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authorRanke Johannes <johannes.ranke@agroscope.admin.ch>2025-10-22 16:27:37 +0200
committerRanke Johannes <johannes.ranke@agroscope.admin.ch>2025-10-22 16:27:37 +0200
commit7c0e06c053303ea3f35fad3236ee5b3d930e7f08 (patch)
tree2843596590b70d2e892a3f325b0af04cb54c8387
parentb9a839f29beb9c10f22ace4b0dd4eee167ae6836 (diff)
Improve test coverage and use testthat 3rd editionHEADmain
Diffstat
-rw-r--r--DESCRIPTION3
-rw-r--r--docs/coverage/coverage.html1251
-rw-r--r--tests/testthat.R8
-rw-r--r--tests/testthat/_snaps/chent.md18
-rw-r--r--tests/testthat/test_chent.R30
-rw-r--r--tests/testthat/test_pai.R29
6 files changed, 671 insertions, 668 deletions
diff --git a/DESCRIPTION b/DESCRIPTION
index 2201b9a..71c6c42 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -19,7 +19,7 @@ Imports:
reticulate
Suggests:
knitr,
- testthat,
+ testthat (>= 3.0.0),
covr,
devEMF
License: GPL
@@ -29,3 +29,4 @@ Encoding: UTF-8
URL: https://pkgdown.jrwb.de/chents, https://github.com/jranke/chents
Roxygen: list(markdown = TRUE, r6 = TRUE)
RoxygenNote: 7.3.3
+Config/testthat/edition: 3
diff --git a/docs/coverage/coverage.html b/docs/coverage/coverage.html
index f881440..1e9d0ad 100644
--- a/docs/coverage/coverage.html
+++ b/docs/coverage/coverage.html
@@ -95,7 +95,7 @@ table.table-condensed {
font-size: 11px;
}</style>
<div class="col-md-8 col-md-offset-2">
- <h2>chents coverage - 32.25%</h2>
+ <h2>chents coverage - 34.64%</h2>
<div class="tabbable">
<ul class="nav nav-tabs" data-tabsetid="covr">
<li class="active">
@@ -107,8 +107,8 @@ table.table-condensed {
</ul>
<div class="tab-content" data-tabsetid="covr">
<div class="tab-pane active" title="Files" data-value="Files" id="tab-covr-1">
- <div class="datatables html-widget html-fill-item" id="htmlwidget-c7fabdeba8b81e642b4e" style="width:100%;height:500px;"></div>
- <script type="application/json" data-for="htmlwidget-c7fabdeba8b81e642b4e">{"x":{"filter":"none","vertical":false,"fillContainer":false,"data":[["<a href=\"#\">R/zzz.R<\/a>","<a href=\"#\">R/chent.R<\/a>"],[9,829],[7,300],[0,99],[7,201],["0","1"],["0.00%","33.00%"]],"container":"<table class=\"row-border\">\n <thead>\n <tr>\n <th>File<\/th>\n <th>Lines<\/th>\n <th>Relevant<\/th>\n <th>Covered<\/th>\n <th>Missed<\/th>\n <th>Hits / Line<\/th>\n <th>Coverage<\/th>\n <\/tr>\n <\/thead>\n<\/table>","options":{"searching":false,"dom":"t","paging":false,"columnDefs":[{"targets":6,"createdCell":"function(td, cellData, rowData, row, col) {\n var percent = cellData.replace(\"%\", \"\");\n if (percent > 90) {\n var grad = \"linear-gradient(90deg, #edfde7 \" + cellData + \", white \" + cellData + \")\";\n } else if (percent > 75) {\n var grad = \"linear-gradient(90deg, #f9ffe5 \" + cellData + \", white \" + cellData + \")\";\n } else {\n var grad = \"linear-gradient(90deg, #fcece9 \" + cellData + \", white \" + cellData + \")\";\n }\n $(td).css(\"background\", grad);\n}\n"},{"className":"dt-right","targets":[1,2,3,4]},{"name":"File","targets":0},{"name":"Lines","targets":1},{"name":"Relevant","targets":2},{"name":"Covered","targets":3},{"name":"Missed","targets":4},{"name":"Hits / Line","targets":5},{"name":"Coverage","targets":6}],"order":[],"autoWidth":false,"orderClasses":false},"callback":"function(table) {\ntable.on('click.dt', 'a', function() {\n files = $('div#files div');\n files.not('div.hidden').addClass('hidden');\n id = $(this).text();\n files.filter('div[id=\\'' + id + '\\']').removeClass('hidden');\n $('ul.nav a[data-value=Source]').text(id).tab('show');\n});\n}"},"evals":["options.columnDefs.0.createdCell","callback"],"jsHooks":[]}</script>
+ <div class="datatables html-widget html-fill-item" id="htmlwidget-702167ad1bbf5cac83c0" style="width:100%;height:500px;"></div>
+ <script type="application/json" data-for="htmlwidget-702167ad1bbf5cac83c0">{"x":{"filter":"none","vertical":false,"fillContainer":false,"data":[["<a href=\"#\">R/zzz.R<\/a>","<a href=\"#\">R/chent.R<\/a>"],[9,828],[7,299],[0,106],[7,193],["0","1"],["0.00%","35.45%"]],"container":"<table class=\"row-border\">\n <thead>\n <tr>\n <th>File<\/th>\n <th>Lines<\/th>\n <th>Relevant<\/th>\n <th>Covered<\/th>\n <th>Missed<\/th>\n <th>Hits / Line<\/th>\n <th>Coverage<\/th>\n <\/tr>\n <\/thead>\n<\/table>","options":{"searching":false,"dom":"t","paging":false,"columnDefs":[{"targets":6,"createdCell":"function(td, cellData, rowData, row, col) {\n var percent = cellData.replace(\"%\", \"\");\n if (percent > 90) {\n var grad = \"linear-gradient(90deg, #edfde7 \" + cellData + \", white \" + cellData + \")\";\n } else if (percent > 75) {\n var grad = \"linear-gradient(90deg, #f9ffe5 \" + cellData + \", white \" + cellData + \")\";\n } else {\n var grad = \"linear-gradient(90deg, #fcece9 \" + cellData + \", white \" + cellData + \")\";\n }\n $(td).css(\"background\", grad);\n}\n"},{"className":"dt-right","targets":[1,2,3,4]},{"name":"File","targets":0},{"name":"Lines","targets":1},{"name":"Relevant","targets":2},{"name":"Covered","targets":3},{"name":"Missed","targets":4},{"name":"Hits / Line","targets":5},{"name":"Coverage","targets":6}],"order":[],"autoWidth":false,"orderClasses":false},"callback":"function(table) {\ntable.on('click.dt', 'a', function() {\n files = $('div#files div');\n files.not('div.hidden').addClass('hidden');\n id = $(this).text();\n files.filter('div[id=\\'' + id + '\\']').removeClass('hidden');\n $('ul.nav a[data-value=Source]').text(id).tab('show');\n});\n}"},"evals":["options.columnDefs.0.createdCell","callback"],"jsHooks":[]}</script>
</div>
<div class="tab-pane" title="Source" data-value="Source" id="tab-covr-2">
<div id="files">
@@ -1218,14 +1218,14 @@ table.table-condensed {
<td class="num">158</td>
<td class="coverage"></td>
<td class="col-sm-12">
- <pre class="language-r"> try_pubchem = function(query, from = 'name') {</pre>
+ <pre class="language-r"> try_pubchem = function(query = self$identifier, from = 'name') {</pre>
</td>
</tr>
<tr class="covered">
<td class="num">159</td>
<td class="coverage">2<em>x</em></td>
<td class="col-sm-12">
- <pre class="language-r"> message("PubChem:")</pre>
+ <pre class="language-r"> message("Querying PubChem for ", from , " ", query, " ...")</pre>
</td>
</tr>
<tr class="covered">
@@ -1260,7 +1260,7 @@ table.table-condensed {
<td class="num">164</td>
<td class="coverage">!</td>
<td class="col-sm-12">
- <pre class="language-r"> message("Query ", query, " did not give results at PubChem")</pre>
+ <pre class="language-r"> message("Querying for ", query, " as ", from, " did not give results at PubChem")</pre>
</td>
</tr>
<tr class="never">
@@ -1729,7 +1729,7 @@ table.table-condensed {
<td class="num">231</td>
<td class="coverage">2<em>x</em></td>
<td class="col-sm-12">
- <pre class="language-r"> message("Trying to get chemical information from RDKit using ",</pre>
+ <pre class="language-r"> message("Get chemical information from RDKit using ",</pre>
</td>
</tr>
<tr class="covered">
@@ -1771,12 +1771,12 @@ table.table-condensed {
<td class="num">237</td>
<td class="coverage">2<em>x</em></td>
<td class="col-sm-12">
- <pre class="language-r"> if (!is.na(self$mw)) {</pre>
+ <pre class="language-r"> if (!is.null(self$mw) &amp;&amp; !is.na(self$mw)) {</pre>
</td>
</tr>
<tr class="covered">
<td class="num">238</td>
- <td class="coverage">1<em>x</em></td>
+ <td class="coverage">2<em>x</em></td>
<td class="col-sm-12">
<pre class="language-r"> if (round(self$rdkit$mw, 1) != round(self$mw, 1)) {</pre>
</td>
@@ -1785,4134 +1785,4127 @@ table.table-condensed {
<td class="num">239</td>
<td class="coverage">!</td>
<td class="col-sm-12">
- <pre class="language-r"> message("RDKit mw is ", self$rdkit$mw)</pre>
- </td>
- </tr>
- <tr class="missed">
- <td class="num">240</td>
- <td class="coverage">!</td>
- <td class="col-sm-12">
- <pre class="language-r"> message("mw is ", self$mw)</pre>
+ <pre class="language-r"> warning("RDKit mw is ", self$rdkit$mw, " while mw is ", self$mw)</pre>
</td>
</tr>
<tr class="never">
- <td class="num">241</td>
+ <td class="num">240</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> }</pre>
</td>
</tr>
<tr class="never">
- <td class="num">242</td>
+ <td class="num">241</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> } else {</pre>
</td>
</tr>
- <tr class="covered">
- <td class="num">243</td>
- <td class="coverage">1<em>x</em></td>
+ <tr class="missed">
+ <td class="num">242</td>
+ <td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> self$mw &lt;- self$rdkit$mw</pre>
</td>
</tr>
- <tr class="covered">
- <td class="num">244</td>
- <td class="coverage">1<em>x</em></td>
+ <tr class="missed">
+ <td class="num">243</td>
+ <td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> attr(self$mw, "source") &lt;- "rdkit"</pre>
</td>
</tr>
<tr class="never">
- <td class="num">245</td>
+ <td class="num">244</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> }</pre>
</td>
</tr>
<tr class="never">
- <td class="num">246</td>
+ <td class="num">245</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"></pre>
</td>
</tr>
<tr class="never">
- <td class="num">247</td>
+ <td class="num">246</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> # Create an SVG representation</pre>
</td>
</tr>
<tr class="covered">
- <td class="num">248</td>
+ <td class="num">247</td>
<td class="coverage">2<em>x</em></td>
<td class="col-sm-12">
<pre class="language-r"> rdkit_module$Chem$rdDepictor$Compute2DCoords(self$mol)</pre>
</td>
</tr>
<tr class="covered">
- <td class="num">249</td>
+ <td class="num">248</td>
<td class="coverage">2<em>x</em></td>
<td class="col-sm-12">
<pre class="language-r"> if (!is.null(template)) {</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">250</td>
+ <td class="num">249</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> rdkit_template &lt;- rdkit_module$Chem$MolFromSmiles(template)</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">251</td>
+ <td class="num">250</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> rdkit_module$Chem$rdDepictor$Compute2DCoords(template)</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">252</td>
+ <td class="num">251</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> rdkit$Chem$AllChem$GenerateDepictionMatching2DStructure(self$mol, template)</pre>
</td>
</tr>
<tr class="never">
- <td class="num">253</td>
+ <td class="num">252</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> }</pre>
</td>
</tr>
<tr class="covered">
- <td class="num">254</td>
+ <td class="num">253</td>
<td class="coverage">2<em>x</em></td>
<td class="col-sm-12">
<pre class="language-r"> d2d &lt;- rdkit_module$Chem$Draw$rdMolDraw2D$MolDraw2DSVG(400L, 400L)</pre>
</td>
</tr>
<tr class="covered">
- <td class="num">255</td>
+ <td class="num">254</td>
<td class="coverage">2<em>x</em></td>
<td class="col-sm-12">
<pre class="language-r"> d2d$DrawMolecule(self$mol)</pre>
</td>
</tr>
<tr class="covered">
- <td class="num">256</td>
+ <td class="num">255</td>
<td class="coverage">2<em>x</em></td>
<td class="col-sm-12">
<pre class="language-r"> d2d$FinishDrawing()</pre>
</td>
</tr>
<tr class="covered">
- <td class="num">257</td>
+ <td class="num">256</td>
<td class="coverage">2<em>x</em></td>
<td class="col-sm-12">
<pre class="language-r"> self$svg &lt;- d2d$GetDrawingText()</pre>
</td>
</tr>
<tr class="covered">
- <td class="num">258</td>
+ <td class="num">257</td>
<td class="coverage">2<em>x</em></td>
<td class="col-sm-12">
<pre class="language-r"> svgfile &lt;- tempfile(fileext = ".svg")</pre>
</td>
</tr>
<tr class="covered">
- <td class="num">259</td>
+ <td class="num">258</td>
<td class="coverage">2<em>x</em></td>
<td class="col-sm-12">
<pre class="language-r"> psfile &lt;- tempfile(fileext = ".ps")</pre>
</td>
</tr>
<tr class="covered">
- <td class="num">260</td>
+ <td class="num">259</td>
<td class="coverage">2<em>x</em></td>
<td class="col-sm-12">
<pre class="language-r"> writeLines(self$svg, svgfile)</pre>
</td>
</tr>
<tr class="covered">
- <td class="num">261</td>
+ <td class="num">260</td>
<td class="coverage">2<em>x</em></td>
<td class="col-sm-12">
<pre class="language-r"> rsvg::rsvg_ps(svgfile, psfile)</pre>
</td>
</tr>
<tr class="never">
- <td class="num">262</td>
+ <td class="num">261</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"></pre>
</td>
</tr>
<tr class="never">
- <td class="num">263</td>
+ <td class="num">262</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> # Get size properties useful for plotting</pre>
</td>
</tr>
<tr class="covered">
- <td class="num">264</td>
+ <td class="num">263</td>
<td class="coverage">2<em>x</em></td>
<td class="col-sm-12">
<pre class="language-r"> ps_font_line &lt;- grep("Tm$", readLines(psfile), value = TRUE)[1]</pre>
</td>
</tr>
<tr class="covered">
- <td class="num">265</td>
+ <td class="num">264</td>
<td class="coverage">2<em>x</em></td>
<td class="col-sm-12">
<pre class="language-r"> ps_font_size &lt;- gsub(" .*$", "", ps_font_line)</pre>
</td>
</tr>
<tr class="covered">
- <td class="num">266</td>
+ <td class="num">265</td>
<td class="coverage">2<em>x</em></td>
<td class="col-sm-12">
<pre class="language-r"> self$Pict_font_size = as.numeric(ps_font_size)</pre>
</td>
</tr>
<tr class="never">
- <td class="num">267</td>
+ <td class="num">266</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"></pre>
</td>
</tr>
<tr class="never">
- <td class="num">268</td>
+ <td class="num">267</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> # Read in to create Picture</pre>
</td>
</tr>
<tr class="covered">
- <td class="num">269</td>
+ <td class="num">268</td>
<td class="coverage">2<em>x</em></td>
<td class="col-sm-12">
<pre class="language-r"> xmlfile &lt;- tempfile(fileext = ".xml")</pre>
</td>
</tr>
<tr class="covered">
- <td class="num">270</td>
+ <td class="num">269</td>
<td class="coverage">2<em>x</em></td>
<td class="col-sm-12">
<pre class="language-r"> PostScriptTrace(psfile, outfilename = xmlfile)</pre>
</td>
</tr>
<tr class="covered">
- <td class="num">271</td>
+ <td class="num">270</td>
<td class="coverage">2<em>x</em></td>
<td class="col-sm-12">
<pre class="language-r"> unlink(paste0("capture", basename(psfile)))</pre>
</td>
</tr>
<tr class="covered">
- <td class="num">272</td>
+ <td class="num">271</td>
<td class="coverage">2<em>x</em></td>
<td class="col-sm-12">
<pre class="language-r"> self$Picture &lt;- readPicture(xmlfile)</pre>
</td>
</tr>
<tr class="covered">
- <td class="num">273</td>
+ <td class="num">272</td>
<td class="coverage">2<em>x</em></td>
<td class="col-sm-12">
<pre class="language-r"> unlink(c(xmlfile, psfile, svgfile))</pre>
</td>
</tr>
