li> + <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/"> + </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 --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>R6 class for holding a product with at least one active ingredient</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/chents/blob/master/R/chent.R'><code>R/chent.R</code></a></small> + <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>pp.Rd</code></div> </div> @@ -118,89 +50,105 @@ </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> - <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> - <p>An <code>R6Class</code> generator object.</p> - <h2 class="hasAnchor" id="public-fields"><a class="anchor" href="#public-fields"></a>Public fields</h2> +<dt><code>ais</code></dt> +<dd><p>A list of active ingredients</p></dd> - <p><div class="r6-fields"></p><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>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>concentration_units</code></dt> +<dd><p>Defaults to g/L</p></dd> -</dl><p></div></p> - <h2 class="hasAnchor" id="methods"><a class="anchor" href="#methods"></a>Methods</h2> +</dl><p></p></div> + </div> + <div id="methods"> + <h2>Methods</h2> -<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Public methods</h3> +<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-pp-new"><code>pp$new()</code></a></p></li> +<li><p><a href="#method-pp-print"><code>pp$print()</code></a></p></li> +<li><p><a href="#method-pp-clone"><code>pp$clone()</code></a></p></li> +</ul></div><p></p><hr><a id="method-pp-new"></a><div class="section"> +<h3 id="method-new-">Method <code>new()</code><a class="anchor" aria-label="anchor" href="#method-new-"></a></h3> + +<div class="section"> +<h4 id="usage">Usage<a class="anchor" aria-label="anchor" href="#usage"></a></h4> +<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va"><a href="../reference/pp.html">pp</a></span><span class="op">$</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> -<ul> -<li><p><a href='#method-new'><code>pp$new()</code></a></p></li> -<li><p><a href='#method-print'><code>pp$print()</code></a></p></li> -<li><p><a href='#method-clone'><code>pp$clone()</code></a></p></li> -</ul> -<p><hr> -<a id="method-new"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>new()</code></h3> -<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4> -<p><div class="r"></p><pre><span class='va'>pp</span><span class='op'>$</span><span class='fu'>new</span><span class='op'>(</span> - <span class='va'>name</span>, - <span class='va'>...</span>, - <span class='va'>concentrations</span>, - concentration_units <span class='op'>=</span> <span class='st'>"g/L"</span>, - density <span class='op'>=</span> <span class='fl'>1000</span>, - density_units <span class='op'>=</span> <span class='st'>"g/L"</span> -<span class='op'>)</span></pre><p></div></p> +</div><p></p><hr><a id="method-pp-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> -<p><hr> -<a id="method-print"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code><a href='https://rdrr.io/r/base/print.html'>print()</a></code></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">pp</span><span class="op">$</span><span class="fu">print</span><span class="op">(</span><span class="op">)</span></span></code></pre></div><p></p></div> +</div> -<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4> -<p><div class="r"></p><pre><span class='va'>pp</span><span class='op'>$</span><span class='fu'>print</span><span class='op'>(</span><span class='op'>)</span></pre><p></div></p> -<p><hr> -<a id="method-clone"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>clone()</code></h3> -<p>The objects of this class are cloneable with this method.</p><h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4> -<p><div class="r"></p><pre><span class='va'>pp</span><span class='op'>$</span><span class='fu'>clone</span><span class='op'>(</span>deep <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span></pre><p></div></p> +</div><p></p><hr><a id="method-pp-clone"></a><div class="section"> +<h3 id="method-clone-">Method <code>clone()</code><a class="anchor" aria-label="anchor" href="#method-clone-"></a></h3> +<p>The objects of this class are cloneable with this method.</p><div class="section"> +<h4 id="usage-2">Usage<a class="anchor" aria-label="anchor" href="#usage-2"></a></h4> +<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">pp</span><span class="op">$</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> -<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Arguments</h4> -<p><div class="arguments"></p><dl> -<dt><code>deep</code></dt><dd><p>Whether to make a deep clone.</p></dd> -</dl><p></div></p> +</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> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <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> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/reference/print.chent.html b/docs/reference/print.chent.html index b188ed9..08497dd 100644 --- a/docs/reference/print.chent.html +++ b/docs/reference/print.chent.html @@ -1,67 +1,12 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<meta http-equiv="X-UA-Compatible" content="IE=edge"> -<meta name="viewport" content="width=device-width, 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content="Printing method for chent objects"><!-- 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]--> - +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - - </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"> + <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"> @@ -72,44 +17,31 @@ </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="Released version">0.3.1</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.3.1</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> - <a href="../index.html"> - <span class="fas fa-home fa-lg"></span> - - </a> -</li> -<li> + <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/"> + </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 --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Printing method for chent objects</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/chents/blob/master/R/chent.R'><code>R/chent.R</code></a></small> + <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>print.chent.Rd</code></div> </div> @@ -117,48 +49,43 @@ <p>Printing method for chent objects</p> </div> - <pre class="usage"><span class='co'># S3 method for chent</span> -<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>...</span><span class='op'>)</span></pre> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for chent</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>x</dt> +<dd><p>The chent object to be printed</p></dd> + - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <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> +<dt>...</dt> +<dd><p>Further arguments for compatibility with the S3 method</p></dd> +</dl></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> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <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> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/reference/print.pai.html b/docs/reference/print.pai.html index 284792f..3faa5f7 100644 --- a/docs/reference/print.pai.html +++ b/docs/reference/print.pai.html @@ -1,67 +1,12 @@ -<!-- Generated by pkgdown: do 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+<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - - </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"> + <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"> @@ -72,44 +17,31 @@ </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="Released version">0.3.1</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.3.1</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> - <a href="../index.html"> - <span class="fas fa-home fa-lg"></span> - - </a> -</li> -<li> + <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/"> + </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 --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Printing method for pai objects (pesticidal active ingredients)</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/chents/blob/master/R/chent.R'><code>R/chent.R</code></a></small> + <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>print.pai.Rd</code></div> </div> @@ -117,48 +49,43 @@ <p>Printing method for pai objects (pesticidal active ingredients)</p> </div> - <pre class="usage"><span class='co'># S3 method for pai</span> -<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>...</span><span class='op'>)</span></pre> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for pai</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>x</dt> +<dd><p>The chent object to be printed</p></dd> + - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <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> +<dt>...</dt> +<dd><p>Further arguments for compatibility with the S3 method</p></dd> +</dl></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> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 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