diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2022-05-18 21:26:17 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2022-05-18 21:26:17 +0200 |
| commit | 91c5db736a4d3f2290a0cc5698fb4e35ae7bda59 (patch) | |
| tree | 8e9e34d18f055936172329c1248e6e2ff136bff9 /docs/reference/mkinmod.html | |
| parent | ea57db98cef3fb882f7bd9656b44f270e7bded38 (diff) | |
Remove outdated comment in FOCUS L vignette, update docs
This also adds the first benchmark results obtained on my laptop system
Diffstat (limited to 'docs/reference/mkinmod.html')
| -rw-r--r-- | docs/reference/mkinmod.html | 8 |
1 files changed, 5 insertions, 3 deletions
diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index 72a9ea52..3a29b39b 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -258,6 +258,7 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p> <span class="r-in"></span> <span class="r-in"><span class="co"># \dontrun{</span></span> <span class="r-in"> <span class="va">fit_sfo_sfo</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, solution_type <span class="op">=</span> <span class="st">"deSolve"</span><span class="op">)</span></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span> <span class="r-in"></span> <span class="r-in"> <span class="co"># Now supplying compound names used for plotting, and write to user defined location</span></span> <span class="r-in"> <span class="co"># We need to choose a path outside the session tempdir because this gets removed</span></span> @@ -267,13 +268,14 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p> <span class="r-in"> parent <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span>, full_name <span class="op">=</span> <span class="st">"Test compound"</span><span class="op">)</span>,</span> <span class="r-in"> m1 <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span>, full_name <span class="op">=</span> <span class="st">"Metabolite M1"</span><span class="op">)</span>,</span> <span class="r-in"> name <span class="op">=</span> <span class="st">"SFO_SFO"</span>, dll_dir <span class="op">=</span> <span class="va">DLL_dir</span>, unload <span class="op">=</span> <span class="cn">TRUE</span>, overwrite <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span class="r-msg co"><span class="r-pr">#></span> Copied DLL from /tmp/Rtmp1TiIZY/file1180516cafe4a2.so to /home/jranke/.local/share/mkin/SFO_SFO.so</span> +<span class="r-msg co"><span class="r-pr">#></span> Copied DLL from /tmp/RtmpkcKjUM/file8dd657f864c2.so to /home/jranke/.local/share/mkin/SFO_SFO.so</span> <span class="r-in"><span class="co"># Now we can save the model and restore it in a new session</span></span> <span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/readRDS.html" class="external-link">saveRDS</a></span><span class="op">(</span><span class="va">SFO_SFO.2</span>, file <span class="op">=</span> <span class="st">"~/SFO_SFO.rds"</span><span class="op">)</span></span> <span class="r-in"><span class="co"># Terminate the R session here if you would like to check, and then do</span></span> <span class="r-in"><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://pkgdown.jrwb.de/mkin/">mkin</a></span><span class="op">)</span></span> <span class="r-in"><span class="va">SFO_SFO.3</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/readRDS.html" class="external-link">readRDS</a></span><span class="op">(</span><span class="st">"~/SFO_SFO.rds"</span><span class="op">)</span></span> <span class="r-in"><span class="va">fit_sfo_sfo</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO.3</span>, <span class="va">FOCUS_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, solution_type <span class="op">=</span> <span class="st">"deSolve"</span><span class="op">)</span></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span> <span class="r-in"></span> <span class="r-in"><span class="co"># Show details of creating the C function</span></span> <span class="r-in"><span class="va">SFO_SFO</span> <span class="op"><-</span> <span class="fu">mkinmod</span><span class="op">(</span></span> @@ -319,7 +321,7 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p> <span class="r-out co"><span class="r-pr">#></span> })</span> <span class="r-out co"><span class="r-pr">#></span> return(predicted)</span> <span class="r-out co"><span class="r-pr">#></span> }</span> -<span class="r-out co"><span class="r-pr">#></span> <environment: 0x55555f6c4cd8></span> +<span class="r-out co"><span class="r-pr">#></span> <environment: 0x55cc1a5f8ad8></span> <span class="r-in"></span> <span class="r-in"><span class="co"># If we have several parallel metabolites</span></span> <span class="r-in"><span class="co"># (compare tests/testthat/test_synthetic_data_for_UBA_2014.R)</span></span> @@ -348,7 +350,7 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> |