<tr class="never">
- <td class="num">274</td>
+ <td class="num">273</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> },</pre>
</td>
</tr>
<tr class="never">
- <td class="num">275</td>
+ <td class="num">274</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"></pre>
</td>
</tr>
<tr class="never">
- <td class="num">276</td>
+ <td class="num">275</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' @description</pre>
</td>
</tr>
<tr class="never">
- <td class="num">277</td>
+ <td class="num">276</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' Obtain information from a YAML file</pre>
</td>
</tr>
<tr class="never">
- <td class="num">278</td>
+ <td class="num">277</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' @param repo Should the file be looked for in the current working</pre>
</td>
</tr>
<tr class="never">
- <td class="num">279</td>
+ <td class="num">278</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' directory, a local git repository under `~/git/chyaml`, or from</pre>
</td>
</tr>
<tr class="never">
- <td class="num">280</td>
+ <td class="num">279</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' the web (not implemented).</pre>
</td>
</tr>
<tr class="never">
- <td class="num">281</td>
+ <td class="num">280</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' @param chyaml The filename to be looked for</pre>
</td>
</tr>
<tr class="never">
- <td class="num">282</td>
+ <td class="num">281</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> get_chyaml = function(repo = c("wd", "local", "web"),</pre>
</td>
</tr>
<tr class="never">
- <td class="num">283</td>
+ <td class="num">282</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> chyaml = paste0(URLencode(self$identifier), ".yaml"))</pre>
</td>
</tr>
<tr class="never">
- <td class="num">284</td>
+ <td class="num">283</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> {</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">285</td>
+ <td class="num">284</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> repo = match.arg(repo)</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">286</td>
+ <td class="num">285</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> paths = c(</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">287</td>
+ <td class="num">286</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> wd = ".",</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">288</td>
+ <td class="num">287</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> local = file.path("~", "git/chyaml"))</pre>
</td>
</tr>
<tr class="never">
- <td class="num">289</td>
+ <td class="num">288</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"></pre>
</td>
</tr>
<tr class="missed">
- <td class="num">290</td>
+ <td class="num">289</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> chyaml_handlers = list(</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">291</td>
+ <td class="num">290</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> expr = function(x) NULL, # To avoid security risks from reading chyaml files</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">292</td>
+ <td class="num">291</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> dataframe = function(x)</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">293</td>
+ <td class="num">292</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> eval(parse(text = paste0("data.frame(", x, ", stringsAsFactors = FALSE)"))))</pre>
</td>
</tr>
<tr class="never">
- <td class="num">294</td>
+ <td class="num">293</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"></pre>
</td>
</tr>
<tr class="missed">
- <td class="num">295</td>
+ <td class="num">294</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> if (repo %in% c("wd", "local")) {</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">296</td>
+ <td class="num">295</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> path = paths[repo]</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">297</td>
+ <td class="num">296</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> full = file.path(path, chyaml)</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">298</td>
+ <td class="num">297</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> if (!file.exists(full)) {</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">299</td>
+ <td class="num">298</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> message("Did not find chyaml file ", full)</pre>
</td>
</tr>
<tr class="never">
- <td class="num">300</td>
+ <td class="num">299</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> } else {</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">301</td>
+ <td class="num">300</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> if (is(try(self$chyaml &lt;- yaml.load_file(chyaml, handlers = chyaml_handlers)),</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">302</td>
+ <td class="num">301</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> "try-error")) {</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">303</td>
+ <td class="num">302</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> message("Could not load ", full)</pre>
</td>
</tr>
<tr class="never">
- <td class="num">304</td>
+ <td class="num">303</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> } else {</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">305</td>
+ <td class="num">304</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> message("Loaded ", full)</pre>
</td>
</tr>
<tr class="never">
- <td class="num">306</td>
+ <td class="num">305</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> }</pre>
</td>
</tr>
<tr class="never">
- <td class="num">307</td>
+ <td class="num">306</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> }</pre>
</td>
</tr>
<tr class="never">
- <td class="num">308</td>
+ <td class="num">307</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> } else {</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">309</td>
+ <td class="num">308</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> message("web repositories not implemented")</pre>
</td>
</tr>
<tr class="never">
- <td class="num">310</td>
+ <td class="num">309</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> }</pre>
</td>
</tr>
<tr class="never">
- <td class="num">311</td>
+ <td class="num">310</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> },</pre>
</td>
</tr>
<tr class="never">
- <td class="num">312</td>
+ <td class="num">311</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"></pre>
</td>
</tr>
<tr class="never">
- <td class="num">313</td>
+ <td class="num">312</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' @description</pre>
</td>
</tr>
<tr class="never">
- <td class="num">314</td>
+ <td class="num">313</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' Add a vapour pressure</pre>
</td>
</tr>
<tr class="never">
- <td class="num">315</td>
+ <td class="num">314</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' @param p0 The vapour pressure in Pa</pre>
</td>
</tr>
<tr class="never">
- <td class="num">316</td>
+ <td class="num">315</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> add_p0 = function(p0, T = NA, source = NA, page = NA, remark = "") {</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">317</td>
+ <td class="num">316</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> self$p0 &lt;- p0</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">318</td>
+ <td class="num">317</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> attr(self$p0, "T") &lt;- T</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">319</td>
+ <td class="num">318</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> attr(self$p0, "source") &lt;- source</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">320</td>
+ <td class="num">319</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> attr(self$p0, "page") &lt;- page</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">321</td>
+ <td class="num">320</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> attr(self$p0, "remark") &lt;- remark</pre>
</td>
</tr>
<tr class="never">
- <td class="num">322</td>
+ <td class="num">321</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> },</pre>
</td>
</tr>
<tr class="never">
- <td class="num">323</td>
+ <td class="num">322</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"></pre>
</td>
</tr>
<tr class="never">
- <td class="num">324</td>
+ <td class="num">323</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' @description</pre>
</td>
</tr>
<tr class="never">
- <td class="num">325</td>
+ <td class="num">324</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' Add a water solubility</pre>
</td>
</tr>
<tr class="never">
- <td class="num">326</td>
+ <td class="num">325</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' @param cwsat The water solubility in mg/L</pre>
</td>
</tr>
<tr class="never">
- <td class="num">327</td>
+ <td class="num">326</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> add_cwsat = function(cwsat, T = NA, pH = NA,</pre>
</td>
</tr>
<tr class="never">
- <td class="num">328</td>
+ <td class="num">327</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> source = NA, page = NA, remark = "")</pre>
</td>
</tr>
<tr class="never">
- <td class="num">329</td>
+ <td class="num">328</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> {</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">330</td>
+ <td class="num">329</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> self$cwsat &lt;- cwsat</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">331</td>
+ <td class="num">330</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> attr(self$cwsat, "T") &lt;- T</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">332</td>
+ <td class="num">331</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> attr(self$cwsat, "pH") &lt;- pH</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">333</td>
+ <td class="num">332</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> attr(self$cwsat, "source") &lt;- source</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">334</td>
+ <td class="num">333</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> attr(self$cwsat, "page") &lt;- page</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">335</td>
+ <td class="num">334</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> attr(self$cwsat, "remark") &lt;- remark</pre>
</td>
</tr>
<tr class="never">
- <td class="num">336</td>
+ <td class="num">335</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> },</pre>
</td>
</tr>
<tr class="never">
- <td class="num">337</td>
+ <td class="num">336</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"></pre>
</td>
</tr>
<tr class="never">
- <td class="num">338</td>
+ <td class="num">337</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' @description</pre>
</td>
</tr>
<tr class="never">
- <td class="num">339</td>
+ <td class="num">338</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' Add a plant uptake factor</pre>
</td>
</tr>
<tr class="never">
- <td class="num">340</td>
+ <td class="num">339</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' @param PUF The plant uptake factor, a number between 0 and 1</pre>
</td>
</tr>
<tr class="never">
- <td class="num">341</td>
+ <td class="num">340</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> add_PUF = function(PUF = 0,</pre>
</td>
</tr>
<tr class="never">
- <td class="num">342</td>
+ <td class="num">341</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> source = "focus_generic_gw_2014", page = 41,</pre>
</td>
</tr>
<tr class="never">
- <td class="num">343</td>
+ <td class="num">342</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> remark = "Conservative default value")</pre>
</td>
</tr>
<tr class="never">
- <td class="num">344</td>
+ <td class="num">343</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> {</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">345</td>
+ <td class="num">344</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> self$PUF &lt;- PUF</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">346</td>
+ <td class="num">345</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> attr(self$PUF, "source") &lt;- source</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">347</td>
+ <td class="num">346</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> attr(self$PUF, "page") &lt;- page</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">348</td>
+ <td class="num">347</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> attr(self$PUF, "remark") &lt;- remark</pre>
</td>
</tr>
<tr class="never">
- <td class="num">349</td>
+ <td class="num">348</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> },</pre>
</td>
</tr>
<tr class="never">
- <td class="num">350</td>
+ <td class="num">349</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"></pre>
</td>
</tr>
<tr class="never">
- <td class="num">351</td>
+ <td class="num">350</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' @field TPs List of transformation products as chent objects</pre>
</td>
</tr>
<tr class="never">
- <td class="num">352</td>
+ <td class="num">351</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> TPs = list(),</pre>
</td>
</tr>
<tr class="never">
- <td class="num">353</td>
+ <td class="num">352</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"></pre>
</td>
</tr>
<tr class="never">
- <td class="num">354</td>
+ <td class="num">353</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' @description</pre>
</td>
</tr>
<tr class="never">
- <td class="num">355</td>
+ <td class="num">354</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' Add a transformation product to the internal list</pre>
</td>
</tr>
<tr class="never">
- <td class="num">356</td>
+ <td class="num">355</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' @param x A [chent] object, or an identifier to generate a [chent] object</pre>
</td>
</tr>
<tr class="never">
- <td class="num">357</td>
+ <td class="num">356</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' @param pubchem Should chemical information be obtained from PubChem?</pre>
</td>
</tr>
<tr class="never">
- <td class="num">358</td>
+ <td class="num">357</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> add_TP = function(x, smiles = NULL, pubchem = FALSE) {</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">359</td>
