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-rw-r--r--docs/reference/mccall81_245T.html113
1 files changed, 49 insertions, 64 deletions
diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html
index ce2d40cd..06fcd79e 100644
--- a/docs/reference/mccall81_245T.html
+++ b/docs/reference/mccall81_245T.html
@@ -10,23 +10,27 @@
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@@ -39,7 +43,6 @@
<meta property="og:description" content="Time course of 2,4,5-trichlorophenoxyacetic acid, and the corresponding
2,4,5-trichlorophenol and 2,4,5-trichloroanisole as recovered in diethylether
extracts." />
-<meta name="twitter:card" content="summary" />
@@ -57,7 +60,7 @@
</head>
- <body>
+ <body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -71,7 +74,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.6</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50.2</span>
</span>
</div>
@@ -115,7 +118,12 @@
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
-
+ <li>
+ <a href="http://github.com/jranke/mkin/">
+ <span class="fab fa fab fa-github fa-lg"></span>
+
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+</li>
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</div><!--/.nav-collapse -->
@@ -145,7 +153,7 @@
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
- <p>A dataframe containing the following variables.</p><dl class='dl-horizontal'>
+ <p>A dataframe containing the following variables.</p><dl'>
<dt><code>name</code></dt><dd><p>the name of the compound observed. Note that T245 is used as
an acronym for 2,4,5-T. T245 is a legitimate object name
in R, which is necessary for specifying models using
@@ -159,34 +167,31 @@
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
- <p>McCall P, Vrona SA, Kelley SS (1981) Fate of uniformly carbon-14 ring labeled 2,4,5-Trichlorophenoxyacetic acid and 2,4-dichlorophenoxyacetic acid. J Agric Chem 29, 100-107
+ <p>McCall P, Vrona SA, Kelley SS (1981) Fate of uniformly carbon-14 ring labelled 2,4,5-Trichlorophenoxyacetic acid and 2,4-dichlorophenoxyacetic acid. J Agric Chem 29, 100-107
<a href='http://dx.doi.org/10.1021/jf00103a026'>http://dx.doi.org/10.1021/jf00103a026</a></p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'> <span class='no'>SFO_SFO_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>T245</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"phenol"</span>),
<span class='kw'>phenol</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"anisole"</span>),
<span class='kw'>anisole</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> <span class='co'># \dontrun{</span>
- <span class='no'>fit.1</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO_SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>), <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>fit.1</span>)$<span class='no'>bpar</span></div><div class='output co'>#&gt; <span class='warning'>Warning: NaNs wurden erzeugt</span></div><div class='output co'>#&gt; Estimate se_notrans t value Pr(&gt;t) Lower
-#&gt; T245_0 1.038550e+02 2.1508110557 48.286452 3.542232e-18 99.246062215
-#&gt; k_T245_sink 1.636106e-02 NaN NaN NaN 0.012661558
-#&gt; k_T245_phenol 2.700936e-02 NaN NaN NaN 0.024487315
-#&gt; k_phenol_sink 1.788604e-10 NaN NaN NaN 0.000000000
-#&gt; k_phenol_anisole 4.050581e-01 0.1053801116 3.843781 7.970202e-04 0.218013982
-#&gt; k_anisole_sink 6.678742e-03 0.0006205844 10.762020 9.428076e-09 0.005370739
-#&gt; sigma 2.514628e+00 0.3383670685 7.431657 1.054101e-06 1.706607296
-#&gt; Upper
-#&gt; T245_0 1.084640e+02
-#&gt; k_T245_sink 2.114150e-02
-#&gt; k_T245_phenol 2.979116e-02
-#&gt; k_phenol_sink Inf
-#&gt; k_phenol_anisole 7.525759e-01
-#&gt; k_anisole_sink 8.305299e-03
-#&gt; sigma 3.322649e+00</div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.1</span>)</div><div class='output co'>#&gt; $ff
-#&gt; T245_sink T245_phenol phenol_sink phenol_anisole anisole_sink
-#&gt; 3.772401e-01 6.227599e-01 4.415672e-10 1.000000e+00 1.000000e+00
-#&gt;
-#&gt; $SFORB
-#&gt; logical(0)
+ <span class='no'>fit.1</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO_SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>), <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>fit.1</span>)$<span class='no'>bpar</span></div><div class='output co'>#&gt; Estimate se_notrans t value Pr(&gt;t)
+#&gt; T245_0 1.038550e+02 2.184707514 47.537272 4.472189e-18
+#&gt; k_T245 4.337042e-02 0.001898397 22.845818 2.276912e-13
+#&gt; k_phenol 4.050581e-01 0.298699428 1.356073 9.756994e-02
+#&gt; k_anisole 6.678742e-03 0.000802144 8.326114 2.623179e-07
