diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2023-11-12 22:11:33 +0100 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2023-11-12 22:11:33 +0100 |
| commit | 9828b97fb946104f15e537fc6a53653f1bceb27d (patch) | |
| tree | 2670cb8f6cd9d308b62514367aa0764e66511591 | |
| parent | e4be5e83c8c525b3745d2d7813336319d10f8855 (diff) | |
Add pkgdown url to DESCRIPTON and _pkgdown.yml
| -rw-r--r-- | DESCRIPTION | 2 | ||||
| -rw-r--r-- | _pkgdown.yml | 2 | ||||
| -rw-r--r-- | docs/404.html | 16 | ||||
| -rw-r--r-- | docs/authors.html | 6 | ||||
| -rw-r--r-- | docs/index.html | 2 | ||||
| -rw-r--r-- | docs/pkgdown.yml | 5 | ||||
| -rw-r--r-- | docs/search.json | 2 | ||||
| -rw-r--r-- | docs/sitemap.xml | 24 |
8 files changed, 32 insertions, 27 deletions
diff --git a/DESCRIPTION b/DESCRIPTION index 879bee7..75853cb 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -26,6 +26,6 @@ License: GPL LazyLoad: yes LazyData: yes Encoding: UTF-8 -URL: https://github.com/jranke/chents +URL: https://pkgdown.jrwb.de/chents, https://github.com/jranke/chents Roxygen: list(markdown = TRUE, r6 = TRUE) RoxygenNote: 7.2.3 diff --git a/_pkgdown.yml b/_pkgdown.yml index c70c58b..32b7e3a 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -1,3 +1,5 @@ +url: https://pkgdown.jrwb.de/chents + title: chents template: diff --git a/docs/404.html b/docs/404.html index 2a8d837..00dc371 100644 --- a/docs/404.html +++ b/docs/404.html @@ -6,23 +6,23 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"> <title>Page not found (404) • chents</title> -<script src="deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"> -<link href="deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"> -<script src="deps/bootstrap-5.2.2/bootstrap.bundle.min.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"> +<script src="https://pkgdown.jrwb.de/chents/deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"> +<link href="https://pkgdown.jrwb.de/chents/deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"> +<script src="https://pkgdown.jrwb.de/chents/deps/bootstrap-5.2.2/bootstrap.bundle.min.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"> -<!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" 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><!-- 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><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="pkgdown.js"></script><meta property="og:title" content="Page not found (404)"> +<!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" 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><!-- 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><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="https://pkgdown.jrwb.de/chents/pkgdown.js"></script><meta property="og:title" content="Page not found (404)"> <!-- 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> - <a href="#main" class="visually-hidden-focusable">Skip to contents</a> + <a href="https://pkgdown.jrwb.de/chents/#main" class="visually-hidden-focusable">Skip to contents</a> <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container"> - <a class="navbar-brand me-2" href="index.html">chents</a> + <a class="navbar-brand me-2" href="https://pkgdown.jrwb.de/chents/index.html">chents</a> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.3.2</small> @@ -34,7 +34,7 @@ <div id="navbar" class="collapse navbar-collapse ms-3"> <ul class="navbar-nav me-auto"> <li class="nav-item"> - <a class="nav-link" href="reference/index.html">Reference</a> + <a class="nav-link" href="https://pkgdown.jrwb.de/chents/reference/index.html">Reference</a> </li> </ul> <form class="form-inline my-2 my-lg-0" role="search"> @@ -56,7 +56,7 @@ </nav><div class="container template-title-body"> <div class="row"> <main id="main" class="col-md-9"><div class="page-header"> - <img src="" class="logo" alt=""><h1>Page not found (404)</h1> + <img src="https://pkgdown.jrwb.de/chents/" class="logo" alt=""><h1>Page not found (404)</h1> </div> diff --git a/docs/authors.html b/docs/authors.html index c7be0b2..a6036b4 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -55,14 +55,14 @@ <p>Ranke J (2023). <em>chents: Chemical Entities as R Objects</em>. -R package version 0.3.2, <a href="https://github.com/jranke/chents" class="external-link">https://github.com/jranke/chents</a>. +R package version 0.3.2, https://github.com/jranke/chents, <a href="https://pkgdown.jrwb.de/chents">https://pkgdown.jrwb.de/chents</a>. </p> <pre>@Manual{, title = {chents: Chemical Entities as R Objects}, author = {Johannes Ranke}, year = {2023}, - note = {R package version 0.3.2}, - url = {https://github.com/jranke/chents}, + note = {R package version 0.3.2, https://github.com/jranke/chents}, + url = {https://pkgdown.jrwb.de/chents}, }</pre> </div> </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> diff --git a/docs/index.html b/docs/index.html index 1732af6..70a25fd 100644 --- a/docs/index.html +++ b/docs/index.html @@ -82,7 +82,7 @@ <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> +<p>Some examples are available from the <a href="https://pkgdown.jrwb.de/chents/reference">reference on jrwb.de</a>.</p> </div> </div> </main><aside class="col-md-3"><div class="links"> diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 4bf180b..44cd4ff 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -2,5 +2,8 @@ pandoc: 2.17.1.1 pkgdown: 2.0.7 pkgdown_sha: ~ articles: {} -last_built: 2023-11-12T21:06Z +last_built: 2023-11-12T21:10Z +urls: + reference: https://pkgdown.jrwb.de/chents/reference + article: https://pkgdown.jrwb.de/chents/articles diff --git a/docs/search.json b/docs/search.json index 5f952b5..62e1308 100644 --- a/docs/search.json +++ b/docs/search.json @@ -1 +1 @@ -[{"path":"/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Johannes Ranke. Author, maintainer, copyright holder.","code":""},{"path":"/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Ranke J (2023). chents: Chemical Entities R Objects. R package version 0.3.2, https://github.com/jranke/chents.","code":"@Manual{, title = {chents: Chemical Entities as R Objects}, author = {Johannes Ranke}, year = {2023}, note = {R package version 0.3.2}, url = {https://github.com/jranke/chents}, }"},{"path":"/index.html","id":"chents","dir":"","previous_headings":"","what":"Chemical Entities as R Objects","title":"Chemical Entities as R Objects","text":"R package chents provides utilities working chemical entities