+ <td class="num">358</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> if (inherits(x, "chent")) {</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">360</td>
+ <td class="num">359</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> id &lt;- names(x$identifier)</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">361</td>
+ <td class="num">360</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> chent &lt;- x</pre>
</td>
</tr>
<tr class="never">
- <td class="num">362</td>
+ <td class="num">361</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> } else {</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">363</td>
+ <td class="num">362</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> id &lt;- make.names(x)</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">364</td>
+ <td class="num">363</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> chent &lt;- chent$new(x, smiles = smiles, pubchem = pubchem)</pre>
</td>
</tr>
<tr class="never">
- <td class="num">365</td>
+ <td class="num">364</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> }</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">366</td>
+ <td class="num">365</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> self$TPs[[id]] &lt;- chent</pre>
</td>
</tr>
<tr class="never">
- <td class="num">367</td>
+ <td class="num">366</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> },</pre>
</td>
</tr>
<tr class="never">
- <td class="num">368</td>
+ <td class="num">367</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"></pre>
</td>
</tr>
<tr class="never">
- <td class="num">369</td>
+ <td class="num">368</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' @field transformations Data frame of observed transformations</pre>
</td>
</tr>
<tr class="never">
- <td class="num">370</td>
+ <td class="num">369</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> transformations = data.frame(study_type = character(0),</pre>
</td>
</tr>
<tr class="never">
- <td class="num">371</td>
+ <td class="num">370</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> TP_identifier = character(0),</pre>
</td>
</tr>
<tr class="never">
- <td class="num">372</td>
+ <td class="num">371</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> max_occurrence = numeric(0),</pre>
</td>
</tr>
<tr class="never">
- <td class="num">373</td>
+ <td class="num">372</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> source = character(0),</pre>
</td>
</tr>
<tr class="never">
- <td class="num">374</td>
+ <td class="num">373</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> page = character(0),</pre>
</td>
</tr>
<tr class="never">
- <td class="num">375</td>
+ <td class="num">374</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> stringsAsFactors = FALSE),</pre>
</td>
</tr>
<tr class="never">
- <td class="num">376</td>
+ <td class="num">375</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"></pre>
</td>
</tr>
<tr class="never">
- <td class="num">377</td>
+ <td class="num">376</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' @description</pre>
</td>
</tr>
<tr class="never">
- <td class="num">378</td>
+ <td class="num">377</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' Add a line in the internal dataframe holding observed transformations</pre>
</td>
</tr>
<tr class="never">
- <td class="num">379</td>
+ <td class="num">378</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' @param study_type A characterisation of the study type</pre>
</td>
</tr>
<tr class="never">
- <td class="num">380</td>
+ <td class="num">379</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' @param TP_identifier An identifier of one of the transformation products</pre>
</td>
</tr>
<tr class="never">
- <td class="num">381</td>
+ <td class="num">380</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' in `self$TPs`</pre>
</td>
</tr>
<tr class="never">
- <td class="num">382</td>
+ <td class="num">381</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' @param max_occurrence The maximum observed occurrence of the</pre>
</td>
</tr>
<tr class="never">
- <td class="num">383</td>
+ <td class="num">382</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' transformation product, expressed as a fraction of the amount that would</pre>
</td>
</tr>
<tr class="never">
- <td class="num">384</td>
+ <td class="num">383</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' result from stochiometric transformation</pre>
</td>
</tr>
<tr class="never">
- <td class="num">385</td>
+ <td class="num">384</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> add_transformation = function(study_type, TP_identifier, max_occurrence,</pre>
</td>
</tr>
<tr class="never">
- <td class="num">386</td>
+ <td class="num">385</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> remark = "", source = NA, pages = NA)</pre>
</td>
</tr>
<tr class="never">
- <td class="num">387</td>
+ <td class="num">386</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> {</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">388</td>
+ <td class="num">387</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> TP_name = make.names(TP_identifier)</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">389</td>
+ <td class="num">388</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> if (!inherits(self$TPs[[TP_name]], "chent")) {</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">390</td>
+ <td class="num">389</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> stop(paste("Please add the TP", TP_identifier, "first using chent$add_TP()"))</pre>
</td>
</tr>
<tr class="never">
- <td class="num">391</td>
+ <td class="num">390</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> }</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">392</td>
+ <td class="num">391</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> TP_chent &lt;- self$TPs[TP_name]</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">393</td>
+ <td class="num">392</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> if (is.numeric(pages)) pages &lt;- paste(pages, collapse = ", ")</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">394</td>
+ <td class="num">393</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> cn &lt;- colnames(self$transformations)</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">395</td>
+ <td class="num">394</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> self$transformations &lt;- rbind(self$transformations,</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">396</td>
+ <td class="num">395</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> data.frame(study_type = study_type,</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">397</td>
+ <td class="num">396</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> TP_identifier = TP_identifier,</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">398</td>
+ <td class="num">397</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> max_occurrence = max_occurrence,</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">399</td>
+ <td class="num">398</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> remark = remark,</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">400</td>
+ <td class="num">399</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> source = source,</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">401</td>
+ <td class="num">400</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> page = page,</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">402</td>
+ <td class="num">401</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> stringsAsFactors = FALSE))</pre>
</td>
</tr>
<tr class="never">
- <td class="num">403</td>
+ <td class="num">402</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> },</pre>
</td>
</tr>
<tr class="never">
- <td class="num">404</td>
+ <td class="num">403</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"></pre>
</td>
</tr>
<tr class="never">
- <td class="num">405</td>
+ <td class="num">404</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' @field soil_degradation Dataframe of modelling DT50 values</pre>
</td>
</tr>
<tr class="never">
- <td class="num">406</td>
+ <td class="num">405</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> soil_degradation = NULL,</pre>
</td>
</tr>
<tr class="never">
- <td class="num">407</td>
+ <td class="num">406</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"></pre>
</td>
</tr>
<tr class="never">
- <td class="num">408</td>
+ <td class="num">407</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' @description</pre>
</td>
</tr>
<tr class="never">
- <td class="num">409</td>
+ <td class="num">408</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' Add a line in the internal dataframe holding modelling DT50 values</pre>
</td>
</tr>
<tr class="never">
- <td class="num">410</td>
+ <td class="num">409</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' @param DT50_mod The modelling DT50 in the sense of regulatory pesticide</pre>
</td>
</tr>
<tr class="never">
- <td class="num">411</td>
+ <td class="num">410</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' fate modelling</pre>
</td>
</tr>
<tr class="never">
- <td class="num">412</td>
+ <td class="num">411</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' @param DT50_mod_ref The normalised modelling DT50 in the sense of</pre>
</td>
</tr>
<tr class="never">
- <td class="num">413</td>
+ <td class="num">412</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' regulatory pesticide fate modelling</pre>
</td>
</tr>
<tr class="never">
- <td class="num">414</td>
+ <td class="num">413</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' @param country The country (mainly for field studies)</pre>
</td>
</tr>
<tr class="never">
- <td class="num">415</td>
+ <td class="num">414</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' @param temperature The temperature during the study in degrees Celsius</pre>
</td>
</tr>
<tr class="never">
- <td class="num">416</td>
+ <td class="num">415</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' @param moisture The moisture during the study</pre>
</td>
</tr>
<tr class="never">
- <td class="num">417</td>
+ <td class="num">416</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' @param category Is it a laboratory ('lab') or field study ('field')</pre>
</td>
</tr>
<tr class="never">
- <td class="num">418</td>
+ <td class="num">417</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' @param formulation Name of the formulation applied, if it was not</pre>
</td>
</tr>
<tr class="never">
- <td class="num">419</td>
+ <td class="num">418</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' the technical active ingredient</pre>
</td>
</tr>
<tr class="never">
- <td class="num">420</td>
+ <td class="num">419</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' @param model The degradation model used for deriving `DT50_mod`</pre>
</td>
</tr>
<tr class="never">
- <td class="num">421</td>
+ <td class="num">420</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' @param chi2 The relative error as defined in FOCUS kinetics</pre>
</td>
</tr>
<tr class="never">
- <td class="num">422</td>
+ <td class="num">421</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> add_soil_degradation = function(soils, DT50_mod, DT50_mod_ref,</pre>
</td>
</tr>
<tr class="never">
- <td class="num">423</td>
+ <td class="num">422</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> type = NA, country = NA,</pre>
</td>
</tr>
<tr class="never">
- <td class="num">424</td>
+ <td class="num">423</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> pH_orig = NA, pH_medium = NA, pH_H2O = NA,</pre>
</td>
</tr>
<tr class="never">
- <td class="num">425</td>
+ <td class="num">424</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> perc_OC = NA,</pre>
</td>
</tr>
<tr class="never">
- <td class="num">426</td>
+ <td class="num">425</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> temperature = NA, moisture = NA,</pre>
</td>
</tr>
<tr class="never">
- <td class="num">427</td>
+ <td class="num">426</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> category = "lab", formulation = NA,</pre>
</td>
</tr>
<tr class="never">
- <td class="num">428</td>
+ <td class="num">427</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> model = NA, chi2 = NA,</pre>
</td>
</tr>
<tr class="never">
- <td class="num">429</td>
+ <td class="num">428</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> remark = "", source, page = NA)</pre>
</td>
</tr>
<tr class="never">
- <td class="num">430</td>
+ <td class="num">429</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> {</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">431</td>
+ <td class="num">430</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> new_soil_degradation = data.frame(</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">432</td>
+ <td class="num">431</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> soil = soils,</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">433</td>
+ <td class="num">432</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> DT50_mod = DT50_mod,</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">434</td>
+ <td class="num">433</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> DT50_mod_ref = DT50_mod_ref,</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">435</td>
+ <td class="num">434</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> type = type,</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">436</td>
+ <td class="num">435</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> country = country,</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">437</td>
+ <td class="num">436</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> pH_orig = pH_orig,</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">438</td>
+ <td class="num">437</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> pH_medium = pH_medium,</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">439</td>
+ <td class="num">438</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> pH_H2O = pH_H2O,</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">440</td>
+ <td class="num">439</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> perc_OC = perc_OC,</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">441</td>
+ <td class="num">440</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> temperature = temperature,</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">442</td>
