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authorJohannes Ranke <jranke@uni-bremen.de>2020-04-20 18:52:52 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2020-04-20 18:52:52 +0200
commit3a62211d9211cd0aedecec055226d66b55a17958 (patch)
tree23ec36c38f7a17c800c7004610550230bd7e39a5
parent5526bf5ba6b003c6dae842f7f03f33c1648c9551 (diff)
Prepare release to address failed CRAN check
-rw-r--r--DESCRIPTION4
-rw-r--r--NEWS.md2
-rw-r--r--docs/404.html2
-rw-r--r--docs/articles/index.html2
-rw-r--r--docs/authors.html2
-rw-r--r--docs/index.html2
-rw-r--r--docs/news/index.html17
-rw-r--r--docs/reference/index.html2
-rw-r--r--docs/reference/mkinds.html2
-rw-r--r--docs/reference/mkinfit.html44
10 files changed, 42 insertions, 37 deletions
diff --git a/DESCRIPTION b/DESCRIPTION
index 8273c7df..99a9cc76 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
Package: mkin
Type: Package
Title: Kinetic Evaluation of Chemical Degradation Data
-Version: 0.9.49.10
-Date: 2020-04-18
+Version: 0.9.49.11
+Date: 2020-04-20
Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre", "cph"),
email = "jranke@uni-bremen.de",
comment = c(ORCID = "0000-0003-4371-6538")),
diff --git a/NEWS.md b/NEWS.md
index 919f413b..790e2e03 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,5 +1,7 @@
# mkin 0.9.49.11 (unreleased)
+- Increase a test tolerance to make it pass on all CRAN check machines
+
# mkin 0.9.49.10 (2020-04-18)
- 'nlme.mmkin': An nlme method for mmkin row objects and an associated S3 class with print, plot, anova and endpoint methods
diff --git a/docs/404.html b/docs/404.html
index dc3c3c18..b3193a23 100644
--- a/docs/404.html
+++ b/docs/404.html
@@ -67,7 +67,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="https://pkgdown.jrwb.de/mkin/index.html">mkin</a>
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.10</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.11</span>
</span>
</div>
diff --git a/docs/articles/index.html b/docs/articles/index.html
index 4a5087df..9b0cce06 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -67,7 +67,7 @@
</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">0.9.49.10</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.11</span>
</span>
</div>
diff --git a/docs/authors.html b/docs/authors.html
index 20c040f9..55121d7c 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -67,7 +67,7 @@
</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">0.9.49.10</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.11</span>
</span>
</div>
diff --git a/docs/index.html b/docs/index.html
index 99d580c5..5baaa718 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -37,7 +37,7 @@
</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">0.9.49.10</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.11</span>
</span>
</div>
diff --git a/docs/news/index.html b/docs/news/index.html
index 5758c284..853c217f 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -67,7 +67,7 @@
</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">0.9.49.10</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.11</span>
</span>
</div>
@@ -129,9 +129,17 @@
</div>
- <div id="mkin-0-9-49-10-unreleased" class="section level1">
+ <div id="mkin-0-9-49-11-unreleased" class="section level1">
<h1 class="page-header">
-<a href="#mkin-0-9-49-10-unreleased" class="anchor"></a>mkin 0.9.49.10 (unreleased)<small> Unreleased </small>
+<a href="#mkin-0-9-49-11-unreleased" class="anchor"></a>mkin 0.9.49.11 (unreleased)<small> Unreleased </small>
+</h1>
+<ul>
+<li>Increase a test tolerance to make it pass on all CRAN check machines</li>
+</ul>
+</div>
+ <div id="mkin-0-9-49-10-2020-04-18" class="section level1">
+<h1 class="page-header">
+<a href="#mkin-0-9-49-10-2020-04-18" class="anchor"></a>mkin 0.9.49.10 (2020-04-18)<small> 2020-04-18 </small>
</h1>
<ul>
<li><p>‘nlme.mmkin’: An nlme method for mmkin row objects and an associated S3 class with print, plot, anova and endpoint methods</p></li>
@@ -769,7 +777,8 @@
<div id="tocnav">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
- <li><a href="#mkin-0-9-49-10-unreleased">0.9.49.10</a></li>
