From bc3825ae2d12c18ea3d3caf17eb23c93fef180b8 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Thu, 8 Oct 2020 09:31:35 +0200
Subject: Fix issues for release
---
docs/dev/articles/FOCUS_D.html | 31 +++++++++++++++++++------------
1 file changed, 19 insertions(+), 12 deletions(-)
(limited to 'docs/dev/articles/FOCUS_D.html')
diff --git a/docs/dev/articles/FOCUS_D.html b/docs/dev/articles/FOCUS_D.html
index 7d5dd732..02701431 100644
--- a/docs/dev/articles/FOCUS_D.html
+++ b/docs/dev/articles/FOCUS_D.html
@@ -101,7 +101,7 @@
<h1 data-toc-skip>Example evaluation of FOCUS Example Dataset D</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2020-05-27</h4>
+ <h4 class="date">2020-10-08</h4>
<small class="dont-index">Source: <a href="http://github.com/jranke/mkin/blob/master/vignettes/FOCUS_D.rmd"><code>vignettes/FOCUS_D.rmd</code></a></small>
<div class="hidden name"><code>FOCUS_D.rmd</code></div>
@@ -171,18 +171,20 @@
<div class="sourceCode" id="cb7"><html><body><pre class="r"><span class="no">fit</span> <span class="kw"><-</span> <span class="fu"><a href="../reference/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>)</pre></body></html></div>
<pre><code>## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE): Observations with value
## of zero were removed from the data</code></pre>
+<pre><code>## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE): Shapiro-Wilk test for
+## standardized residuals: p = 0.0165</code></pre>
<p>A plot of the fit including a residual plot for both observed variables is obtained using the <code>plot_sep</code> method for <code>mkinfit</code> objects, which shows separate graphs for all compounds and their residuals.</p>
-<div class="sourceCode" id="cb9"><html><body><pre class="r"><span class="fu"><a href="../reference/plot.mkinfit.html">plot_sep</a></span>(<span class="no">fit</span>, <span class="kw">lpos</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"topright"</span>, <span class="st">"bottomright"</span>))</pre></body></html></div>
+<div class="sourceCode" id="cb10"><html><body><pre class="r"><span class="fu"><a href="../reference/plot.mkinfit.html">plot_sep</a></span>(<span class="no">fit</span>, <span class="kw">lpos</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"topright"</span>, <span class="st">"bottomright"</span>))</pre></body></html></div>
<p><img src="FOCUS_D_files/figure-html/plot-1.png" width="768"></p>
<p>Confidence intervals for the parameter estimates are obtained using the <code>mkinparplot</code> function.</p>
-<div class="sourceCode" id="cb10"><html><body><pre class="r"><span class="fu"><a href="../reference/mkinparplot.html">mkinparplot</a></span>(<span class="no">fit</span>)</pre></body></html></div>
+<div class="sourceCode" id="cb11"><html><body><pre class="r"><span class="fu"><a href="../reference/mkinparplot.html">mkinparplot</a></span>(<span class="no">fit</span>)</pre></body></html></div>
<p><img src="FOCUS_D_files/figure-html/plot_2-1.png" width="768"></p>
<p>A comprehensive report of the results is obtained using the <code>summary</code> method for <code>mkinfit</code> objects.</p>
-<div class="sourceCode" id="cb11"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(<span class="no">fit</span>)</pre></body></html></div>
+<div class="sourceCode" id="cb12"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(<span class="no">fit</span>)</pre></body></html></div>
<pre><code>## mkin version used for fitting: 0.9.50.3
-## R version used for fitting: 4.0.0
-## Date of fit: Wed May 27 07:51:36 2020
-## Date of summary: Wed May 27 07:51:37 2020
+## R version used for fitting: 4.0.2
+## Date of fit: Thu Oct 8 09:14:03 2020
+## Date of summary: Thu Oct 8 09:14:03 2020
##
## Equations:
## d_parent/dt = - k_parent * parent
@@ -190,7 +192,7 @@
##
## Model predictions using solution type analytical
##
-## Fitted using 421 model solutions performed in 0.173 s
+## Fitted using 421 model solutions performed in 0.171 s
##
## Error model: Constant variance
##
@@ -214,6 +216,11 @@
## value type
## m1_0 0 state
##
+##
+## Warning(s):
+## Observations with value of zero were removed from the data
+## Shapiro-Wilk test for standardized residuals: p = 0.0165
+##
## Results:
##
## AIC BIC logLik
@@ -229,11 +236,11 @@
##
## Parameter correlation:
## parent_0 log_k_parent log_k_m1 f_parent_ilr_1 sigma
-## parent_0 1.000e+00 5.174e-01 -1.688e-01 -5.471e-01 -3.190e-07
+## parent_0 1.000e+00 5.174e-01 -1.688e-01 -5.471e-01 -3.214e-07
## log_k_parent 5.174e-01 1.000e+00 -3.263e-01 -5.426e-01 3.168e-07
-## log_k_m1 -1.688e-01 -3.263e-01 1.000e+00 7.478e-01 -1.406e-07
-## f_parent_ilr_1 -5.471e-01 -5.426e-01 7.478e-01 1.000e+00 -1.587e-10
-## sigma -3.190e-07 3.168e-07 -1.406e-07 -1.587e-10 1.000e+00
+## log_k_m1 -1.688e-01 -3.263e-01 1.000e+00 7.478e-01 -1.410e-07
+## f_parent_ilr_1 -5.471e-01 -5.426e-01 7.478e-01 1.000e+00 5.093e-10
+## sigma -3.214e-07 3.168e-07 -1.410e-07 5.093e-10 1.000e+00
##
## Backtransformed parameters:
## Confidence intervals for internally transformed parameters are asymmetric.
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