R.","code":""},{"path":"/index.html","id":"features","dir":"","previous_headings":"","what":"Features","title":"Chemical Entities as R Objects","text":"chemical information retrieved PubChem website using webchem package Python RDKit (> 2015.03) installed configured use ‘reticulate’, basic chemoinformatics functions additional chemical information computed 2D graph can plotted Additional information can read local .yaml file","code":""},{"path":"/index.html","id":"examples","dir":"","previous_headings":"","what":"Examples","title":"Chemical Entities as R Objects","text":"examples available reference jrwb.de.","code":""},{"path":"/reference/chent.html","id":null,"dir":"Reference","previous_headings":"","what":"An R6 class for chemical entities with associated data — chent","title":"An R6 class for chemical entities with associated data — chent","text":"class initialised identifier. Chemical information retrieved internet. Additionally, can generated using RDKit RDKit python bindings installed.","code":""},{"path":"/reference/chent.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"An R6 class for chemical entities with associated data — chent","text":"R6Class generator object","code":""},{"path":"/reference/chent.html","id":"public-fields","dir":"Reference","previous_headings":"","what":"Public fields","title":"An R6 class for chemical entities with associated data — chent","text":"identifier (character(1)) identifier used initiate object, attribute 'source' inchikey (character(1)) InChI Key, attribute 'source' smiles (character()) SMILES code(s), attribute 'source' mw (numeric(1)) Molecular weight, attribute 'source' pubchem (list()) List information retrieved PubChem rdkit List information obtained RDKit mol <rdkit.Chem.rdchem.Mol> object svg SVG code Picture Graph picture object obtained using grImport Pict_font_size Font size extracted intermediate PostScript file pdf_height Height MediaBox pdf cropping p0 Vapour pressure Pa cwsat Water solubility mg/L PUF Plant uptake factor chyaml List information obtained YAML file TPs List transformation products chent objects Add transformation product internal list transformations Data frame observed transformations Add line internal dataframe holding observed transformations soil_degradation Dataframe modelling DT50 values Add line internal dataframe holding modelling DT50 values soil_ff Dataframe formation fractions soil_sorption Dataframe soil sorption data Add soil sorption data","code":""},{"path":[]},{"path":"/reference/chent.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"An R6 class for chemical entities with associated data — chent","text":"chent$new() chent$try_pubchem() chent$get_pubchem() chent$get_rdkit() chent$get_chyaml() chent$add_p0() chent$add_cwsat() chent$add_PUF() chent$add_TP() chent$add_transformation() chent$add_soil_degradation() chent$add_soil_ff() chent$add_soil_sorption() chent$pdf() chent$png() chent$emf() chent$clone()","code":""},{"path":"/reference/chent.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"An R6 class for chemical entities with associated data — chent","text":"Creates new instance R6 class.","code":""},{"path":"/reference/chent.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$new( identifier, smiles = NULL, inchikey = NULL, pubchem = TRUE, pubchem_from = c(\"name\", \"smiles\", \"inchikey\"), rdkit = TRUE, template = NULL, chyaml = TRUE )"},{"path":"/reference/chent.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"identifier Identifier stored object smiles Optional user provided SMILES code inchikey Optional user provided InChI Key pubchem attempt made retrieve chemical information PubChem via webchem package? pubchem_from Possibility select argument used query pubchem rdkit attempt made retrieve chemical information local rdkit installation via python reticulate package? template optional SMILES code used template RDKit chyaml look identifier.yaml file working directory? Try get chemical information PubChem","code":""},{"path":[]},{"path":"/reference/chent.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$try_pubchem(query, from = \"name\")"},{"path":"/reference/chent.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"query Query string passed get_cid Passed get_cid Get chemical information PubChem known PubChem CID","code":""},{"path":[]},{"path":"/reference/chent.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$get_pubchem(pubchem_cid)"},{"path":"/reference/chent.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"pubchem_cid CID Get chemical information RDKit available","code":""},{"path":[]},{"path":"/reference/chent.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$get_rdkit(template = NULL)"},{"path":"/reference/chent.html","id":"arguments-3","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"template Optional template specified SMILES code Obtain information YAML file","code":""},{"path":[]},{"path":"/reference/chent.html","id":"usage-4","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$get_chyaml( repo = c(\"wd\", \"local\", \"web\"), chyaml = paste0(URLencode(self$identifier), \".yaml\") )"},{"path":"/reference/chent.html","id":"arguments-4","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"repo file looked current working directory, local git repository ~/git/chyaml, web (implemented). chyaml filename looked Add vapour pressure","code":""},{"path":[]},{"path":"/reference/chent.html","id":"usage-5","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$add_p0(p0, T = NA, source = NA, page = NA, remark = \"\")"},{"path":"/reference/chent.html","id":"arguments-5","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"p0 vapour pressure Pa T Temperature source acronym specifying source information page page information taken remark remark Add water solubility","code":""},{"path":[]},{"path":"/reference/chent.html","id":"usage-6","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$add_cwsat(cwsat, T = NA, pH = NA, source = NA, page = NA, remark = \"\")"},{"path":"/reference/chent.html","id":"arguments-6","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"cwsat water solubility mg/L T Temperature pH pH value source acronym specifying source information page page information taken remark remark Add plant uptake factor","code":""},{"path":[]},{"path":"/reference/chent.html","id":"usage-7","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$add_PUF( PUF = 0, source = \"focus_generic_gw_2014\", page = 41, remark = \"Conservative default