+ <li><a href="#mkin-0-9-49-11-unreleased">0.9.49.11</a></li>
+ <li><a href="#mkin-0-9-49-10-2020-04-18">0.9.49.10</a></li>
<li><a href="#mkin-0-9-49-9-2020-03-31">0.9.49.9</a></li>
<li><a href="#mkin-0-9-49-8-2020-01-09">0.9.49.8</a></li>
<li><a href="#mkin-0-9-49-7-2019-11-01">0.9.49.7</a></li>
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 04e3b8b9..e6a373d6 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -67,7 +67,7 @@
</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">0.9.49.10</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.11</span>
</span>
</div>
diff --git a/docs/reference/mkinds.html b/docs/reference/mkinds.html
index 946d40a6..4f5d9f67 100644
--- a/docs/reference/mkinds.html
+++ b/docs/reference/mkinds.html
@@ -72,7 +72,7 @@ provided by this package come as mkinds objects nevertheless." />
</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">0.9.49.10</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.11</span>
</span>
</div>
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index ffc8d52b..09837505 100644
--- a/docs/reference/mkinfit.html
+++ b/docs/reference/mkinfit.html
@@ -75,7 +75,7 @@ likelihood function." />
</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">0.9.49.11</span>
</span>
</div>
@@ -415,17 +415,17 @@ estimators.</p>
<pre class="examples"><div class='input'>
<span class='co'># Use shorthand notation for parent only degradation</span>
<span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.49.9
+<span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.49.11
#&gt; R version used for fitting: 3.6.3
-#&gt; Date of fit: Mon Mar 30 21:41:20 2020
-#&gt; Date of summary: Mon Mar 30 21:41:20 2020
+#&gt; Date of fit: Mon Apr 20 18:52:22 2020
+#&gt; Date of summary: Mon Apr 20 18:52:22 2020
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
#&gt;
#&gt; Model predictions using solution type analytical
#&gt;
-#&gt; Fitted using 222 model solutions performed in 0.463 s
+#&gt; Fitted using 222 model solutions performed in 0.473 s
#&gt;
#&gt; Error model: Constant variance
#&gt;
@@ -497,13 +497,10 @@ estimators.</p>
<span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></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='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span>(<span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>,
<span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</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; User System verstrichen
-#&gt; 1.526 0.000 1.530 </div><div class='input'><span class='fu'><a href='https://rdrr.io/r/stats/coef.html'>coef</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; NULL</div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; $ff
+#&gt; 1.465 0.003 1.474 </div><div class='input'><span class='fu'><a href='https://rdrr.io/r/stats/coef.html'>coef</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; NULL</div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; $ff
#&gt; parent_sink parent_m1 m1_sink
#&gt; 0.485524 0.514476 1.000000
#&gt;
-#&gt; $SFORB
-#&gt; logical(0)
-#&gt;
#&gt; $distimes
#&gt; DT50 DT90
#&gt; parent 7.022929 23.32967
@@ -570,13 +567,10 @@ estimators.</p>
#&gt; Sum of squared residuals at call 126: 371.2134
#&gt; Sum of squared residuals at call 135: 371.2134
#&gt; Negative log-likelihood at call 145: 97.22429</div><div class='output co'>#&gt; <span class='message'>Optimisation successfully terminated.</span></div><div class='output co'>#&gt; User System verstrichen
-#&gt; 1.083 0.000 1.084 </div><div class='input'><span class='fu'><a href='https://rdrr.io/r/stats/coef.html'>coef</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#&gt; NULL</div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#&gt; $ff
+#&gt; 1.052 0.000 1.068 </div><div class='input'><span class='fu'><a href='https://rdrr.io/r/stats/coef.html'>coef</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#&gt; NULL</div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#&gt; $ff
#&gt; parent_sink parent_m1 m1_sink
#&gt; 0.485524 0.514476 1.000000
#&gt;
