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-rw-r--r--docs/reference/transform_odeparms.html95
1 files changed, 42 insertions, 53 deletions
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html
index 2a08228d..fc0ffef2 100644
--- a/docs/reference/transform_odeparms.html
+++ b/docs/reference/transform_odeparms.html
@@ -10,23 +10,27 @@
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@@ -42,7 +46,6 @@ constants and other paramters that can only take on positive values, a
simple log transformation is used. For compositional parameters, such as the
formations fractions that should always sum up to 1 and can not be negative,
the ilr transformation is used." />
-<meta name="twitter:card" content="summary" />
@@ -60,7 +63,7 @@ the ilr transformation is used." />
</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">
@@ -74,7 +77,7 @@ the ilr transformation is used." />
</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">0.9.49.9</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50.1</span>
</span>
</div>
@@ -118,7 +121,12 @@ the ilr transformation is used." />
</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>
+
+ </a>
+</li>
</ul>
</div><!--/.nav-collapse -->
@@ -133,7 +141,7 @@ the ilr transformation is used." />
<div class="col-md-9 contents">
<div class="page-header">
<h1>Functions to transform and backtransform kinetic parameters for fitting</h1>
-
+ <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/transform_odeparms.R'><code>R/transform_odeparms.R</code></a></small>
<div class="hidden name"><code>transform_odeparms.Rd</code></div>
</div>
@@ -204,7 +212,7 @@ fitting procedure.</p></td>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>A vector of transformed or backtransformed parameters with the same
- names as the original parameters.</p>
+names as the original parameters.</p>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>The transformation of sets of formation fractions is fragile, as it supposes
@@ -224,39 +232,28 @@ This is no problem for the internal use in <code><a href='mkinfit.html'>mkinfit<
<span class='kw'>m1</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'># Fit the model to the FOCUS example dataset D using defaults</span>
<span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</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='no'>fit.s</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>fit</span>)
<span class='co'># Transformed and backtransformed parameters</span>
-<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>fit.s</span>$<span class='no'>par</span>, <span class='fl'>3</span>)</div><div class='output co'>#&gt; Estimate Std. Error Lower Upper
-#&gt; parent_0 99.60 1.5702 96.40 102.79
-#&gt; log_k_parent_sink -3.04 0.0763 -3.19 -2.88
-#&gt; log_k_parent_m1 -2.98 0.0403 -3.06 -2.90
-#&gt; log_k_m1_sink -5.25 0.1332 -5.52 -4.98
-#&gt; sigma 3.13 0.3585 2.40 3.85</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>fit.s</span>$<span class='no'>bpar</span>, <span class='fl'>3</span>)</div><div class='output co'>#&gt; Estimate se_notrans t value Pr(&gt;t) Lower Upper
-#&gt; parent_0 99.59848 1.57022 63.43 2.30e-36 96.40384 102.7931
-#&gt; k_parent_sink 0.04792 0.00365 13.11 6.13e-15 0.04103 0.0560
-#&gt; k_parent_m1 0.05078 0.00205 24.80 3.27e-23 0.04678 0.0551
-#&gt; k_m1_sink 0.00526 0.00070 7.51 6.16e-09 0.00401 0.0069
-#&gt; sigma 3.12550 0.35852 8.72 2.24e-10 2.39609 3.8549</div><div class='input'>
+<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>fit.s</span>$<span class='no'>par</span>, <span class='fl'>3</span>)</div><div class='output co'>#&gt; Estimate Std. Error Lower Upper
+#&gt; parent_0 99.598 1.5702 96.4038 102.793
+#&gt; log_k_parent -2.316 0.0409 -2.3988 -2.233
+#&gt; log_k_m1 -5.248 0.1332 -5.5184 -4.977
+#&gt; f_parent_ilr_1 0.041 0.0631 -0.0875 0.169
+#&gt; sigma 3.126 0.3585 2.3961 3.855</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>fit.s</span>$<span class='no'>bpar</span>, <span class='fl'>3</span>)</div><div class='output co'>#&gt; Estimate se_notrans t value Pr(&gt;t) Lower Upper
+#&gt; parent_0 99.59848 1.57022 63.43 2.30e-36 96.40384 102.7931
+#&gt; k_parent 0.09870 0.00403 24.47 4.96e-23 0.09082 0.1073
+#&gt; k_m1 0.00526 0.00070 7.51 6.16e-09 0.00401 0.0069
+#&gt; f_parent_to_m1 0.51448 0.02230 23.07 3.10e-22 0.46912 0.5596
+#&gt; sigma 3.12550 0.35852 8.72 2.24e-10 2.39609 3.8549</div><div class='input'>
<span class='co'># \dontrun{</span>
<span class='co'># Compare to the version without transforming rate parameters</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</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>transform_rates</span> <span class='kw'>=</span> <span class='fl'>FALSE</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='no'>fit.2.s</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>fit.2</span>)
-<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>fit.2.s</span>$<span class='no'>par</span>, <span class='fl'>3</span>)</div><div class='output co'>#&gt; Estimate Std. Error Lower Upper