+ <td class="num">441</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> moisture = moisture,</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">443</td>
+ <td class="num">442</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> category = category,</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">444</td>
+ <td class="num">443</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> formulation = formulation,</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">445</td>
+ <td class="num">444</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> model = model,</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">446</td>
+ <td class="num">445</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> chi2 = chi2,</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">447</td>
+ <td class="num">446</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> remark = remark,</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">448</td>
+ <td class="num">447</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> source = source,</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">449</td>
+ <td class="num">448</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> page = page,</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">450</td>
+ <td class="num">449</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> stringsAsFactors = FALSE)</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">451</td>
+ <td class="num">450</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> if (is.null(self$soil_degradation)) {</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">452</td>
+ <td class="num">451</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> self$soil_degradation &lt;- new_soil_degradation</pre>
</td>
</tr>
<tr class="never">
- <td class="num">453</td>
+ <td class="num">452</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> } else {</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">454</td>
+ <td class="num">453</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> self$soil_degradation &lt;- rbind(self$soil_degradation, new_soil_degradation)</pre>
</td>
</tr>
<tr class="never">
- <td class="num">455</td>
+ <td class="num">454</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> }</pre>
</td>
</tr>
<tr class="never">
- <td class="num">456</td>
+ <td class="num">455</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> },</pre>
</td>
</tr>
<tr class="never">
- <td class="num">457</td>
+ <td class="num">456</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"></pre>
</td>
</tr>
<tr class="never">
- <td class="num">458</td>
+ <td class="num">457</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' @field soil_ff Dataframe of formation fractions</pre>
</td>
</tr>
<tr class="never">
- <td class="num">459</td>
+ <td class="num">458</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> soil_ff = NULL,</pre>
</td>
</tr>
<tr class="never">
- <td class="num">460</td>
+ <td class="num">459</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"></pre>
</td>
</tr>
<tr class="never">
- <td class="num">461</td>
+ <td class="num">460</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' @description</pre>
</td>
</tr>
<tr class="never">
- <td class="num">462</td>
+ <td class="num">461</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' Add one or more formation fractions for degradation in soil</pre>
</td>
</tr>
<tr class="never">
- <td class="num">463</td>
+ <td class="num">462</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' @param target The identifier(s) of the transformation product</pre>
</td>
</tr>
<tr class="never">
- <td class="num">464</td>
+ <td class="num">463</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' @param soils The soil name(s) in which the transformation was observed</pre>
</td>
</tr>
<tr class="never">
- <td class="num">465</td>
+ <td class="num">464</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' @param ff The formation fraction(s)</pre>
</td>
</tr>
<tr class="never">
- <td class="num">466</td>
+ <td class="num">465</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> add_soil_ff = function(target, soils, ff = 1,</pre>
</td>
</tr>
<tr class="never">
- <td class="num">467</td>
+ <td class="num">466</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> remark = "", source, page = NA)</pre>
</td>
</tr>
<tr class="never">
- <td class="num">468</td>
+ <td class="num">467</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> {</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">469</td>
+ <td class="num">468</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> new_soil_ff = data.frame(</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">470</td>
+ <td class="num">469</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> target = target,</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">471</td>
+ <td class="num">470</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> target = target,</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">472</td>
+ <td class="num">471</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> soil = soils,</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">473</td>
+ <td class="num">472</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> ff = ff,</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">474</td>
+ <td class="num">473</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> remark = remark,</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">475</td>
+ <td class="num">474</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> source = source,</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">476</td>
+ <td class="num">475</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> page = page,</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">477</td>
+ <td class="num">476</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> stringsAsFactors = FALSE)</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">478</td>
+ <td class="num">477</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> if (is.null(self$soil_ff)) {</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">479</td>
+ <td class="num">478</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> self$soil_ff &lt;- new_soil_ff</pre>
</td>
</tr>
<tr class="never">
- <td class="num">480</td>
+ <td class="num">479</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> } else {</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">481</td>
+ <td class="num">480</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> self$soil_ff &lt;- rbind(self$soil_ff, new_soil_ff)</pre>
</td>
</tr>
<tr class="never">
- <td class="num">482</td>
+ <td class="num">481</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> }</pre>
</td>
</tr>
<tr class="never">
- <td class="num">483</td>
+ <td class="num">482</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> },</pre>
</td>
</tr>
<tr class="never">
- <td class="num">484</td>
+ <td class="num">483</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"></pre>
</td>
</tr>
<tr class="never">
- <td class="num">485</td>
+ <td class="num">484</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' @field soil_sorption Dataframe of soil sorption data</pre>
</td>
</tr>
<tr class="never">
- <td class="num">486</td>
+ <td class="num">485</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> soil_sorption = NULL,</pre>
</td>
</tr>
<tr class="never">
- <td class="num">487</td>
+ <td class="num">486</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"></pre>
</td>
</tr>
<tr class="never">
- <td class="num">488</td>
+ <td class="num">487</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' @description</pre>
</td>
</tr>
<tr class="never">
- <td class="num">489</td>
+ <td class="num">488</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' Add soil sorption data</pre>
</td>
</tr>
<tr class="never">
- <td class="num">490</td>
+ <td class="num">489</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' @param Kf The sorption constant in L/kg, either linear (then `N` is 1)</pre>
</td>
</tr>
<tr class="never">
- <td class="num">491</td>
+ <td class="num">490</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' or according to Freundlich</pre>
</td>
</tr>
<tr class="never">
- <td class="num">492</td>
+ <td class="num">491</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' @param Kfoc The constant from above, normalised to soil organic carbon</pre>
</td>
</tr>
<tr class="never">
- <td class="num">493</td>
+ <td class="num">492</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' @param N The Freundlich exponent</pre>
</td>
</tr>
<tr class="never">
- <td class="num">494</td>
+ <td class="num">493</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' @param perc_clay The percentage of clay in the soil</pre>
</td>
</tr>
<tr class="never">
- <td class="num">495</td>
+ <td class="num">494</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' @param CEC The cation exchange capacity</pre>
</td>
</tr>
<tr class="never">
- <td class="num">496</td>
+ <td class="num">495</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> add_soil_sorption = function(soils, </pre>
</td>
</tr>
<tr class="never">
- <td class="num">497</td>
+ <td class="num">496</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> Kf, Kfoc, N,</pre>
</td>
</tr>
<tr class="never">
- <td class="num">498</td>
+ <td class="num">497</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> type = NA, pH_orig = NA, pH_medium = NA,</pre>
</td>
</tr>
<tr class="never">
- <td class="num">499</td>
+ <td class="num">498</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> pH_H2O = NA,</pre>
</td>
</tr>
<tr class="never">
- <td class="num">500</td>
+ <td class="num">499</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> perc_OC = NA, perc_clay = NA, CEC = NA,</pre>
</td>
</tr>
<tr class="never">
- <td class="num">501</td>
+ <td class="num">500</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> remark = "", source, page = NA)</pre>
</td>
</tr>
<tr class="never">
- <td class="num">502</td>
+ <td class="num">501</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> {</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">503</td>
+ <td class="num">502</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> new_soil_sorption = data.frame(</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">504</td>
+ <td class="num">503</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> soils = soils,</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">505</td>
+ <td class="num">504</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> Kf = Kf, Kfoc = Kfoc, N = N,</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">506</td>
+ <td class="num">505</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> type = type,</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">507</td>
+ <td class="num">506</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> pH_orig = pH_orig,</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">508</td>
+ <td class="num">507</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> pH_medium = pH_medium,</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">509</td>
+ <td class="num">508</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> pH_H2O = pH_H2O,</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">510</td>
+ <td class="num">509</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> perc_OC = perc_OC, perc_clay = perc_clay, CEC = CEC,</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">511</td>
+ <td class="num">510</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> remark = remark,</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">512</td>
+ <td class="num">511</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> source = source,</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">513</td>
+ <td class="num">512</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> page = page,</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">514</td>
+ <td class="num">513</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> stringsAsFactors = FALSE)</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">515</td>
+ <td class="num">514</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> if (is.null(self$soil_sorption)) {</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">516</td>
+ <td class="num">515</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> self$soil_sorption &lt;- new_soil_sorption</pre>
</td>
</tr>
<tr class="never">
- <td class="num">517</td>
+ <td class="num">516</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> } else {</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">518</td>
+ <td class="num">517</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> self$soil_sorption &lt;- rbind(self$soil_sorption, new_soil_sorption)</pre>
</td>
</tr>
<tr class="never">
- <td class="num">519</td>
+ <td class="num">518</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> }</pre>
</td>
</tr>
<tr class="never">
- <td class="num">520</td>
+ <td class="num">519</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> },</pre>
</td>
</tr>
<tr class="never">
- <td class="num">521</td>
+ <td class="num">520</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"></pre>
</td>
</tr>
<tr class="never">
- <td class="num">522</td>
+ <td class="num">521</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' @description</pre>
</td>
</tr>
<tr class="never">
- <td class="num">523</td>
+ <td class="num">522</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' Write a PDF image of the structure</pre>
</td>
</tr>
<tr class="never">
- <td class="num">524</td>
+ <td class="num">523</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> pdf = function(file = paste0(self$identifier, ".pdf"),</pre>
</td>
</tr>
<tr class="never">
- <td class="num">525</td>
+ <td class="num">524</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> dir = "structures/pdf", template = NULL) {</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">526</td>
+ <td class="num">525</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> if (!dir.exists(dir)) {</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">527</td>
+ <td class="num">526</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> message("Directory '", dir, "' does not exist")</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">528</td>
+ <td class="num">527</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> message("Trying to create directory '", dir, "'")</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">529</td>