-#&gt; $SFORB
-#&gt; logical(0)
-#&gt;
#&gt; $distimes
#&gt; DT50 DT90
#&gt; parent 7.022929 23.32967
@@ -604,10 +598,10 @@ estimators.</p>
<span class='co'># \dontrun{</span>
<span class='co'># Weighted fits, including IRLS</span>
<span class='no'>SFO_SFO.ff</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>),
- <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</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='no'>f.noweight</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</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='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>f.noweight</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.49.9
+ <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</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='no'>f.noweight</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</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='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>f.noweight</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.49.11
#&gt; R version used for fitting: 3.6.3
-#&gt; Date of fit: Mon Mar 30 21:41:36 2020
-#&gt; Date of summary: Mon Mar 30 21:41:36 2020
+#&gt; Date of fit: Mon Apr 20 18:52:37 2020
+#&gt; Date of summary: Mon Apr 20 18:52:37 2020
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -615,7 +609,7 @@ estimators.</p>
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted using 422 model solutions performed in 1.144 s
+#&gt; Fitted using 422 model solutions performed in 1.087 s
#&gt;
#&gt; Error model: Constant variance
#&gt;
@@ -721,10 +715,10 @@ estimators.</p>
#&gt; 100 m1 31.04 31.98163 -9.416e-01
#&gt; 100 m1 33.13 31.98163 1.148e+00
#&gt; 120 m1 25.15 28.78984 -3.640e+00
-#&gt; 120 m1 33.31 28.78984 4.520e+00</div><div class='input'><span class='no'>f.obs</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"obs"</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'>f.obs</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.49.9
+#&gt; 120 m1 33.31 28.78984 4.520e+00</div><div class='input'><span class='no'>f.obs</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"obs"</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'>f.obs</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.49.11
#&gt; R version used for fitting: 3.6.3
-#&gt; Date of fit: Mon Mar 30 21:41:39 2020
-#&gt; Date of summary: Mon Mar 30 21:41:39 2020
+#&gt; Date of fit: Mon Apr 20 18:52:40 2020
+#&gt; Date of summary: Mon Apr 20 18:52:40 2020
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -732,7 +726,7 @@ estimators.</p>
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted using 979 model solutions performed in 2.576 s
+#&gt; Fitted using 979 model solutions performed in 2.518 s
#&gt;
#&gt; Error model: Variance unique to each observed variable
#&gt;
@@ -853,10 +847,10 @@ estimators.</p>
#&gt; 100 m1 31.04 31.98773 -9.477e-01
#&gt; 100 m1 33.13 31.98773 1.142e+00
#&gt; 120 m1 25.15 28.80429 -3.654e+00
-#&gt; 120 m1 33.31 28.80429 4.506e+00</div><div class='input'><span class='no'>f.tc</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</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'>f.tc</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.49.9
+#&gt; 120 m1 33.31 28.80429 4.506e+00</div><div class='input'><span class='no'>f.tc</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</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'>f.tc</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.49.11
#&gt; R version used for fitting: 3.6.3
-#&gt; Date of fit: Mon Mar 30 21:41:50 2020
-#&gt; Date of summary: Mon Mar 30 21:41:50 2020
+#&gt; Date of fit: Mon Apr 20 18:52:50 2020
+#&gt; Date of summary: Mon Apr 20 18:52:50 2020
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -864,7 +858,7 @@ estimators.</p>
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted using 2552 model solutions performed in 10.593 s
+#&gt; Fitted using 2552 model solutions performed in 10.186 s
#&gt;
#&gt; Error model: Two-component variance function
#&gt;

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