value\" )"},{"path":"/reference/chent.html","id":"arguments-7","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"PUF plant uptake factor, number 0 1 source acronym specifying source information page page information taken remark remark","code":""},{"path":[]},{"path":"/reference/chent.html","id":"usage-8","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$add_TP(x, smiles = NULL, pubchem = FALSE)"},{"path":"/reference/chent.html","id":"arguments-8","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"x chent object, identifier generate chent object smiles SMILES code defining chent object pubchem chemical information obtained PubChem?","code":""},{"path":[]},{"path":"/reference/chent.html","id":"usage-9","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$add_transformation( study_type, TP_identifier, max_occurrence, remark = \"\", source = NA, pages = NA )"},{"path":"/reference/chent.html","id":"arguments-9","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"study_type characterisation study type TP_identifier identifier one transformation products self$TPs max_occurrence maximum observed occurrence transformation product, expressed fraction amount result stochiometric transformation remark remark source acronym specifying source information pages page information taken","code":""},{"path":[]},{"path":"/reference/chent.html","id":"usage-10","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$add_soil_degradation( soils, DT50_mod, DT50_mod_ref, type = NA, country = NA, pH_orig = NA, pH_medium = NA, pH_H2O = NA, perc_OC = NA, temperature = NA, moisture = NA, category = \"lab\", formulation = NA, model = NA, chi2 = NA, remark = \"\", source, page = NA )"},{"path":"/reference/chent.html","id":"arguments-10","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"soils Names soils DT50_mod modelling DT50 sense regulatory pesticide fate modelling DT50_mod_ref normalised modelling DT50 sense regulatory pesticide fate modelling type soil type country country (mainly field studies) pH_orig pH stated study pH_medium medium pH measured pH_H2O pH extrapolated pure water perc_OC percentage organic carbon soil temperature temperature study degrees Celsius moisture moisture study category laboratory ('lab') field study ('field') formulation Name formulation applied, technical active ingredient model degradation model used deriving DT50_mod chi2 relative error defined FOCUS kinetics remark remark source acronym specifying source information page page information taken","code":""},{"path":[]},{"path":"/reference/chent.html","id":"usage-11","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$add_soil_ff(target, soils, ff = 1, remark = \"\", source, page = NA)"},{"path":"/reference/chent.html","id":"arguments-11","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"target identifier(s) transformation product soils soil name(s) transformation observed ff formation fraction(s)","code":""},{"path":[]},{"path":"/reference/chent.html","id":"usage-12","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$add_soil_sorption( soils, Kf, Kfoc, N, type = NA, pH_orig = NA, pH_medium = NA, pH_H2O = NA, perc_OC = NA, perc_clay = NA, CEC = NA, remark = \"\", source, page = NA )"},{"path":"/reference/chent.html","id":"arguments-12","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"Kf sorption constant L/kg, either linear (N 1) according Freundlich Kfoc constant , normalised soil organic carbon N Freundlich exponent perc_clay percentage clay soil CEC cation exchange capacity Write PDF image structure","code":""},{"path":[]},{"path":"/reference/chent.html","id":"usage-13","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$pdf( file = paste0(self$identifier, \".pdf\"), dir = \"structures/pdf\", template = NULL )"},{"path":"/reference/chent.html","id":"arguments-13","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"file file write dir directory write file template template expressed SMILES use RDKit Write PNG image structure","code":""},{"path":[]},{"path":"/reference/chent.html","id":"usage-14","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$png( file = paste0(self$identifier, \".png\"), dir = \"structures/png\", antialias = \"gray\" )"},{"path":"/reference/chent.html","id":"arguments-14","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"antialias Passed png Write EMF image structure using emf","code":""},{"path":[]},{"path":"/reference/chent.html","id":"usage-15","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$emf(file = paste0(self$identifier, \".emf\"), dir = \"structures/emf\")"},{"path":"/reference/chent.html","id":"arguments-15","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"file file write ","code":""},{"path":"/reference/chent.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"An R6 class for chemical entities with associated data — chent","text":"objects class cloneable method.","code":""},{"path":"/reference/chent.html","id":"usage-16","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$clone(deep = FALSE)"},{"path":"/reference/chent.html","id":"arguments-16","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"deep Whether make deep clone.","code":""},{"path":"/reference/chent.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"oct <- chent$new(\"1-octanol\", smiles = \"CCCCCCCCO\", pubchem = FALSE) #> Trying to get chemical information from RDKit using user SMILES #> CCCCCCCCO #> Error in URLencode(self$identifier): could not find function \"URLencode\" print(oct) #> Error in eval(expr, envir, enclos): object 'oct' not found if (!is.null(oct$Picture)) { plot(oct) } #> Error in eval(expr, envir, enclos): object 'oct' not found caffeine <- chent$new(\"caffeine\") #> PubChem: #> Trying to get chemical information from RDKit using PubChem_Canonical SMILES #> CN1C=NC2=C1C(=O)N(C(=O)N2C)C #> Error in URLencode(self$identifier): could not find function \"URLencode\" print(caffeine) #> Error in eval(expr, envir, enclos): object 'caffeine' not found if (!is.null(caffeine$Picture)) { plot(caffeine) } #> Error in eval(expr, envir, enclos): object 'caffeine' not found"},{"path":"/reference/draw_svg.chent.html","id":null,"dir":"Reference","previous_headings":"","what":"Draw SVG graph from a chent object using RDKit — draw_svg.chent","title":"Draw SVG graph from a chent object using RDKit — draw_svg.chent","text":"Draw SVG graph chent object using RDKit","code":""},{"path":"/reference/draw_svg.chent.