+ <td class="num">528</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> dir.create(dir, recursive = TRUE)</pre>
</td>
</tr>
<tr class="never">
- <td class="num">530</td>
+ <td class="num">529</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> }</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">531</td>
+ <td class="num">530</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> path = file.path(dir, file)</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">532</td>
+ <td class="num">531</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> message("Creating file '", path, "'")</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">533</td>
+ <td class="num">532</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> pdf(path)</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">534</td>
+ <td class="num">533</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> plot(self)</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">535</td>
+ <td class="num">534</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> dev.off()</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">536</td>
+ <td class="num">535</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> message("Cropping file '", path, "' using pdfcrop")</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">537</td>
+ <td class="num">536</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> bash_path &lt;- shQuote(path)</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">538</td>
+ <td class="num">537</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> system(paste("pdfcrop --margin 10", bash_path, bash_path, "&gt; /dev/null"))</pre>
</td>
</tr>
<tr class="never">
- <td class="num">539</td>
+ <td class="num">538</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"></pre>
</td>
</tr>
<tr class="never">
- <td class="num">540</td>
+ <td class="num">539</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> # Get the height of the MediaBox</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">541</td>
+ <td class="num">540</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> head &lt;- readLines(path, n = 20, skipNul = TRUE)</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">542</td>
+ <td class="num">541</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> m_line &lt;- suppressWarnings(grep("MediaBox", head, value = TRUE))</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">543</td>
+ <td class="num">542</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> self$pdf_height &lt;- as.numeric(gsub("/MediaBox \\[.* (.*)\\]", "\\1", m_line))</pre>
</td>
</tr>
<tr class="never">
- <td class="num">544</td>
+ <td class="num">543</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> },</pre>
</td>
</tr>
<tr class="never">
- <td class="num">545</td>
+ <td class="num">544</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"></pre>
</td>
</tr>
<tr class="never">
- <td class="num">546</td>
+ <td class="num">545</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' @description</pre>
</td>
</tr>
<tr class="never">
- <td class="num">547</td>
+ <td class="num">546</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' Write a PNG image of the structure</pre>
</td>
</tr>
<tr class="never">
- <td class="num">548</td>
+ <td class="num">547</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' @param antialias Passed to [png][grDevices::png]</pre>
</td>
</tr>
<tr class="never">
- <td class="num">549</td>
+ <td class="num">548</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> png = function(file = paste0(self$identifier, ".png"),</pre>
</td>
</tr>
<tr class="never">
- <td class="num">550</td>
+ <td class="num">549</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> dir = "structures/png", antialias = 'gray')</pre>
</td>
</tr>
<tr class="never">
- <td class="num">551</td>
+ <td class="num">550</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> {</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">552</td>
+ <td class="num">551</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> if (!dir.exists(dir)) {</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">553</td>
+ <td class="num">552</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> message("Directory '", dir, "' does not exist")</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">554</td>
+ <td class="num">553</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> message("Trying to create directory '", dir, "'")</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">555</td>
+ <td class="num">554</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> dir.create(dir, recursive = TRUE)</pre>
</td>
</tr>
<tr class="never">
- <td class="num">556</td>
+ <td class="num">555</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> }</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">557</td>
+ <td class="num">556</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> path = file.path(dir, file)</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">558</td>
+ <td class="num">557</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> message("Creating file '", path, "'")</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">559</td>
+ <td class="num">558</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> png(path, antialias = antialias)</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">560</td>
+ <td class="num">559</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> plot(self)</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">561</td>
+ <td class="num">560</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> dev.off()</pre>
</td>
</tr>
<tr class="never">
- <td class="num">562</td>
+ <td class="num">561</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> },</pre>
</td>
</tr>
<tr class="never">
- <td class="num">563</td>
+ <td class="num">562</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"></pre>
</td>
</tr>
<tr class="never">
- <td class="num">564</td>
+ <td class="num">563</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' @description</pre>
</td>
</tr>
<tr class="never">
- <td class="num">565</td>
+ <td class="num">564</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' Write an EMF image of the structure using [emf][devEMF::emf]</pre>
</td>
</tr>
<tr class="never">
- <td class="num">566</td>
+ <td class="num">565</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> emf = function(file = paste0(self$identifier, ".emf"),</pre>
</td>
</tr>
<tr class="never">
- <td class="num">567</td>
+ <td class="num">566</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> dir = "structures/emf")</pre>
</td>
</tr>
<tr class="never">
- <td class="num">568</td>
+ <td class="num">567</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> {</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">569</td>
+ <td class="num">568</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> if (!requireNamespace("devEMF")) {</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">570</td>
+ <td class="num">569</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> stop("You need to have the devEMF package installed for this function")</pre>
</td>
</tr>
<tr class="never">
- <td class="num">571</td>
+ <td class="num">570</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> }</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">572</td>
+ <td class="num">571</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> if (!dir.exists(dir)) {</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">573</td>
+ <td class="num">572</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> message("Directory '", dir, "' does not exist")</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">574</td>
+ <td class="num">573</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> message("Trying to create directory '", dir, "'")</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">575</td>
+ <td class="num">574</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> dir.create(dir, recursive = TRUE)</pre>
</td>
</tr>
<tr class="never">
- <td class="num">576</td>
+ <td class="num">575</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> }</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">577</td>
+ <td class="num">576</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> path = file.path(dir, file)</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">578</td>
+ <td class="num">577</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> message("Creating file '", path, "'")</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">579</td>
+ <td class="num">578</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> devEMF::emf(path)</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">580</td>
+ <td class="num">579</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> plot(self)</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">581</td>
+ <td class="num">580</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> dev.off()</pre>
</td>
</tr>
<tr class="never">
- <td class="num">582</td>
+ <td class="num">581</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> }</pre>
</td>
</tr>
<tr class="never">
- <td class="num">583</td>
+ <td class="num">582</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> )</pre>
</td>
</tr>
<tr class="never">
- <td class="num">584</td>
+ <td class="num">583</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r">)</pre>
</td>
</tr>
<tr class="never">
- <td class="num">585</td>
+ <td class="num">584</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"></pre>
</td>
</tr>
<tr class="never">
- <td class="num">586</td>
+ <td class="num">585</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r">#' Printing method for chent objects</pre>
</td>
</tr>
<tr class="never">
- <td class="num">587</td>
+ <td class="num">586</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r">#'</pre>
</td>
</tr>
<tr class="never">
- <td class="num">588</td>
+ <td class="num">587</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r">#' @param x The chent object to be printed</pre>
</td>
</tr>
<tr class="never">
- <td class="num">589</td>
+ <td class="num">588</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r">#' @param ... Further arguments for compatibility with the S3 method</pre>
</td>
</tr>
<tr class="never">
- <td class="num">590</td>
+ <td class="num">589</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r">#' @importFrom utils head</pre>
</td>
</tr>
<tr class="never">
- <td class="num">591</td>
+ <td class="num">590</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r">#' @export</pre>
</td>
</tr>
<tr class="never">
- <td class="num">592</td>
+ <td class="num">591</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r">print.chent = function(x, ...) {</pre>
</td>
</tr>
- <tr class="missed">
- <td class="num">593</td>
- <td class="coverage">!</td>
+ <tr class="covered">
+ <td class="num">592</td>
+ <td class="coverage">1<em>x</em></td>
<td class="col-sm-12">
<pre class="language-r"> cat("&lt;chent&gt;\n")</pre>
</td>
</tr>
- <tr class="missed">
- <td class="num">594</td>
- <td class="coverage">!</td>
+ <tr class="covered">
+ <td class="num">593</td>
+ <td class="coverage">1<em>x</em></td>
<td class="col-sm-12">
<pre class="language-r"> cat("Identifier $identifier", x$identifier, "\n")</pre>
</td>
</tr>
- <tr class="missed">
- <td class="num">595</td>
- <td class="coverage">!</td>
+ <tr class="covered">
+ <td class="num">594</td>
+ <td class="coverage">1<em>x</em></td>
<td class="col-sm-12">
<pre class="language-r"> cat ("InChI Key $inchikey", x$inchikey, "\n")</pre>
</td>
</tr>
- <tr class="missed">
- <td class="num">596</td>
- <td class="coverage">!</td>
+ <tr class="covered">
+ <td class="num">595</td>
+ <td class="coverage">1<em>x</em></td>
<td class="col-sm-12">
<pre class="language-r"> cat ("SMILES string $smiles:\n")</pre>
</td>
</tr>
- <tr class="missed">
- <td class="num">597</td>
- <td class="coverage">!</td>
+ <tr class="covered">
+ <td class="num">596</td>
+ <td class="coverage">1<em>x</em></td>
<td class="col-sm-12">
<pre class="language-r"> print(x$smiles)</pre>
</td>
</tr>
- <tr class="missed">
- <td class="num">598</td>
- <td class="coverage">!</td>
+ <tr class="covered">
+ <td class="num">597</td>
+ <td class="coverage">1<em>x</em></td>
<td class="col-sm-12">
<pre class="language-r"> if (!is.null(x$mw)) cat ("Molecular weight $mw:", round(x$mw, 1), "\n")</pre>
</td>
</tr>
- <tr class="missed">
- <td class="num">599</td>
- <td class="coverage">!</td>
+ <tr class="covered">
+ <td class="num">598</td>
+ <td class="coverage">1<em>x</em></td>
<td class="col-sm-12">
<pre class="language-r"> if (!is.null(x$pubchem$synonyms)) {</pre>
</td>
</tr>
- <tr class="missed">
- <td class="num">600</td>
- <td class="coverage">!</td>
+ <tr class="covered">
+ <td class="num">599</td>
+ <td class="coverage">1<em>x</em></td>
<td class="col-sm-12">
<pre class="language-r"> cat ("PubChem synonyms (up to 10):\n")</pre>
</td>
</tr>
- <tr class="missed">
- <td class="num">601</td>
- <td class="coverage">!</td>
+ <tr class="covered">
+ <td class="num">600</td>
+ <td class="coverage">1<em>x</em></td>
<td class="col-sm-12">
<pre class="language-r"> print(head(x$pubchem$synonyms, n = 10L))</pre>
</td>
</tr>
<tr class="never">
- <td class="num">602</td>
+ <td class="num">601</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> }</pre>
</td>
</tr>
<tr class="never">
- <td class="num">603</td>
+ <td class="num">602</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r">}</pre>
</td>
</tr>
<tr class="never">
- <td class="num">604</td>
+ <td class="num">603</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"></pre>
</td>
</tr>
<tr class="never">
- <td class="num">605</td>
+ <td class="num">604</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r">#' Draw SVG graph from a chent object using RDKit</pre>
</td>
</tr>
<tr class="never">
- <td class="num">606</td>
+ <td class="num">605</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r">#'</pre>
</td>
</tr>
<tr class="never">
- <td class="num">607</td>
+ <td class="num">606</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r">#' @param x The chent object to be plotted</pre>
</td>
</tr>
<tr class="never">
- <td class="num">608</td>
+ <td class="num">607</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r">#' @param width The desired width in pixels</pre>
</td>
</tr>
<tr class="never">
- <td class="num">609</td>
