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authorJohannes Ranke <jranke@uni-bremen.de>2019-01-31 15:46:04 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2019-01-31 15:46:04 +0100
commit54eb679cb599042b33d67e101687dd451c4b53fe (patch)
tree841336729f31bb28bb756dc4f066278daffa09c5
parentde040ca33f6b13ef89be89718510f30631b67903 (diff)
Correct title for CAKE_export
Add NEWS entry. Static documentation rebuilt by pkgdown
-rw-r--r--NEWS.md4
-rw-r--r--docs/articles/FOCUS_L.html38
-rw-r--r--docs/articles/web_only/compiled_models.html12
-rw-r--r--docs/news/index.html7
-rw-r--r--docs/reference/CAKE_export.html6
-rw-r--r--docs/reference/index.html2
-rw-r--r--docs/reference/mkinpredict.html2
-rw-r--r--docs/reference/mmkin.html2
-rw-r--r--man/CAKE_export.Rd2
9 files changed, 39 insertions, 36 deletions
diff --git a/NEWS.md b/NEWS.md
index f799a749..8ca0e89c 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,4 @@
-# mkin 0.9.47.6 (2018-11-26)
+# mkin 0.9.47.6 (2019-01-31)
- Add the function 'logLik.mkinfit' which makes it possible to calculate an AIC for mkinfit objects
@@ -14,6 +14,8 @@
- 'tests/testthat/test_irls.R': Test if the components of the error model used to generate the data can be reproduced with moderate accuracy
+- Add the function 'CAKE_export' to facilitate cross-checking of results
+
# mkin 0.9.47.5 (2018-09-14)
- Make the two-component error model stop in cases where it is inadequate to avoid nls crashes on windows
diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html
index daf887e6..b53ab0d0 100644
--- a/docs/articles/FOCUS_L.html
+++ b/docs/articles/FOCUS_L.html
@@ -111,15 +111,15 @@
<a class="sourceLine" id="cb2-2" data-line-number="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.L1.SFO)</a></code></pre></div>
<pre><code>## mkin version used for fitting: 0.9.47.5
## R version used for fitting: 3.5.2
-## Date of fit: Thu Jan 31 15:37:32 2019
-## Date of summary: Thu Jan 31 15:37:32 2019
+## Date of fit: Thu Jan 31 15:43:40 2019
+## Date of summary: Thu Jan 31 15:43:40 2019
##
## Equations:
## d_parent/dt = - k_parent_sink * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 37 model solutions performed in 0.095 s
+## Fitted with method Port using 37 model solutions performed in 0.094 s
##
## Weighting: none
##
@@ -202,15 +202,15 @@
<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.L1.FOMC, <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div>
<pre><code>## mkin version used for fitting: 0.9.47.5
## R version used for fitting: 3.5.2
-## Date of fit: Thu Jan 31 15:37:34 2019
-## Date of summary: Thu Jan 31 15:37:34 2019
+## Date of fit: Thu Jan 31 15:43:42 2019
+## Date of summary: Thu Jan 31 15:43:42 2019
##
## Equations:
## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 611 model solutions performed in 1.492 s
+## Fitted with method Port using 611 model solutions performed in 1.502 s
##
## Weighting: none
##
@@ -297,15 +297,15 @@
<div class="sourceCode" id="cb12"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb12-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.L2.FOMC, <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div>
<pre><code>## mkin version used for fitting: 0.9.47.5
## R version used for fitting: 3.5.2
-## Date of fit: Thu Jan 31 15:37:35 2019
-## Date of summary: Thu Jan 31 15:37:35 2019
+## Date of fit: Thu Jan 31 15:43:42 2019
+## Date of summary: Thu Jan 31 15:43:42 2019
##
## Equations:
## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 81 model solutions performed in 0.196 s
+## Fitted with method Port using 81 model solutions performed in 0.195 s
##
## Weighting: none
##
@@ -368,8 +368,8 @@
<div class="sourceCode" id="cb15"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb15-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.L2.DFOP, <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div>
<pre><code>## mkin version used for fitting: 0.9.47.5
## R version used for fitting: 3.5.2
-## Date of fit: Thu Jan 31 15:37:36 2019
-## Date of summary: Thu Jan 31 15:37:36 2019
+## Date of fit: Thu Jan 31 15:43:43 2019
+## Date of summary: Thu Jan 31 15:43:43 2019
##
## Equations:
## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -378,7 +378,7 @@
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 336 model solutions performed in 0.837 s
+## Fitted with method Port using 336 model solutions performed in 0.836 s
##
## Weighting: none
##
@@ -460,8 +460,8 @@
<div class="sourceCode" id="cb21"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb21-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(mm.L3[[<span class="st">"DFOP"</span>, <span class="dv">1</span>]])</a></code></pre></div>