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Draw SVG graph from a chent object using RDKit — draw_svg.chent","text":"","code":"draw_svg.chent( x, width = 300, height = 150, filename = paste0(names(x$identifier), \".svg\"), subdir = \"svg\" )"},{"path":"/reference/draw_svg.chent.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Draw SVG graph from a chent object using RDKit — draw_svg.chent","text":"x chent object plotted width desired width pixels height desired height pixels filename filename subdir path file written","code":""},{"path":"/reference/pai.html","id":null,"dir":"Reference","previous_headings":"","what":"An R6 class for pesticidal active ingredients and associated data — pai","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"class initialised identifier generally ISO common name. Additional chemical information retrieved internet available.","code":""},{"path":"/reference/pai.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"R6Class generator object","code":""},{"path":"/reference/pai.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"chents::chent -> pai","code":""},{"path":"/reference/pai.html","id":"public-fields","dir":"Reference","previous_headings":"","what":"Public fields","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"iso ISO common name active ingredient according ISO 1750 bcpc Information retrieved BCPC compendium available online <pesticidecompendium.bcpc.org> Creates new instance R6 class.","code":""},{"path":"/reference/pai.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"chents::chent$add_PUF() chents::chent$add_TP() chents::chent$add_cwsat() chents::chent$add_p0() chents::chent$add_soil_degradation() chents::chent$add_soil_ff() chents::chent$add_soil_sorption() chents::chent$add_transformation() chents::chent$emf() chents::chent$get_chyaml() chents::chent$get_pubchem() chents::chent$get_rdkit() chents::chent$pdf() chents::chent$png() chents::chent$try_pubchem()","code":""},{"path":"/reference/pai.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"pai$new() pai$clone()","code":""},{"path":"/reference/pai.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"class derived chent. makes easy create chent ISO common name pesticide active ingredient, additionally stores ISO name well complete result querying BCPC compendium using bcpc_query.","code":""},{"path":"/reference/pai.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"","code":"pai$new( iso, identifier = iso, smiles = NULL, inchikey = NULL, bcpc = TRUE, pubchem = TRUE, pubchem_from = \"auto\", rdkit = TRUE, template = NULL, chyaml = TRUE )"},{"path":"/reference/pai.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"iso ISO common name used query BCPC compendium identifier Alternative identifier used querying pubchem","code":""},{"path":"/reference/pai.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"objects class cloneable method.","code":""},{"path":"/reference/pai.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"","code":"pai$clone(deep = FALSE)"},{"path":"/reference/pai.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"deep Whether make deep clone.","code":""},{"path":"/reference/pai.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"","code":"# On Travis, we get a certificate validation error, # likely because the system (xenial) is so old, # therefore don't run this example on Travis if (Sys.getenv(\"TRAVIS\") == \"\") { atr <- pai$new(\"atrazine\") print(atr) if (!is.null(atr$Picture)) { plot(atr) } } #> BCPC: #> PubChem: #> Trying to get chemical information from RDKit using PubChem_Canonical SMILES #> CCNC1=NC(=NC(=N1)Cl)NC(C)C #> Error in URLencode(self$identifier): could not find function \"URLencode\""},{"path":"/reference/plot.chent.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot method for chent objects — plot.chent","title":"Plot method for chent objects — plot.chent","text":"Plot method chent objects","code":""},{"path":"/reference/plot.chent.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot method for chent objects — plot.chent","text":"","code":"# S3 method for chent plot(x, ...)"},{"path":"/reference/plot.chent.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot method for chent objects — plot.chent","text":"x chent object plotted ... arguments passed grid.picture","code":""},{"path":"/reference/plot.chent.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Plot method for chent objects — plot.chent","text":"","code":"caffeine <- chent$new(\"caffeine\") #> PubChem: #> Trying to get chemical information from RDKit using PubChem_Canonical SMILES #> CN1C=NC2=C1C(=O)N(C(=O)N2C)C #> Error in URLencode(self$identifier): could not find function \"URLencode\" print(caffeine) #> Error in eval(expr, envir, enclos): object 'caffeine' not found if (!is.null(caffeine$Picture)) { plot(caffeine) } #> Error in eval(expr, envir, enclos): object 'caffeine' not found"},{"path":"/reference/ppp.html","id":null,"dir":"Reference","previous_headings":"","what":"R6 class for a plant protection product with at least one active ingredient — ppp","title":"R6 class for a plant protection product with at least one active ingredient — ppp","text":"Contains basic information active ingredients product","code":""},{"path":"/reference/ppp.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"R6 class for a plant protection product with at least one active ingredient — ppp","text":"R6Class generator object.","code":""},{"path":"/reference/ppp.html","id":"public-fields","dir":"Reference","previous_headings":"","what":"Public fields","title":"R6 class for a plant protection product with at least one active ingredient — ppp","text":"name name product ais list active ingredients concentrations concentration ais concentration_units Defaults g/L density density product density_units Defaults g/L Creates new instance R6 class. ... Identifiers active ingredients concentrations Concentrations active ingredients concentration_units Defaults g/L density density density_units Defaults g/L Printing method","code":""},{"path":"/reference/ppp.html","id":"active-bindings","dir":"Reference","previous_headings":"","what":"Active bindings","title":"R6 class for a plant protection product with at least one active ingredient — ppp","text":"... Identifiers active ingredients","code":""},{"path":[]},{"path":"/reference/ppp.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"R6 class for a plant protection product with at least one active ingredient — ppp","text":"ppp$new() ppp$print() ppp$clone()","code":""},{"path":[]},{"path":"/reference/ppp.