+ <td class="num">608</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r">#' @param height The desired height in pixels</pre>
</td>
</tr>
<tr class="never">
- <td class="num">610</td>
+ <td class="num">609</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r">#' @param filename The filename</pre>
</td>
</tr>
<tr class="never">
- <td class="num">611</td>
+ <td class="num">610</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r">#' @param subdir The path to which the file should be written</pre>
</td>
</tr>
<tr class="never">
- <td class="num">612</td>
+ <td class="num">611</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r">#' @export</pre>
</td>
</tr>
<tr class="never">
- <td class="num">613</td>
+ <td class="num">612</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r">draw_svg.chent = function(x, width = 300, height = 150,</pre>
</td>
</tr>
<tr class="never">
- <td class="num">614</td>
+ <td class="num">613</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> filename = paste0(names(x$identifier), ".svg"),</pre>
</td>
</tr>
<tr class="never">
- <td class="num">615</td>
+ <td class="num">614</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> subdir = "svg") {</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">616</td>
+ <td class="num">615</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> if (!rdkit_available) {</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">617</td>
+ <td class="num">616</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> stop("RDkit is not available via reticulate")</pre>
</td>
</tr>
<tr class="never">
- <td class="num">618</td>
+ <td class="num">617</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> } else {</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">619</td>
+ <td class="num">618</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> if (!dir.exists(subdir)) dir.create(subdir)</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">620</td>
+ <td class="num">619</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> mol &lt;- rdkit_module$Chem$MolFromSmiles(x$smiles)</pre>
</td>
</tr>
<tr class="never">
- <td class="num">621</td>
+ <td class="num">620</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"></pre>
</td>
</tr>
<tr class="missed">
- <td class="num">622</td>
+ <td class="num">621</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> rdkit_module$Chem$Draw$MolToFile(mol, file.path(subdir, filename),</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">623</td>
+ <td class="num">622</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> size = c(as.integer(width), as.integer(height)))</pre>
</td>
</tr>
<tr class="never">
- <td class="num">624</td>
+ <td class="num">623</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> }</pre>
</td>
</tr>
<tr class="never">
- <td class="num">625</td>
+ <td class="num">624</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r">}</pre>
</td>
</tr>
<tr class="never">
- <td class="num">626</td>
+ <td class="num">625</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"></pre>
</td>
</tr>
<tr class="never">
- <td class="num">627</td>
+ <td class="num">626</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r">#' Plot method for chent objects</pre>
</td>
</tr>
<tr class="never">
- <td class="num">628</td>
+ <td class="num">627</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r">#'</pre>
</td>
</tr>
<tr class="never">
- <td class="num">629</td>
+ <td class="num">628</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r">#' @importFrom grImport grid.picture</pre>
</td>
</tr>
<tr class="never">
- <td class="num">630</td>
+ <td class="num">629</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r">#' @param x The chent object to be plotted</pre>
</td>
</tr>
<tr class="never">
- <td class="num">631</td>
+ <td class="num">630</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r">#' @param ... Further arguments passed to [grImport::grid.picture]</pre>
</td>
</tr>
<tr class="never">
- <td class="num">632</td>
+ <td class="num">631</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r">#' @export</pre>
</td>
</tr>
<tr class="never">
- <td class="num">633</td>
+ <td class="num">632</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r">#' @examples</pre>
</td>
</tr>
<tr class="never">
- <td class="num">634</td>
+ <td class="num">633</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r">#' caffeine &lt;- chent$new("caffeine")</pre>
</td>
</tr>
<tr class="never">
- <td class="num">635</td>
+ <td class="num">634</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r">#' print(caffeine)</pre>
</td>
</tr>
<tr class="never">
- <td class="num">636</td>
+ <td class="num">635</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r">#' if (!is.null(caffeine$Picture)) {</pre>
</td>
</tr>
<tr class="never">
- <td class="num">637</td>
+ <td class="num">636</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r">#' plot(caffeine)</pre>
</td>
</tr>
<tr class="never">
- <td class="num">638</td>
+ <td class="num">637</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r">#' }</pre>
</td>
</tr>
<tr class="never">
- <td class="num">639</td>
+ <td class="num">638</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r">plot.chent = function(x, ...) {</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">640</td>
+ <td class="num">639</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> if (is.null(x$Picture)) stop("No Picture object in chent, was RDKit available during creation?")</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">641</td>
+ <td class="num">640</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> grid.picture(x$Picture)</pre>
</td>
</tr>
<tr class="never">
- <td class="num">642</td>
+ <td class="num">641</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r">}</pre>
</td>
</tr>
<tr class="never">
- <td class="num">643</td>
+ <td class="num">642</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"></pre>
</td>
</tr>
<tr class="never">
- <td class="num">644</td>
+ <td class="num">643</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r">#' @title An R6 class for pesticidal active ingredients and associated data</pre>
</td>
</tr>
<tr class="never">
- <td class="num">645</td>
+ <td class="num">644</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r">#'</pre>
</td>
</tr>
<tr class="never">
- <td class="num">646</td>
+ <td class="num">645</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r">#' @description This class is derived from [chent]. It makes it easy</pre>
</td>
</tr>
<tr class="never">
- <td class="num">647</td>
+ <td class="num">646</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r">#' to create a [chent] from the ISO common name of a pesticide active</pre>
</td>
</tr>
<tr class="never">
- <td class="num">648</td>
+ <td class="num">647</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r">#' ingredient, and additionally stores the ISO name as well as</pre>
</td>
</tr>
<tr class="never">
- <td class="num">649</td>
+ <td class="num">648</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r">#' the complete result of querying the BCPC compendium using</pre>
</td>
</tr>
<tr class="never">
- <td class="num">650</td>
+ <td class="num">649</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r">#' [bcpc_query][webchem::bcpc_query].</pre>
</td>
</tr>
<tr class="never">
- <td class="num">651</td>
+ <td class="num">650</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r">#'</pre>
</td>
</tr>
<tr class="never">
- <td class="num">652</td>
+ <td class="num">651</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r">#' @export</pre>
</td>
</tr>
<tr class="never">
- <td class="num">653</td>
+ <td class="num">652</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r">#' @format An [R6::R6Class] generator object</pre>
</td>
</tr>
<tr class="never">
- <td class="num">654</td>
+ <td class="num">653</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r">#' @examples</pre>
</td>
</tr>
<tr class="never">
- <td class="num">655</td>
+ <td class="num">654</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r">#' # On Travis, we get a certificate validation error,</pre>
</td>
</tr>
<tr class="never">
- <td class="num">656</td>
+ <td class="num">655</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r">#' # likely because the system (xenial) is so old,</pre>
</td>
</tr>
<tr class="never">
- <td class="num">657</td>
+ <td class="num">656</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r">#' # therefore don't run this example on Travis</pre>
</td>
</tr>
<tr class="never">
- <td class="num">658</td>
+ <td class="num">657</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r">#' if (Sys.getenv("TRAVIS") == "") {</pre>
</td>
</tr>
<tr class="never">
- <td class="num">659</td>
+ <td class="num">658</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r">#'</pre>
</td>
</tr>
<tr class="never">
- <td class="num">660</td>
+ <td class="num">659</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r">#' atr &lt;- pai$new("atrazine")</pre>
</td>
</tr>
<tr class="never">
- <td class="num">661</td>
+ <td class="num">660</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r">#' print(atr)</pre>
</td>
</tr>
<tr class="never">
- <td class="num">662</td>
+ <td class="num">661</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r">#' if (!is.null(atr$Picture)) {</pre>
</td>
</tr>
<tr class="never">
- <td class="num">663</td>
+ <td class="num">662</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r">#' plot(atr)</pre>
</td>
</tr>
<tr class="never">
- <td class="num">664</td>
+ <td class="num">663</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r">#' }</pre>
</td>
</tr>
<tr class="never">
- <td class="num">665</td>
+ <td class="num">664</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r">#'</pre>
</td>
</tr>
<tr class="never">
- <td class="num">666</td>
+ <td class="num">665</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r">#' }</pre>
</td>
</tr>
<tr class="never">
- <td class="num">667</td>
+ <td class="num">666</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r">pai &lt;- R6Class("pai",</pre>
</td>
</tr>
<tr class="never">
- <td class="num">668</td>
+ <td class="num">667</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> inherit = chent,</pre>
</td>
</tr>
<tr class="never">
- <td class="num">669</td>
+ <td class="num">668</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> public = list(</pre>
</td>
</tr>
<tr class="never">
- <td class="num">670</td>
+ <td class="num">669</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"></pre>
</td>
</tr>
<tr class="never">
- <td class="num">671</td>
+ <td class="num">670</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' @field iso ISO common name of the active ingredient according to ISO 1750</pre>
</td>
</tr>
<tr class="never">
- <td class="num">672</td>
+ <td class="num">671</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> iso = NULL,</pre>
</td>
</tr>
<tr class="never">
- <td class="num">673</td>
+ <td class="num">672</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"></pre>
</td>
</tr>
<tr class="never">
- <td class="num">674</td>
+ <td class="num">673</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' @field bcpc Information retrieved from the BCPC compendium available online</pre>
</td>
</tr>
<tr class="never">
- <td class="num">675</td>
+ <td class="num">674</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' at &lt;pesticidecompendium.bcpc.org&gt;</pre>
</td>
</tr>
<tr class="never">
- <td class="num">676</td>
+ <td class="num">675</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> bcpc = NULL,</pre>
</td>
</tr>
<tr class="never">
- <td class="num">677</td>
+ <td class="num">676</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"></pre>
</td>
</tr>
<tr class="never">
- <td class="num">678</td>
+ <td class="num">677</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' @description</pre>
</td>
</tr>
<tr class="never">
- <td class="num">679</td>
+ <td class="num">678</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' Create a new pai object</pre>
</td>
</tr>
<tr class="never">
- <td class="num">680</td>
+ <td class="num">679</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' @param iso The ISO common name to be used in the query of the</pre>
</td>
</tr>
<tr class="never">
- <td class="num">681</td>
+ <td class="num">680</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' BCPC compendium</pre>
</td>
</tr>
<tr class="never">
- <td class="num">682</td>
+ <td class="num">681</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' @param identifier Alternative identifier used for querying pubchem</pre>
</td>
</tr>
<tr class="never">
- <td class="num">683</td>
+ <td class="num">682</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' @param smiles Optional user provided SMILES code</pre>
</td>
</tr>
<tr class="never">
- <td class="num">684</td>
+ <td class="num">683</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' @param inchikey Optional user provided InChI Key</pre>
</td>
</tr>
<tr class="never">
- <td class="num">685</td>
+ <td class="num">684</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' @param bcpc Should the BCPC compendium be queried?</pre>
</td>
</tr>
<tr class="never">
- <td class="num">686</td>
+ <td class="num">685</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' @param pubchem Should an attempt be made to retrieve chemical</pre>
</td>
</tr>
<tr class="never">
- <td class="num">687</td>
+ <td class="num">686</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' information from PubChem via the webchem package?</pre>
</td>
</tr>
<tr class="never">
- <td class="num">688</td>
+ <td class="num">687</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' @param pubchem_from Possibility to select the argument</pre>
</td>
</tr>
<tr class="never">
- <td class="num">689</td>
+ <td class="num">688</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' that is used to query pubchem</pre>
</td>
</tr>
<tr class="never">
- <td class="num">690</td>
+ <td class="num">689</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' @param rdkit Should an attempt be made to retrieve chemical</pre>
</td>
</tr>
<tr class="never">
- <td class="num">691</td>
+ <td class="num">690</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' information from a local rdkit installation via python</pre>
</td>
</tr>
<tr class="never">
- <td class="num">692</td>
+ <td class="num">691</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' and the reticulate package?</pre>