<pre><code>## mkin version used for fitting: 0.9.47.5
## R version used for fitting: 3.5.2
-## Date of fit: Thu Jan 31 15:37:37 2019
-## Date of summary: Thu Jan 31 15:37:37 2019
+## Date of fit: Thu Jan 31 15:43:44 2019
+## Date of summary: Thu Jan 31 15:43:45 2019
##
## Equations:
## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -470,7 +470,7 @@
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 137 model solutions performed in 0.344 s
+## Fitted with method Port using 137 model solutions performed in 0.34 s
##
## Weighting: none
##
@@ -561,8 +561,8 @@
<div class="sourceCode" id="cb26"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb26-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(mm.L4[[<span class="st">"SFO"</span>, <span class="dv">1</span>]], <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div>
<pre><code>## mkin version used for fitting: 0.9.47.5
## R version used for fitting: 3.5.2
-## Date of fit: Thu Jan 31 15:37:37 2019
-## Date of summary: Thu Jan 31 15:37:38 2019
+## Date of fit: Thu Jan 31 15:43:45 2019
+## Date of summary: Thu Jan 31 15:43:45 2019
##
## Equations:
## d_parent/dt = - k_parent_sink * parent
@@ -621,8 +621,8 @@
<div class="sourceCode" id="cb28"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb28-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(mm.L4[[<span class="st">"FOMC"</span>, <span class="dv">1</span>]], <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div>
<pre><code>## mkin version used for fitting: 0.9.47.5
## R version used for fitting: 3.5.2
-## Date of fit: Thu Jan 31 15:37:37 2019
-## Date of summary: Thu Jan 31 15:37:38 2019
+## Date of fit: Thu Jan 31 15:43:45 2019
+## Date of summary: Thu Jan 31 15:43:45 2019
##
## Equations:
## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html
index a1fa69f5..d7d76b49 100644
--- a/docs/articles/web_only/compiled_models.html
+++ b/docs/articles/web_only/compiled_models.html
@@ -126,14 +126,14 @@
<a class="sourceLine" id="cb5-16" data-line-number="16">}</a></code></pre></div>
<pre><code>## Lade nötiges Paket: rbenchmark</code></pre>
<pre><code>## test replications elapsed relative user.self sys.self
-## 3 deSolve, compiled 3 2.319 1.000 2.317 0.000
-## 1 deSolve, not compiled 3 17.483 7.539 17.473 0.000
-## 2 Eigenvalue based 3 2.857 1.232 2.852 0.003
+## 3 deSolve, compiled 3 2.331 1.000 2.330 0
+## 1 deSolve, not compiled 3 17.369 7.451 17.360 0
+## 2 Eigenvalue based 3 2.878 1.235 2.876 0
## user.child sys.child
## 3 0 0
## 1 0 0
## 2 0 0</code></pre>
-<p>We see that using the compiled model is by a factor of around 8 faster than using the R version with the default ode solver, and it is even faster than the Eigenvalue based solution implemented in R which does not need iterative solution of the ODEs.</p>
+<p>We see that using the compiled model is by a factor of around 7 faster than using the R version with the default ode solver, and it is even faster than the Eigenvalue based solution implemented in R which does not need iterative solution of the ODEs.</p>
</div>
<div id="model-that-can-not-be-solved-with-eigenvalues" class="section level2">
<h2 class="hasAnchor">
@@ -157,8 +157,8 @@
<a class="sourceLine" id="cb8-16" data-line-number="16">}</a></code></pre></div>
<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre>
<pre><code>## test replications elapsed relative user.self sys.self
-## 2 deSolve, compiled 3 4.102 1.000 4.100 0
-## 1 deSolve, not compiled 3 37.059 9.034 37.041 0
+## 2 deSolve, compiled 3 4.120 1.000 4.116 0
+## 1 deSolve, not compiled 3 37.011 8.983 36.993 0
## user.child sys.child
## 2 0 0
## 1 0 0</code></pre>
diff --git a/docs/news/index.html b/docs/news/index.html
index 1aa9e7a5..7736a28d 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -119,9 +119,9 @@
</div>
- <div id="mkin-0-9-47-6-2018-11-26" class="section level1">
+ <div id="mkin-0-9-47-6-2019-01-31" class="section level1">
<h1 class="page-header">
-<a href="#mkin-0-9-47-6-2018-11-26" class="anchor"></a>mkin 0.9.47.6 (2018-11-26)<small> Unreleased </small>
+<a href="#mkin-0-9-47-6-2019-01-31" class="anchor"></a>mkin 0.9.47.6 (2019-01-31)<small> Unreleased </small>
</h1>
<ul>
<li><p>Add the function ‘logLik.mkinfit’ which makes it possible to calculate an AIC for mkinfit objects</p></li>
@@ -131,6 +131,7 @@
<li><p>‘mkinpredict’: Make the function generic and create a method for mkinfit objects</p></li>
<li><p>‘mkinfit’: Improve the correctness of the fitted two component error model by fitting the mean absolute deviance at each observation against the observed values, weighting with the current two-component error model</p></li>
<li><p>‘tests/testthat/test_irls.R’: Test if the components of the error model used to generate the data can be reproduced with moderate accuracy</p></li>