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 class for a plant protection product with at least one active ingredient — ppp","text":"","code":"ppp$new( name, ..., concentrations, concentration_units = \"g/L\", density = 1000, density_units = \"g/L\" )"},{"path":[]},{"path":"/reference/ppp.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 class for a plant protection product with at least one active ingredient — ppp","text":"","code":"ppp$print()"},{"path":"/reference/ppp.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"R6 class for a plant protection product with at least one active ingredient — ppp","text":"objects class cloneable method.","code":""},{"path":"/reference/ppp.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 class for a plant protection product with at least one active ingredient — ppp","text":"","code":"ppp$clone(deep = FALSE)"},{"path":"/reference/ppp.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 class for a plant protection product with at least one active ingredient — ppp","text":"deep Whether make deep clone.","code":""},{"path":"/reference/print.chent.html","id":null,"dir":"Reference","previous_headings":"","what":"Printing method for chent objects — print.chent","title":"Printing method for chent objects — print.chent","text":"Printing method chent objects","code":""},{"path":"/reference/print.chent.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Printing method for chent objects — print.chent","text":"","code":"# S3 method for chent print(x, ...)"},{"path":"/reference/print.chent.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Printing method for chent objects — print.chent","text":"x chent object printed ... arguments compatibility S3 method","code":""},{"path":"/reference/print.pai.html","id":null,"dir":"Reference","previous_headings":"","what":"Printing method for pai objects (pesticidal active ingredients) — print.pai","title":"Printing method for pai objects (pesticidal active ingredients) — print.pai","text":"Printing method pai objects (pesticidal active ingredients)","code":""},{"path":"/reference/print.pai.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Printing method for pai objects (pesticidal active ingredients) — print.pai","text":"","code":"# S3 method for pai print(x, ...)"},{"path":"/reference/print.pai.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Printing method for pai objects (pesticidal active ingredients) — print.pai","text":"x chent object printed ... arguments compatibility S3 method","code":""}] +[{"path":"https://pkgdown.jrwb.de/chents/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Johannes Ranke. Author, maintainer, copyright holder.","code":""},{"path":"https://pkgdown.jrwb.de/chents/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Ranke J (2023). chents: Chemical Entities R Objects. R package version 0.3.2, https://github.com/jranke/chents, https://pkgdown.jrwb.de/chents.","code":"@Manual{, title = {chents: Chemical Entities as R Objects}, author = {Johannes Ranke}, year = {2023}, note = {R package version 0.3.2, https://github.com/jranke/chents}, url = {https://pkgdown.jrwb.de/chents}, }"},{"path":"https://pkgdown.jrwb.de/chents/index.html","id":"chents","dir":"","previous_headings":"","what":"Chemical Entities as R Objects","title":"Chemical Entities as R Objects","text":"R package chents provides utilities working chemical entities R.","code":""},{"path":"https://pkgdown.jrwb.de/chents/index.html","id":"features","dir":"","previous_headings":"","what":"Features","title":"Chemical Entities as R Objects","text":"chemical information retrieved PubChem website using webchem package Python RDKit (> 2015.03) installed configured use ‘reticulate’, basic chemoinformatics functions additional chemical information computed 2D graph can plotted Additional information can read local .yaml file","code":""},{"path":"https://pkgdown.jrwb.de/chents/index.html","id":"examples","dir":"","previous_headings":"","what":"Examples","title":"Chemical Entities as R Objects","text":"examples available reference jrwb.de.","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":null,"dir":"Reference","previous_headings":"","what":"An R6 class for chemical entities with associated data — chent","title":"An R6 class for chemical entities with associated data — chent","text":"class initialised identifier. Chemical information retrieved internet. Additionally, can generated using RDKit RDKit python bindings installed.","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"An R6 class for chemical entities with associated data — chent","text":"R6Class generator object","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"public-fields","dir":"Reference","previous_headings":"","what":"Public fields","title":"An R6 class for chemical entities with associated data — chent","text":"identifier (character(1)) identifier used initiate object, attribute 'source' inchikey (character(1)) InChI Key, attribute 'source' smiles (character()) SMILES code(s), attribute 'source' mw (numeric(1)) Molecular weight, attribute 'source' pubchem (list()) List information retrieved PubChem rdkit List information obtained RDKit mol <rdkit.Chem.rdchem.Mol> object svg SVG code Picture Graph picture object obtained using grImport Pict_font_size Font size extracted intermediate PostScript file pdf_height Height MediaBox pdf cropping p0 Vapour pressure Pa cwsat Water solubility mg/L PUF Plant uptake factor chyaml List information obtained YAML file TPs List transformation products chent objects Add transformation product internal list transformations Data frame observed transformations Add line internal dataframe holding observed transformations soil_degradation Dataframe modelling DT50 values Add line internal dataframe holding modelling DT50 values soil_ff Dataframe formation fractions soil_sorption Dataframe soil sorption data Add soil sorption data","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"An R6 class for chemical entities with associated data — chent","text":"chent$new() chent$try_pubchem() chent$get_pubchem() chent$get_rdkit() chent$get_chyaml() chent$add_p0() chent$add_cwsat() chent$add_PUF() chent$add_TP() chent$add_transformation() chent$add_soil_degradation() chent$add_soil_ff() chent$add_soil_sorption() chent$pdf() chent$png() chent$emf() chent$clone()","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"An R6 class for