-#&gt; parent_0 99.59848 1.57022 96.40384 1.03e+02
-#&gt; k_parent_sink 0.04792 0.00365 0.04049 5.54e-02
-#&gt; k_parent_m1 0.05078 0.00205 0.04661 5.49e-02
-#&gt; k_m1_sink 0.00526 0.00070 0.00384 6.69e-03
-#&gt; sigma 3.12550 0.35852 2.39609 3.85e+00</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>fit.2.s</span>$<span class='no'>bpar</span>, <span class='fl'>3</span>)</div><div class='output co'>#&gt; Estimate se_notrans t value Pr(&gt;t) Lower Upper
-#&gt; parent_0 99.59848 1.57022 63.43 2.30e-36 96.40384 1.03e+02
-#&gt; k_parent_sink 0.04792 0.00365 13.11 6.13e-15 0.04049 5.54e-02
-#&gt; k_parent_m1 0.05078 0.00205 24.80 3.27e-23 0.04661 5.49e-02
-#&gt; k_m1_sink 0.00526 0.00070 7.51 6.16e-09 0.00384 6.69e-03
-#&gt; sigma 3.12550 0.35852 8.72 2.24e-10 2.39609 3.85e+00</div><div class='input'><span class='co'># }</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</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>transform_rates</span> <span class='kw'>=</span> <span class='fl'>FALSE</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='error'>Error in if (cost &lt; cost.current) { assign("cost.current", cost, inherits = TRUE) if (!quiet) cat(ifelse(OLS, "Sum of squared residuals", "Negative log-likelihood"), " at call ", calls, ": ", cost.current, "\n", sep = "")}: Fehlender Wert, wo TRUE/FALSE nötig ist</span></div><div class='output co'>#&gt; <span class='message'>Timing stopped at: 0.002 0 0.003</span></div><div class='input'><span class='no'>fit.2.s</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>fit.2</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='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>fit.2.s</span>$<span class='no'>par</span>, <span class='fl'>3</span>)</div><div class='output co'>#&gt; <span class='error'>Error in print(fit.2.s$par, 3): Objekt 'fit.2.s' nicht gefunden</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>fit.2.s</span>$<span class='no'>bpar</span>, <span class='fl'>3</span>)</div><div class='output co'>#&gt; <span class='error'>Error in print(fit.2.s$bpar, 3): Objekt 'fit.2.s' nicht gefunden</span></div><div class='input'><span class='co'># }</span>
<span class='no'>initials</span> <span class='kw'>&lt;-</span> <span class='no'>fit</span>$<span class='no'>start</span>$<span class='no'>value</span>
<span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span>(<span class='no'>initials</span>) <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/colnames.html'>rownames</a></span>(<span class='no'>fit</span>$<span class='no'>start</span>)
<span class='no'>transformed</span> <span class='kw'>&lt;-</span> <span class='no'>fit</span>$<span class='no'>start_transformed</span>$<span class='no'>value</span>
<span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span>(<span class='no'>transformed</span>) <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/colnames.html'>rownames</a></span>(<span class='no'>fit</span>$<span class='no'>start_transformed</span>)
-<span class='fu'>transform_odeparms</span>(<span class='no'>initials</span>, <span class='no'>SFO_SFO</span>)</div><div class='output co'>#&gt; parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink
-#&gt; 100.750000 -2.302585 -2.301586 -2.300587 </div><div class='input'><span class='fu'>backtransform_odeparms</span>(<span class='no'>transformed</span>, <span class='no'>SFO_SFO</span>)</div><div class='output co'>#&gt; parent_0 k_parent_sink k_parent_m1 k_m1_sink
-#&gt; 100.7500 0.1000 0.1001 0.1002 </div><div class='input'>
+<span class='fu'>transform_odeparms</span>(<span class='no'>initials</span>, <span class='no'>SFO_SFO</span>)</div><div class='output co'>#&gt; parent_0 log_k_parent log_k_m1 f_parent_ilr_1
+#&gt; 100.750000 -2.302585 -2.301586 0.000000 </div><div class='input'><span class='fu'>backtransform_odeparms</span>(<span class='no'>transformed</span>, <span class='no'>SFO_SFO</span>)</div><div class='output co'>#&gt; parent_0 k_parent k_m1 f_parent_to_m1
+#&gt; 100.7500 0.1000 0.1001 0.5000 </div><div class='input'>
<span class='co'># \dontrun{</span>
<span class='co'># The case of formation fractions</span>
<span class='no'>SFO_SFO.ff</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(
@@ -297,18 +294,10 @@ This is no problem for the internal use in <code><a href='mkinfit.html'>mkinfit<
</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="#arguments">Arguments</a></li>
- <li><a href="#value">Value</a></li>
- <li><a href="#details">Details</a></li>
- <li><a href="#functions">Functions</a></li>
- <li><a href="#examples">Examples</a></li>
- </ul>
-
- <h2>Author</h2>
- <p>Johannes Ranke</p>
+ <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>
</div>
@@ -319,7 +308,7 @@ This is no problem for the internal use in <code><a href='mkinfit.html'>mkinfit<
</div>
<div class="pkgdown">
- <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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