+<li><p>Add the function ‘CAKE_export’ to facilitate cross-checking of results</p></li>
</ul>
</div>
<div id="mkin-0-9-47-5-2018-09-14" class="section level1">
@@ -674,7 +675,7 @@
<div id="tocnav">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
- <li><a href="#mkin-0-9-47-6-2018-11-26">0.9.47.6</a></li>
+ <li><a href="#mkin-0-9-47-6-2019-01-31">0.9.47.6</a></li>
<li><a href="#mkin-0-9-47-5-2018-09-14">0.9.47.5</a></li>
<li><a href="#mkin-0-9-47-3">0.9.47.3</a></li>
<li><a href="#mkin-0-9-47-2-2018-07-19">0.9.47.2</a></li>
diff --git a/docs/reference/CAKE_export.html b/docs/reference/CAKE_export.html
index f1768ecc..21dd46a9 100644
--- a/docs/reference/CAKE_export.html
+++ b/docs/reference/CAKE_export.html
@@ -6,7 +6,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>Export a list of datasets in wide format to a CAKE study file — CAKE_export • mkin</title>
+<title>Export a list of datasets format to a CAKE study file — CAKE_export • mkin</title>
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
@@ -30,7 +30,7 @@
-<meta property="og:title" content="Export a list of datasets in wide format to a CAKE study file — CAKE_export" />
+<meta property="og:title" content="Export a list of datasets format to a CAKE study file — CAKE_export" />
<meta property="og:description" content="In addition to the datasets, the pathways in the degradation
model can be specified as well." />
@@ -119,7 +119,7 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
- <h1>Export a list of datasets in wide format to a CAKE study file</h1>
+ <h1>Export a list of datasets format to a CAKE study file</h1>
<div class="hidden name"><code>CAKE_export.Rd</code></div>
</div>
diff --git a/docs/reference/index.html b/docs/reference/index.html
index fb47d33e..7dd32430 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -374,7 +374,7 @@
<td>
<p><code><a href="CAKE_export.html">CAKE_export()</a></code> </p>
</td>
- <td><p>Export a list of datasets in wide format to a CAKE study file</p></td>
+ <td><p>Export a list of datasets format to a CAKE study file</p></td>
</tr>
</tbody><tbody>
<tr>
diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html
index 294a90de..c126eec9 100644
--- a/docs/reference/mkinpredict.html
+++ b/docs/reference/mkinpredict.html
@@ -232,7 +232,7 @@
<span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>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='error'>Error in mkinmod(parent = list(type = "SFO", to = "m1"), m1 = list(type = "SFO")): konnte Funktion "mkinmod" nicht finden</span></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></span>(
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='kw'>k_parent_m1</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>k_m1_sink</span> <span class='kw'>=</span> <span class='fl'>0.01</span>),
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/seq'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
- <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#&gt; <span class='error'>Error in mkinpredict(SFO_SFO, c(k_parent_m1 = 0.05, k_parent_sink = 0.1, k_m1_sink = 0.01), c(parent = 100, m1 = 0), seq(0, 20, by = 0.1), solution_type = "eigen"): konnte Funktion "mkinpredict" nicht finden</span></div><div class='output co'>#&gt; <span class='message'>Timing stopped at: 0 0 0</span></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></span>(
+ <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#&gt; <span class='error'>Error in mkinpredict(SFO_SFO, c(k_parent_m1 = 0.05, k_parent_sink = 0.1, k_m1_sink = 0.01), c(parent = 100, m1 = 0), seq(0, 20, by = 0.1), solution_type = "eigen"): konnte Funktion "mkinpredict" nicht finden</span></div><div class='output co'>#&gt; <span class='message'>Timing stopped at: 0 0 0.001</span></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></span>(
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='kw'>k_parent_m1</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>k_m1_sink</span> <span class='kw'>=</span> <span class='fl'>0.01</span>),
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/seq'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
<span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#&gt; <span class='error'>Error in mkinpredict(SFO_SFO, c(k_parent_m1 = 0.05, k_parent_sink = 0.1, k_m1_sink = 0.01), c(parent = 100, m1 = 0), seq(0, 20, by = 0.1), solution_type = "deSolve"): konnte Funktion "mkinpredict" nicht finden</span></div><div class='output co'>#&gt; <span class='message'>Timing stopped at: 0 0 0</span></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></span>(
diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html