chemical entities with associated data — chent","text":"Creates new instance R6 class.","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$new( identifier, smiles = NULL, inchikey = NULL, pubchem = TRUE, pubchem_from = c(\"name\", \"smiles\", \"inchikey\"), rdkit = TRUE, template = NULL, chyaml = TRUE )"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"identifier Identifier stored object smiles Optional user provided SMILES code inchikey Optional user provided InChI Key pubchem attempt made retrieve chemical information PubChem via webchem package? pubchem_from Possibility select argument used query pubchem rdkit attempt made retrieve chemical information local rdkit installation via python reticulate package? template optional SMILES code used template RDKit chyaml look identifier.yaml file working directory? Try get chemical information PubChem","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$try_pubchem(query, from = \"name\")"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"query Query string passed get_cid Passed get_cid Get chemical information PubChem known PubChem CID","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$get_pubchem(pubchem_cid)"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"pubchem_cid CID Get chemical information RDKit available","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$get_rdkit(template = NULL)"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-3","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"template Optional template specified SMILES code Obtain information YAML file","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-4","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$get_chyaml( repo = c(\"wd\", \"local\", \"web\"), chyaml = paste0(URLencode(self$identifier), \".yaml\") )"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-4","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"repo file looked current working directory, local git repository ~/git/chyaml, web (implemented). chyaml filename looked Add vapour pressure","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-5","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$add_p0(p0, T = NA, source = NA, page = NA, remark = \"\")"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-5","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"p0 vapour pressure Pa T Temperature source acronym specifying source information page page information taken remark remark Add water solubility","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-6","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$add_cwsat(cwsat, T = NA, pH = NA, source = NA, page = NA, remark = \"\")"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-6","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"cwsat water solubility mg/L T Temperature pH pH value source acronym specifying source information page page information taken remark remark Add plant uptake factor","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-7","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$add_PUF( PUF = 0, source = \"focus_generic_gw_2014\", page = 41, remark = \"Conservative default value\" )"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-7","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"PUF plant uptake factor, number 0 1 source acronym specifying source information page page information taken remark remark","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-8","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$add_TP(x, smiles = NULL, pubchem = FALSE)"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-8","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"x chent object, identifier generate chent object smiles SMILES code defining chent object pubchem chemical information obtained PubChem?","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-9","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$add_transformation( study_type, TP_identifier, max_occurrence, remark = \"\", source = NA, pages = NA )"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-9","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"study_type characterisation study type TP_identifier identifier one transformation products self$TPs max_occurrence maximum observed occurrence transformation product, expressed fraction amount result stochiometric transformation remark remark source acronym specifying source information pages page information taken","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-10","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$add_soil_degradation( soils, DT50_mod, DT50_mod_ref, type = NA, country = NA, pH_orig = NA, pH_medium = NA, pH_H2O = NA, perc_OC = NA, temperature = NA, moisture = NA, category = \"lab\", formulation = NA, model = NA, chi2 = NA, remark = \"\", source, page = NA )"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-10","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"soils Names soils DT50_mod modelling DT50 sense regulatory pesticide fate modelling DT50_mod_ref normalised modelling DT50 sense regulatory pesticide fate modelling type soil type country country (mainly field studies) pH_orig pH stated study pH_medium medium pH measured pH_H2O pH extrapolated pure water perc_OC percentage organic carbon soil temperature temperature study degrees Celsius moisture moisture study category laboratory ('lab') field study ('field') formulation Name formulation applied, technical active ingredient model degradation model used deriving DT50_mod chi2 relative error defined FOCUS kinetics remark remark source acronym specifying source information page page information taken","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-11","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$add_soil_ff(target, soils, ff = 1, remark = \"\", source, page = NA)"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-11","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"target identifier(s) transformation product soils soil name(s) transformation observed ff formation fraction(s)","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-12","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$add_soil_sorption( soils, Kf, Kfoc, N, type = NA, pH_orig = NA, pH_medium = NA, pH_H2O = NA, perc_OC = NA, perc_clay = NA, CEC = NA, remark = \"\", source, page = NA )"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-12","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"Kf sorption constant L/kg, either