</td>
</tr>
<tr class="never">
- <td class="num">693</td>
+ <td class="num">692</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' @param template An optional SMILES code to be used as template for RDKit</pre>
</td>
</tr>
<tr class="never">
- <td class="num">694</td>
+ <td class="num">693</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' @param chyaml Should we look for a identifier.yaml file in the working</pre>
</td>
</tr>
<tr class="never">
- <td class="num">695</td>
+ <td class="num">694</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> initialize = function(iso, identifier = iso,</pre>
</td>
</tr>
<tr class="never">
- <td class="num">696</td>
+ <td class="num">695</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> smiles = NULL, inchikey = NULL, bcpc = TRUE,</pre>
</td>
</tr>
<tr class="never">
- <td class="num">697</td>
+ <td class="num">696</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> pubchem = TRUE, pubchem_from = 'auto',</pre>
</td>
</tr>
<tr class="never">
- <td class="num">698</td>
+ <td class="num">697</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> rdkit = TRUE, template = NULL,</pre>
</td>
</tr>
<tr class="never">
- <td class="num">699</td>
+ <td class="num">698</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> chyaml = FALSE)</pre>
</td>
</tr>
<tr class="never">
- <td class="num">700</td>
+ <td class="num">699</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> {</pre>
</td>
</tr>
<tr class="never">
- <td class="num">701</td>
+ <td class="num">700</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"></pre>
</td>
</tr>
<tr class="covered">
- <td class="num">702</td>
+ <td class="num">701</td>
<td class="coverage">1<em>x</em></td>
<td class="col-sm-12">
<pre class="language-r"> if (!is.null(inchikey)) {</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">703</td>
+ <td class="num">702</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> self$inchikey = inchikey</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">704</td>
+ <td class="num">703</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> attr(self$inchikey, "source") &lt;- "user"</pre>
</td>
</tr>
<tr class="never">
- <td class="num">705</td>
+ <td class="num">704</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> }</pre>
</td>
</tr>
<tr class="never">
- <td class="num">706</td>
+ <td class="num">705</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"></pre>
</td>
</tr>
<tr class="covered">
- <td class="num">707</td>
+ <td class="num">706</td>
<td class="coverage">1<em>x</em></td>
<td class="col-sm-12">
<pre class="language-r"> if (!missing(iso) &amp; bcpc) {</pre>
</td>
</tr>
<tr class="covered">
- <td class="num">708</td>
+ <td class="num">707</td>
<td class="coverage">1<em>x</em></td>
<td class="col-sm-12">
- <pre class="language-r"> message("BCPC:")</pre>
+ <pre class="language-r"> message("Querying BCPC for ", identifier, " ...")</pre>
</td>
</tr>
<tr class="covered">
- <td class="num">709</td>
+ <td class="num">708</td>
<td class="coverage">1<em>x</em></td>
<td class="col-sm-12">
<pre class="language-r"> bcpc_result = webchem::bcpc_query(identifier, from = "name")</pre>
</td>
</tr>
<tr class="never">
- <td class="num">710</td>
+ <td class="num">709</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"></pre>
</td>
</tr>
<tr class="never">
- <td class="num">711</td>
+ <td class="num">710</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> # Use first element of list, as we passed a query of length one</pre>
</td>
</tr>
<tr class="covered">
- <td class="num">712</td>
+ <td class="num">711</td>
<td class="coverage">1<em>x</em></td>
<td class="col-sm-12">
<pre class="language-r"> if (is.na(bcpc_result[[1]][1])) {</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">713</td>
+ <td class="num">712</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> message("Common name ", identifier, " is not known at the BCPC compendium, trying PubChem")</pre>
</td>
</tr>
<tr class="never">
- <td class="num">714</td>
+ <td class="num">713</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> } else {</pre>
</td>
</tr>
<tr class="covered">
- <td class="num">715</td>
+ <td class="num">714</td>
<td class="coverage">1<em>x</em></td>
<td class="col-sm-12">
<pre class="language-r"> self$bcpc = bcpc_result[[1]]</pre>
</td>
</tr>
<tr class="covered">
- <td class="num">716</td>
+ <td class="num">715</td>
<td class="coverage">1<em>x</em></td>
<td class="col-sm-12">
<pre class="language-r"> self$iso = self$bcpc$cname</pre>
</td>
</tr>
<tr class="covered">
- <td class="num">717</td>
+ <td class="num">716</td>
<td class="coverage">1<em>x</em></td>
<td class="col-sm-12">
<pre class="language-r"> attr(self$iso, "source") &lt;- "bcpc"</pre>
</td>
</tr>
<tr class="covered">
- <td class="num">718</td>
+ <td class="num">717</td>
<td class="coverage">1<em>x</em></td>
<td class="col-sm-12">
<pre class="language-r"> attr(self$iso, "status") &lt;- self$bcpc$status</pre>
</td>
</tr>
<tr class="covered">
- <td class="num">719</td>
+ <td class="num">718</td>
<td class="coverage">1<em>x</em></td>
<td class="col-sm-12">
<pre class="language-r"> bcpc_ik = self$bcpc$inchikey</pre>
</td>
</tr>
<tr class="covered">
- <td class="num">720</td>
+ <td class="num">719</td>
<td class="coverage">1<em>x</em></td>
<td class="col-sm-12">
<pre class="language-r"> if (length(bcpc_ik) == 1 &amp;&amp; !is.na(bcpc_ik)) {</pre>
</td>
</tr>
<tr class="covered">
- <td class="num">721</td>
+ <td class="num">720</td>
<td class="coverage">1<em>x</em></td>
<td class="col-sm-12">
<pre class="language-r"> if (is.null(self$inchikey)) {</pre>
</td>
</tr>
<tr class="covered">
- <td class="num">722</td>
+ <td class="num">721</td>
<td class="coverage">1<em>x</em></td>
<td class="col-sm-12">
<pre class="language-r"> self$inchikey = substr(self$bcpc$inchikey, 1, 27)</pre>
</td>
</tr>
<tr class="covered">
- <td class="num">723</td>
+ <td class="num">722</td>
<td class="coverage">1<em>x</em></td>
<td class="col-sm-12">
<pre class="language-r"> attr(self$inchikey, "source") &lt;- "bcpc"</pre>
</td>
</tr>
<tr class="never">
- <td class="num">724</td>
+ <td class="num">723</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> } else {</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">725</td>
+ <td class="num">724</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> if (bcpc_ik == self$inchikey) {</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">726</td>
+ <td class="num">725</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> attr(self$inchikey, "source") = c(attr(self$inchikey, "source"), "bcpc")</pre>
</td>
</tr>
<tr class="never">
- <td class="num">727</td>
+ <td class="num">726</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> } else {</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">728</td>
+ <td class="num">727</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> warning("InChIKey ", self$inchikey, " differs from ", bcpc_ik, " obtained from bcpc.org")</pre>
</td>
</tr>
<tr class="never">
- <td class="num">729</td>
+ <td class="num">728</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> }</pre>
</td>
</tr>
<tr class="never">
- <td class="num">730</td>
+ <td class="num">729</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> }</pre>
</td>
</tr>
<tr class="never">
- <td class="num">731</td>
+ <td class="num">730</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> }</pre>
</td>
</tr>
<tr class="never">
- <td class="num">732</td>
+ <td class="num">731</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> }</pre>
</td>
</tr>
<tr class="never">
- <td class="num">733</td>
+ <td class="num">732</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> }</pre>
</td>
</tr>
<tr class="never">
- <td class="num">734</td>
+ <td class="num">733</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"></pre>
</td>
</tr>
<tr class="never">
- <td class="num">735</td>
+ <td class="num">734</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> # Set pubchem_from if not specified</pre>
</td>
</tr>
<tr class="covered">
- <td class="num">736</td>
+ <td class="num">735</td>
<td class="coverage">1<em>x</em></td>
<td class="col-sm-12">
<pre class="language-r"> if (pubchem_from == 'auto') {</pre>
</td>
</tr>
<tr class="covered">
- <td class="num">737</td>
+ <td class="num">736</td>
<td class="coverage">1<em>x</em></td>
<td class="col-sm-12">
<pre class="language-r"> pubchem_from = 'name'</pre>
</td>
</tr>
<tr class="covered">
- <td class="num">738</td>
+ <td class="num">737</td>
<td class="coverage">1<em>x</em></td>
<td class="col-sm-12">
<pre class="language-r"> if (!is.null(self$inchikey)) {</pre>
</td>
</tr>
<tr class="covered">
- <td class="num">739</td>
+ <td class="num">738</td>
<td class="coverage">1<em>x</em></td>
<td class="col-sm-12">
<pre class="language-r"> pubchem_from = 'inchikey'</pre>
</td>
</tr>
<tr class="never">
- <td class="num">740</td>
+ <td class="num">739</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> }</pre>
</td>
</tr>
<tr class="never">
- <td class="num">741</td>
+ <td class="num">740</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> }</pre>
</td>
</tr>
<tr class="never">
- <td class="num">742</td>
+ <td class="num">741</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"></pre>
</td>
</tr>
<tr class="covered">
- <td class="num">743</td>
+ <td class="num">742</td>
<td class="coverage">1<em>x</em></td>
<td class="col-sm-12">
<pre class="language-r"> super$initialize(identifier = identifier,</pre>
</td>
</tr>
<tr class="covered">
- <td class="num">744</td>
+ <td class="num">743</td>
<td class="coverage">1<em>x</em></td>
<td class="col-sm-12">
<pre class="language-r"> smiles = smiles, inchikey = self$inchikey,</pre>
</td>
</tr>
<tr class="covered">
- <td class="num">745</td>
+ <td class="num">744</td>
<td class="coverage">1<em>x</em></td>
<td class="col-sm-12">
<pre class="language-r"> pubchem = pubchem, pubchem_from = pubchem_from,</pre>
</td>
</tr>
<tr class="covered">
- <td class="num">746</td>
+ <td class="num">745</td>
<td class="coverage">1<em>x</em></td>
<td class="col-sm-12">
<pre class="language-r"> rdkit = rdkit, template = template, chyaml = chyaml)</pre>
</td>
</tr>
<tr class="never">
- <td class="num">747</td>
+ <td class="num">746</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"></pre>
</td>
</tr>
<tr class="covered">
- <td class="num">748</td>
+ <td class="num">747</td>
<td class="coverage">1<em>x</em></td>
<td class="col-sm-12">
<pre class="language-r"> invisible(self)</pre>
</td>
</tr>
<tr class="never">
- <td class="num">749</td>
+ <td class="num">748</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> }</pre>
</td>
</tr>
<tr class="never">
- <td class="num">750</td>
+ <td class="num">749</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> )</pre>
</td>
</tr>
<tr class="never">
- <td class="num">751</td>
+ <td class="num">750</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r">)</pre>
</td>
</tr>
<tr class="never">
- <td class="num">752</td>
+ <td class="num">751</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"></pre>
</td>
</tr>
<tr class="never">
- <td class="num">753</td>
+ <td class="num">752</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r">#' Printing method for pai objects (pesticidal active ingredients)</pre>
</td>
</tr>
<tr class="never">
- <td class="num">754</td>
+ <td class="num">753</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r">#'</pre>
</td>
</tr>
<tr class="never">
- <td class="num">755</td>
+ <td class="num">754</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r">#' @param x The chent object to be printed</pre>
</td>
</tr>
<tr class="never">
- <td class="num">756</td>
+ <td class="num">755</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r">#' @param ... Further arguments for compatibility with the S3 method</pre>
</td>
</tr>
<tr class="never">
- <td class="num">757</td>
+ <td class="num">756</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r">#' @export</pre>
</td>
</tr>
<tr class="never">
- <td class="num">758</td>
+ <td class="num">757</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r">print.pai = function(x, ...) {</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">759</td>
+ <td class="num">758</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> cat("&lt;pai&gt; with ISO common name $iso", x$iso, "\n")</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">760</td>
+ <td class="num">759</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> print.chent(x)</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">761</td>
+ <td class="num">760</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> if (length(x$TPs) &gt; 0) {</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">762</td>
+ <td class="num">761</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> cat("\nTransformation products:\n")</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">763</td>
+ <td class="num">762</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> print(x$TPs)</pre>
</td>
</tr>
<tr class="never">
- <td class="num">764</td>
+ <td class="num">763</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> }</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">765</td>
+ <td class="num">764</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> if (nrow(x$transformations) &gt; 0) {</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">766</td>
+ <td class="num">765</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> cat("\nTransformations:\n")</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">767</td>
+ <td class="num">766</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> print(x$transformations)</pre>
</td>
</tr>
<tr class="never">
- <td class="num">768</td>
+ <td class="num">767</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> }</pre>
</td>
</tr>
<tr class="never">
- <td class="num">769</td>
+ <td class="num">768</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r">}</pre>
</td>
</tr>
<tr class="never">
- <td class="num">770</td>
+ <td class="num">769</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"></pre>
</td>
</tr>
<tr class="never">
- <td class="num">771</td>
+ <td class="num">770</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r">#' @title R6 class for a plant protection product with at least one active ingredient</pre>
</td>
</tr>
<tr class="never">
- <td class="num">772</td>
+ <td class="num">771</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r">#'</pre>
</td>
</tr>
<tr class="never">
- <td class="num">773</td>