index 25f97738..af0b8f6f 100644
--- a/docs/reference/mmkin.html
+++ b/docs/reference/mmkin.html
@@ -186,7 +186,7 @@
<span class='no'>models</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></span>(<span class='kw'>SFO_lin</span> <span class='kw'>=</span> <span class='no'>m_synth_SFO_lin</span>, <span class='kw'>FOMC_lin</span> <span class='kw'>=</span> <span class='no'>m_synth_FOMC_lin</span>)</div><div class='output co'>#&gt; <span class='error'>Error in eval(expr, envir, enclos): Objekt 'm_synth_SFO_lin' nicht gefunden</span></div><div class='input'><span class='no'>datasets</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/lapply'>lapply</a></span>(<span class='no'>synthetic_data_for_UBA_2014</span>[<span class='fl'>1</span>:<span class='fl'>3</span>], <span class='kw'>function</span>(<span class='no'>x</span>) <span class='no'>x</span>$<span class='no'>data</span>)
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/names'>names</a></span>(<span class='no'>datasets</span>) <span class='kw'>&lt;-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/paste'>paste</a></span>(<span class='st'>"Dataset"</span>, <span class='fl'>1</span>:<span class='fl'>3</span>)
-<span class='no'>time_default</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></span>(<span class='no'>fits.0</span> <span class='kw'>&lt;-</span> <span class='fu'>mmkin</span>(<span class='no'>models</span>, <span class='no'>datasets</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))</div><div class='output co'>#&gt; <span class='error'>Error in mmkin(models, datasets, quiet = TRUE): konnte Funktion "mmkin" nicht finden</span></div><div class='output co'>#&gt; <span class='message'>Timing stopped at: 0 0 0.001</span></div><div class='input'><span class='no'>time_1</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></span>(<span class='no'>fits.4</span> <span class='kw'>&lt;-</span> <span class='fu'>mmkin</span>(<span class='no'>models</span>, <span class='no'>datasets</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))</div><div class='output co'>#&gt; <span class='error'>Error in mmkin(models, datasets, cores = 1, quiet = TRUE): konnte Funktion "mmkin" nicht finden</span></div><div class='output co'>#&gt; <span class='message'>Timing stopped at: 0 0 0</span></div><div class='input'>
+<span class='no'>time_default</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></span>(<span class='no'>fits.0</span> <span class='kw'>&lt;-</span> <span class='fu'>mmkin</span>(<span class='no'>models</span>, <span class='no'>datasets</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))</div><div class='output co'>#&gt; <span class='error'>Error in mmkin(models, datasets, quiet = TRUE): konnte Funktion "mmkin" nicht finden</span></div><div class='output co'>#&gt; <span class='message'>Timing stopped at: 0 0 0</span></div><div class='input'><span class='no'>time_1</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></span>(<span class='no'>fits.4</span> <span class='kw'>&lt;-</span> <span class='fu'>mmkin</span>(<span class='no'>models</span>, <span class='no'>datasets</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))</div><div class='output co'>#&gt; <span class='error'>Error in mmkin(models, datasets, cores = 1, quiet = TRUE): konnte Funktion "mmkin" nicht finden</span></div><div class='output co'>#&gt; <span class='message'>Timing stopped at: 0 0 0</span></div><div class='input'>
<span class='no'>time_default</span></div><div class='output co'>#&gt; <span class='error'>Error in eval(expr, envir, enclos): Objekt 'time_default' nicht gefunden</span></div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#&gt; <span class='error'>Error in eval(expr, envir, enclos): Objekt 'time_1' nicht gefunden</span></div><div class='input'>
<span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fits.0</span><span class='kw'>[[</span><span class='st'>"SFO_lin"</span>, <span class='fl'>2</span>]])</div><div class='output co'>#&gt; <span class='error'>Error in endpoints(fits.0[["SFO_lin", 2]]): konnte Funktion "endpoints" nicht finden</span></div><div class='input'>
<span class='co'># plot.mkinfit handles rows or columns of mmkin result objects</span>
diff --git a/man/CAKE_export.Rd b/man/CAKE_export.Rd
index 3a3da4d0..c7111bc8 100644
--- a/man/CAKE_export.Rd
+++ b/man/CAKE_export.Rd
@@ -1,7 +1,7 @@
\name{CAKE_export}
\alias{CAKE_export}
\title{
- Export a list of datasets in wide format to a CAKE study file
+ Export a list of datasets format to a CAKE study file
}
\description{
In addition to the datasets, the pathways in the degradation

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