linear (N 1) according Freundlich Kfoc constant , normalised soil organic carbon N Freundlich exponent perc_clay percentage clay soil CEC cation exchange capacity Write PDF image structure","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-13","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$pdf( file = paste0(self$identifier, \".pdf\"), dir = \"structures/pdf\", template = NULL )"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-13","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"file file write dir directory write file template template expressed SMILES use RDKit Write PNG image structure","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-14","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$png( file = paste0(self$identifier, \".png\"), dir = \"structures/png\", antialias = \"gray\" )"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-14","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"antialias Passed png Write EMF image structure using emf","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-15","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$emf(file = paste0(self$identifier, \".emf\"), dir = \"structures/emf\")"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-15","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"file file write ","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"An R6 class for chemical entities with associated data — chent","text":"objects class cloneable method.","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-16","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$clone(deep = FALSE)"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-16","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"deep Whether make deep clone.","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"oct <- chent$new(\"1-octanol\", smiles = \"CCCCCCCCO\", pubchem = FALSE) #> Trying to get chemical information from RDKit using user SMILES #> CCCCCCCCO #> Error in URLencode(self$identifier): could not find function \"URLencode\" print(oct) #> Error in eval(expr, envir, enclos): object 'oct' not found if (!is.null(oct$Picture)) { plot(oct) } #> Error in eval(expr, envir, enclos): object 'oct' not found caffeine <- chent$new(\"caffeine\") #> PubChem: #> Trying to get chemical information from RDKit using PubChem_Canonical SMILES #> CN1C=NC2=C1C(=O)N(C(=O)N2C)C #> Error in URLencode(self$identifier): could not find function \"URLencode\" print(caffeine) #> Error in eval(expr, envir, enclos): object 'caffeine' not found if (!is.null(caffeine$Picture)) { plot(caffeine) } #> Error in eval(expr, envir, enclos): object 'caffeine' not found"},{"path":"https://pkgdown.jrwb.de/chents/reference/draw_svg.chent.html","id":null,"dir":"Reference","previous_headings":"","what":"Draw SVG graph from a chent object using RDKit — draw_svg.chent","title":"Draw SVG graph from a chent object using RDKit — draw_svg.chent","text":"Draw SVG graph chent object using RDKit","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/draw_svg.chent.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Draw SVG graph from a chent object using RDKit — draw_svg.chent","text":"","code":"draw_svg.chent( x, width = 300, height = 150, filename = paste0(names(x$identifier), \".svg\"), subdir = \"svg\" )"},{"path":"https://pkgdown.jrwb.de/chents/reference/draw_svg.chent.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Draw SVG graph from a chent object using RDKit — draw_svg.chent","text":"x chent object plotted width desired width pixels height desired height pixels filename filename subdir path file written","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":null,"dir":"Reference","previous_headings":"","what":"An R6 class for pesticidal active ingredients and associated data — pai","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"class initialised identifier generally ISO common name. Additional chemical information retrieved internet available.","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"R6Class generator object","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"chents::chent -> pai","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":"public-fields","dir":"Reference","previous_headings":"","what":"Public fields","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"iso ISO common name active ingredient according ISO 1750 bcpc Information retrieved BCPC compendium available online <pesticidecompendium.bcpc.org> Creates new instance R6 class.","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"chents::chent$add_PUF() chents::chent$add_TP() chents::chent$add_cwsat() chents::chent$add_p0() chents::chent$add_soil_degradation() chents::chent$add_soil_ff() chents::chent$add_soil_sorption() chents::chent$add_transformation() chents::chent$emf() chents::chent$get_chyaml() chents::chent$get_pubchem() chents::chent$get_rdkit() chents::chent$pdf() chents::chent$png() chents::chent$try_pubchem()","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"pai$new() pai$clone()","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"class derived chent. makes easy create chent ISO common name pesticide active ingredient, additionally stores ISO name well complete result querying BCPC compendium using bcpc_query.","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"","code":"pai$new( iso, identifier = iso, smiles = NULL, inchikey = NULL, bcpc = TRUE, pubchem = TRUE, pubchem_from = \"auto\", rdkit = TRUE, template = NULL, chyaml = TRUE )"},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"iso ISO common name used query BCPC compendium identifier Alternative identifier used querying pubchem","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"objects class cloneable method.","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"","code":"pai$clone(deep = FALSE)"},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"deep Whether make deep clone.","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"","code":"# On Travis, we get a certificate validation error, # likely because the system (xenial) is so old, # therefore don't run this example on Travis if (Sys.getenv(\"TRAVIS\") == \"\") { atr <- pai$new(\"atrazine\") print(atr) if (!is.null(atr$Picture)) { plot(atr) } } #> BCPC: #> PubChem: #> Trying to get chemical information from RDKit using PubChem_Canonical SMILES #> CCNC1=NC(=NC(=N1)Cl)NC(C)C #> Error in URLencode(self$identifier): could not find function \"URLencode\""},{"path":"https://pkgdown.jrwb.de/chents/reference/plot.chent.