+#&gt; f_T245_to_phenol 6.227599e-01 0.398534167 1.562626 6.949418e-02
+#&gt; f_phenol_to_anisole 1.000000e+00 0.671844168 1.488440 7.867794e-02
+#&gt; sigma 2.514628e+00 0.490755943 5.123989 6.233164e-05
+#&gt; Lower Upper
+#&gt; T245_0 99.246061371 1.084640e+02
+#&gt; k_T245 0.039631621 4.746194e-02
+#&gt; k_phenol 0.218013878 7.525762e-01
+#&gt; k_anisole 0.005370739 8.305299e-03
+#&gt; f_T245_to_phenol 0.547559082 6.924813e-01
+#&gt; f_phenol_to_anisole 0.000000000 1.000000e+00
+#&gt; sigma 1.706607296 3.322649e+00</div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.1</span>)</div><div class='output co'>#&gt; $ff
+#&gt; T245_phenol T245_sink phenol_anisole phenol_sink
+#&gt; 6.227599e-01 3.772401e-01 1.000000e+00 1.748047e-10
#&gt;
#&gt; $distimes
#&gt; DT50 DT90
@@ -196,42 +201,22 @@
#&gt; </div><div class='input'> <span class='co'># k_phenol_sink is really small, therefore fix it to zero</span>
<span class='no'>fit.2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO_SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>),
<span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_phenol_sink</span> <span class='kw'>=</span> <span class='fl'>0</span>),
- <span class='kw'>fixed_parms</span> <span class='kw'>=</span> <span class='st'>"k_phenol_sink"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>fit.2</span>)$<span class='no'>bpar</span></div><div class='output co'>#&gt; Estimate se_notrans t value Pr(&gt;t) Lower
-#&gt; T245_0 1.038550e+02 2.1623653063 48.028441 4.993105e-19 99.271025146
-#&gt; k_T245_sink 1.636106e-02 0.0019676255 8.315130 1.673674e-07 0.012679148
-#&gt; k_T245_phenol 2.700936e-02 0.0012421966 21.743224 1.314080e-13 0.024500319
-#&gt; k_phenol_anisole 4.050581e-01 0.1177235488 3.440757 1.679237e-03 0.218746679
-#&gt; k_anisole_sink 6.678742e-03 0.0006829745 9.778904 1.872892e-08 0.005377084
-#&gt; sigma 2.514628e+00 0.3790944250 6.633250 2.875782e-06 1.710983655
-#&gt; Upper
-#&gt; T245_0 108.43904395
-#&gt; k_T245_sink 0.02111217
-#&gt; k_T245_phenol 0.02977535
-#&gt; k_phenol_anisole 0.75005504
-#&gt; k_anisole_sink 0.00829550
-#&gt; sigma 3.31827222</div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.1</span>)</div><div class='output co'>#&gt; $ff
-#&gt; T245_sink T245_phenol phenol_sink phenol_anisole anisole_sink
-#&gt; 3.772401e-01 6.227599e-01 4.415672e-10 1.000000e+00 1.000000e+00
-#&gt;
-#&gt; $SFORB
-#&gt; logical(0)
+ <span class='kw'>fixed_parms</span> <span class='kw'>=</span> <span class='st'>"k_phenol_sink"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#&gt; <span class='warning'>Warning: Initial parameter(s) k_phenol_sink not used in the model</span></div><div class='output co'>#&gt; <span class='error'>Error in data.frame(value = c(state.ini.fixed, parms.fixed)): Zeilennamen enthalten fehlende Werte</span></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>fit.2</span>)$<span class='no'>bpar</span></div><div class='output co'>#&gt; <span class='error'>Error in summary(fit.2): Objekt 'fit.2' nicht gefunden</span></div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.1</span>)</div><div class='output co'>#&gt; $ff
+#&gt; T245_phenol T245_sink phenol_anisole phenol_sink
+#&gt; 6.227599e-01 3.772401e-01 1.000000e+00 1.748047e-10
#&gt;
#&gt; $distimes
#&gt; DT50 DT90
#&gt; T245 15.982025 53.09114
#&gt; phenol 1.711229 5.68458
#&gt; anisole 103.784092 344.76329
-#&gt; </div><div class='input'> <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>fit.2</span>)</div><div class='img'><img src='mccall81_245T-1.png' alt='' width='700' height='433' /></div><div class='input'> # }
+#&gt; </div><div class='input'> <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>fit.2</span>)</div><div class='output co'>#&gt; <span class='error'>Error in identical(fit$err_mod, "const"): Objekt 'fit.2' nicht gefunden</span></div><div class='input'> # }
</div></pre>
</div>
- <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
- <h2>Contents</h2>
- <ul class="nav nav-pills nav-stacked">
- <li><a href="#format">Format</a></li>
- <li><a href="#source">Source</a></li>
- <li><a href="#examples">Examples</a></li>
- </ul>
-
+ <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
+ <nav id="toc" data-toggle="toc" class="sticky-top">
+ <h2 data-toc-skip>Contents</h2>
+ </nav>
</div>
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@@ -242,7 +227,7 @@
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- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
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