+ <td class="num">772</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r">#' @description Contains basic information about the active ingredients in the</pre>
</td>
</tr>
<tr class="never">
- <td class="num">774</td>
+ <td class="num">773</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r">#' product</pre>
</td>
</tr>
<tr class="never">
- <td class="num">775</td>
+ <td class="num">774</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r">#'</pre>
</td>
</tr>
<tr class="never">
- <td class="num">776</td>
+ <td class="num">775</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r">#' @export</pre>
</td>
</tr>
<tr class="never">
- <td class="num">777</td>
+ <td class="num">776</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r">#' @format An [R6::R6Class] generator object.</pre>
</td>
</tr>
<tr class="never">
- <td class="num">778</td>
+ <td class="num">777</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r">ppp &lt;- R6Class("ppp",</pre>
</td>
</tr>
<tr class="never">
- <td class="num">779</td>
+ <td class="num">778</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> public = list(</pre>
</td>
</tr>
<tr class="never">
- <td class="num">780</td>
+ <td class="num">779</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"></pre>
</td>
</tr>
<tr class="never">
- <td class="num">781</td>
+ <td class="num">780</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' @field name The name of the product</pre>
</td>
</tr>
<tr class="never">
- <td class="num">782</td>
+ <td class="num">781</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> name = NULL,</pre>
</td>
</tr>
<tr class="never">
- <td class="num">783</td>
+ <td class="num">782</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"></pre>
</td>
</tr>
<tr class="never">
- <td class="num">784</td>
+ <td class="num">783</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' @field ais A list of active ingredients</pre>
</td>
</tr>
<tr class="never">
- <td class="num">785</td>
+ <td class="num">784</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> ais = list(),</pre>
</td>
</tr>
<tr class="never">
- <td class="num">786</td>
+ <td class="num">785</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"></pre>
</td>
</tr>
<tr class="never">
- <td class="num">787</td>
+ <td class="num">786</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' @field concentrations The concentration of the ais</pre>
</td>
</tr>
<tr class="never">
- <td class="num">788</td>
+ <td class="num">787</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> concentrations = NULL,</pre>
</td>
</tr>
<tr class="never">
- <td class="num">789</td>
+ <td class="num">788</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"></pre>
</td>
</tr>
<tr class="never">
- <td class="num">790</td>
+ <td class="num">789</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' @field concentration_units Defaults to g/L</pre>
</td>
</tr>
<tr class="never">
- <td class="num">791</td>
+ <td class="num">790</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> concentration_units = NULL,</pre>
</td>
</tr>
<tr class="never">
- <td class="num">792</td>
+ <td class="num">791</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"></pre>
</td>
</tr>
<tr class="never">
- <td class="num">793</td>
+ <td class="num">792</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' @field density The density of the product</pre>
</td>
</tr>
<tr class="never">
- <td class="num">794</td>
+ <td class="num">793</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> density = NULL,</pre>
</td>
</tr>
<tr class="never">
- <td class="num">795</td>
+ <td class="num">794</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"></pre>
</td>
</tr>
<tr class="never">
- <td class="num">796</td>
+ <td class="num">795</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' @field density_units Defaults to g/L</pre>
</td>
</tr>
<tr class="never">
- <td class="num">797</td>
+ <td class="num">796</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> density_units = "g/L",</pre>
</td>
</tr>
<tr class="never">
- <td class="num">798</td>
+ <td class="num">797</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"></pre>
</td>
</tr>
<tr class="never">
- <td class="num">799</td>
+ <td class="num">798</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' @description</pre>
</td>
</tr>
<tr class="never">
- <td class="num">800</td>
+ <td class="num">799</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' Creates a new instance of this [R6][R6::R6Class] class.</pre>
</td>
</tr>
<tr class="never">
- <td class="num">801</td>
+ <td class="num">800</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' @param name The name of the product</pre>
</td>
</tr>
<tr class="never">
- <td class="num">802</td>
+ <td class="num">801</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' @param ... Identifiers of the active ingredients</pre>
</td>
</tr>
<tr class="never">
- <td class="num">803</td>
+ <td class="num">802</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' @param concentrations Concentrations of the active ingredients</pre>
</td>
</tr>
<tr class="never">
- <td class="num">804</td>
+ <td class="num">803</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' @param concentration_units Defaults to g/L</pre>
</td>
</tr>
<tr class="never">
- <td class="num">805</td>
+ <td class="num">804</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' @param density The density</pre>
</td>
</tr>
<tr class="never">
- <td class="num">806</td>
+ <td class="num">805</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> #' @param density_units Defaults to g/L</pre>
</td>
</tr>
<tr class="never">
- <td class="num">807</td>
+ <td class="num">806</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> initialize = function(name, ..., concentrations, concentration_units = "g/L",</pre>
</td>
</tr>
<tr class="never">
- <td class="num">808</td>
+ <td class="num">807</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> density = 1000, density_units = "g/L")</pre>
</td>
</tr>
<tr class="never">
- <td class="num">809</td>
+ <td class="num">808</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> {</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">810</td>
+ <td class="num">809</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> self$name &lt;- name</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">811</td>
+ <td class="num">810</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> self$ais &lt;- list(...)</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">812</td>
+ <td class="num">811</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> self$concentrations &lt;- concentrations</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">813</td>
+ <td class="num">812</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> self$density &lt;- density</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">814</td>
+ <td class="num">813</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> self$density_units &lt;- density_units</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">815</td>
+ <td class="num">814</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> names(self$concentrations) &lt;- names(self$ais)</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">816</td>
+ <td class="num">815</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> self$concentration_units &lt;- concentration_units</pre>
</td>
</tr>
<tr class="never">
- <td class="num">817</td>
+ <td class="num">816</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> }</pre>
</td>
</tr>
<tr class="never">
- <td class="num">818</td>
+ <td class="num">817</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"> )</pre>
</td>
</tr>
<tr class="never">
- <td class="num">819</td>
+ <td class="num">818</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r">)</pre>
</td>
</tr>
<tr class="never">
- <td class="num">820</td>
+ <td class="num">819</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"></pre>
</td>
</tr>
<tr class="never">
- <td class="num">821</td>
+ <td class="num">820</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r">#' Printing method for ppp objects (plant protection products)</pre>
</td>
</tr>
<tr class="never">
- <td class="num">822</td>
+ <td class="num">821</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r">#'</pre>
</td>
</tr>
<tr class="never">
- <td class="num">823</td>
+ <td class="num">822</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r">#' @param x The chent object to be printed</pre>
</td>
</tr>
<tr class="never">
- <td class="num">824</td>
+ <td class="num">823</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r">#' @param ... Further arguments for compatibility with the S3 method</pre>
</td>
</tr>
<tr class="never">
- <td class="num">825</td>
+ <td class="num">824</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r">#' @export</pre>
</td>
</tr>
<tr class="never">
- <td class="num">826</td>
+ <td class="num">825</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r">print.ppp = function(x, ...) {</pre>
</td>
</tr>
<tr class="missed">
- <td class="num">827</td>
+ <td class="num">826</td>
<td class="coverage">!</td>
<td class="col-sm-12">
<pre class="language-r"> cat("&lt;pp&gt; named", x$name, "\n")</pre>
</td>
</tr>
<tr class="never">
- <td class="num">828</td>
+ <td class="num">827</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r">}</pre>
</td>
</tr>
<tr class="never">
- <td class="num">829</td>
+ <td class="num">828</td>
<td class="coverage"></td>
<td class="col-sm-12">
<pre class="language-r"># vim: set ts=2 sw=2 expandtab:</pre>
diff --git a/tests/testthat.R b/tests/testthat.R
index a7a46eb..836723f 100644
--- a/tests/testthat.R
+++ b/tests/testthat.R
@@ -1,3 +1,11 @@
+# This file is part of the standard setup for testthat.
+# It is recommended that you do not modify it.
+#
+# Where should you do additional test configuration?
+# Learn more about the roles of various files in:
+# * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
+# * https://testthat.r-lib.org/articles/special-files.html
+
library(testthat)
library(chents)
diff --git a/tests/testthat/_snaps/chent.md b/tests/testthat/_snaps/chent.md
new file mode 100644
index 0000000..b214852
--- /dev/null
+++ b/tests/testthat/_snaps/chent.md
@@ -0,0 +1,18 @@
+# We can initialise an object and add information
+
+ Code
+ print(oct)
+ Output
+ <chent>
+ Identifier $identifier 1-octanol
+ InChI Key $inchikey KBPLFHHGFOOTCA-UHFFFAOYSA-N
+ SMILES string $smiles:
+ user PubChem
+ "CCCCCCCCO" "CCCCCCCCO"
+ Molecular weight $mw: 130.2
+ PubChem synonyms (up to 10):
+ [1] "1-octanol" "Octan-1-ol" "111-87-5"
+ [4] "N-octanol" "Octyl alcohol" "caprylic alcohol"
+ [7] "n-Octyl alcohol" "Heptyl carbinol" "1-Hydroxyoctane"
+ [10] "Primary octyl alcohol"
+
diff --git a/tests/testthat/test_chent.R b/tests/testthat/test_chent.R
index 4546423..1f4a186 100644
--- a/tests/testthat/test_chent.R
+++ b/tests/testthat/test_chent.R
@@ -1,29 +1,21 @@
-context("Generation of chent objects")
-
# Check if we can use RDKit
skip_if_no_rdkit <- function() {
if (!chents:::rdkit_available) skip("RDKit is not available via reticulate")
}
-oct <- chent$new("1-octanol", smiles = "CCCCCCCCO", rdkit = FALSE, pubchem = FALSE, chyaml = FALSE)
-
-test_that("We can initialise an object only with identifier and SMILES code", {
+test_that("We can initialise an object and add information", {
+ oct <- chent$new("1-octanol", smiles = "CCCCCCCCO", rdkit = FALSE, pubchem = FALSE, chyaml = FALSE)
expect_equal(oct$identifier, c(X1.octanol = "1-octanol")) # The name of the identifier is generated using make.names()
expect_equal(oct$inchikey, structure(NA, source = "user"))
expect_equal(oct$smiles, c(user = "CCCCCCCCO"))
-})
-
-test_that("We can generate a chent object from SMILES using RDKit", {
- skip_if_no_rdkit()
- oct$get_rdkit()
- expect_equivalent(round(oct$mw, 2), 130.23)
-})
-
-test_that("We can add information retrieved from PubChem via webchem", {
- expect_warning(oct$try_pubchem(), "Overwriting uninitialized InChIKey")
- expect_equivalent(round(oct$mw, 2), 130.23)
- ik = "KBPLFHHGFOOTCA-UHFFFAOYSA-N"
- attr(ik, "source") <- "pubchem"
- expect_equal(oct$inchikey, ik)
+ oct$try_pubchem() |>
+ expect_message("Querying PubChem for name 1-octanol") |>
+ expect_warning("Overwriting uninitialized InChIKey")
+ expect_equal(oct$inchikey, structure("KBPLFHHGFOOTCA-UHFFFAOYSA-N", source = "pubchem"))
expect_equal(oct$smiles[["PubChem"]], "CCCCCCCCO")
+ skip_if_no_rdkit()
+ oct$get_rdkit() |>
+ expect_message("Get chemical information from RDKit using user SMILES")
+ expect_equal(round(oct$mw, 2), structure(130.23, source = "pubchem"))
+ expect_snapshot(print(oct))
})
diff --git a/tests/testthat/test_pai.R b/tests/testthat/test_pai.R
index f38672d..0d5264a 100644
--- a/tests/testthat/test_pai.R
+++ b/tests/testthat/test_pai.R
@@ -1,25 +1,16 @@
-# For manual use of this file
-require(chents)
-require(testthat)
-
-context("Generation of pai objects")
-
test_that("a pai object is correctly generated", {
skip_on_travis() # server certificate verification failed in curl_fetch_memory()
- glyphosate <- pai$new("glyphosate")
+ {glyphosate <- pai$new("glyphosate")} |>
+ expect_message("Querying BCPC for glyphosate") |>
+ expect_message("Querying PubChem for inchikey ") |>
+ expect_message("Get chemical information from RDKit using PubChem SMILES")
- # This did not give results at BCPC in previous times, so it was used to test
- # the corresponding warning.
- #bc <- pai$new("benzalkonium chloride")
-
- expect_equivalent(glyphosate$bcpc$cas, "1071-83-6")
- expect_equivalent(glyphosate$bcpc$formula, "C3H8NO5P")
- expect_equivalent(glyphosate$bcpc$iupac_name, "N-(phosphonomethyl)glycine")
+ expect_equal(glyphosate$bcpc$cas, "1071-83-6")
+ expect_equal(glyphosate$bcpc$formula, "C3H8NO5P")
+ expect_equal(glyphosate$bcpc$iupac_name, "N-(phosphonomethyl)glycine")
expect_equal(names(glyphosate$identifier), "glyphosate")
ik = "XDDAORKBJWWYJS-UHFFFAOYSA-N"
- attr(ik, "source") <- c("bcpc", "pubchem")
- expect_equal(glyphosate$inchikey, ik)
- expect_equivalent(round(glyphosate$mw, 2), 169.07)
- smiles <- "C(C(=O)O)NCP(=O)(O)O"
- expect_equal(glyphosate$smiles[["PubChem"]], smiles)
+ expect_equal(glyphosate$inchikey, structure("XDDAORKBJWWYJS-UHFFFAOYSA-N", source = c("bcpc", "pubchem")))
+ expect_equal(round(glyphosate$mw, 2), structure(169.07, source = "pubchem"))
+ expect_equal(glyphosate$smiles[["PubChem"]], "C(C(=O)O)NCP(=O)(O)O")
})

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