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot method for chent objects — plot.chent","title":"Plot method for chent objects — plot.chent","text":"Plot method chent objects","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/plot.chent.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot method for chent objects — plot.chent","text":"","code":"# S3 method for chent plot(x, ...)"},{"path":"https://pkgdown.jrwb.de/chents/reference/plot.chent.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot method for chent objects — plot.chent","text":"x chent object plotted ... arguments passed grid.picture","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/plot.chent.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Plot method for chent objects — plot.chent","text":"","code":"caffeine <- chent$new(\"caffeine\") #> PubChem: #> Trying to get chemical information from RDKit using PubChem_Canonical SMILES #> CN1C=NC2=C1C(=O)N(C(=O)N2C)C #> Error in URLencode(self$identifier): could not find function \"URLencode\" print(caffeine) #> Error in eval(expr, envir, enclos): object 'caffeine' not found if (!is.null(caffeine$Picture)) { plot(caffeine) } #> Error in eval(expr, envir, enclos): object 'caffeine' not found"},{"path":"https://pkgdown.jrwb.de/chents/reference/ppp.html","id":null,"dir":"Reference","previous_headings":"","what":"R6 class for a plant protection product with at least one active ingredient — ppp","title":"R6 class for a plant protection product with at least one active ingredient — ppp","text":"Contains basic information active ingredients product","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/ppp.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"R6 class for a plant protection product with at least one active ingredient — ppp","text":"R6Class generator object.","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/ppp.html","id":"public-fields","dir":"Reference","previous_headings":"","what":"Public fields","title":"R6 class for a plant protection product with at least one active ingredient — ppp","text":"name name product ais list active ingredients concentrations concentration ais concentration_units Defaults g/L density density product density_units Defaults g/L Creates new instance R6 class. ... Identifiers active ingredients concentrations Concentrations active ingredients concentration_units Defaults g/L density density density_units Defaults g/L Printing method","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/ppp.html","id":"active-bindings","dir":"Reference","previous_headings":"","what":"Active bindings","title":"R6 class for a plant protection product with at least one active ingredient — ppp","text":"... Identifiers active ingredients","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/chents/reference/ppp.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"R6 class for a plant protection product with at least one active ingredient — ppp","text":"ppp$new() ppp$print() ppp$clone()","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/chents/reference/ppp.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 class for a plant protection product with at least one active ingredient — ppp","text":"","code":"ppp$new( name, ..., concentrations, concentration_units = \"g/L\", density = 1000, density_units = \"g/L\" )"},{"path":[]},{"path":"https://pkgdown.jrwb.de/chents/reference/ppp.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 class for a plant protection product with at least one active ingredient — ppp","text":"","code":"ppp$print()"},{"path":"https://pkgdown.jrwb.de/chents/reference/ppp.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"R6 class for a plant protection product with at least one active ingredient — ppp","text":"objects class cloneable method.","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/ppp.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 class for a plant protection product with at least one active ingredient — ppp","text":"","code":"ppp$clone(deep = FALSE)"},{"path":"https://pkgdown.jrwb.de/chents/reference/ppp.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 class for a plant protection product with at least one active ingredient — ppp","text":"deep Whether make deep clone.","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/print.chent.html","id":null,"dir":"Reference","previous_headings":"","what":"Printing method for chent objects — print.chent","title":"Printing method for chent objects — print.chent","text":"Printing method chent objects","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/print.chent.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Printing method for chent objects — print.chent","text":"","code":"# S3 method for chent print(x, ...)"},{"path":"https://pkgdown.jrwb.de/chents/reference/print.chent.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Printing method for chent objects — print.chent","text":"x chent object printed ... arguments compatibility S3 method","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/print.pai.html","id":null,"dir":"Reference","previous_headings":"","what":"Printing method for pai objects (pesticidal active ingredients) — print.pai","title":"Printing method for pai objects (pesticidal active ingredients) — print.pai","text":"Printing method pai objects (pesticidal active ingredients)","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/print.pai.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Printing method for pai objects (pesticidal active ingredients) — print.pai","text":"","code":"# S3 method for pai print(x, ...)"},{"path":"https://pkgdown.jrwb.de/chents/reference/print.pai.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Printing method for pai objects (pesticidal active ingredients) — print.pai","text":"x chent object printed ... arguments compatibility S3 method","code":""}] diff --git a/docs/sitemap.xml b/docs/sitemap.xml index 63ab18d..cf96c5e 100644 --- a/docs/sitemap.xml +++ b/docs/sitemap.xml @@ -1,39 +1,39 @@ <?xml version="1.0" encoding="UTF-8"?> <urlset xmlns="http://www.sitemaps.org/schemas/sitemap/0.9"> <url> - 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<loc>/reference/print.chent.html</loc> + <loc>https://pkgdown.jrwb.de/chents/reference/print.chent.html</loc> </url> <url> - <loc>/reference/print.pai.html</loc> + <loc>https://pkgdown.jrwb.de/chents/reference/print.pai.html</loc> </url> </urlset> |