diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2020-04-20 18:52:52 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2020-04-20 18:52:52 +0200 |
| commit | 3a62211d9211cd0aedecec055226d66b55a17958 (patch) | |
| tree | 23ec36c38f7a17c800c7004610550230bd7e39a5 | |
| parent | 5526bf5ba6b003c6dae842f7f03f33c1648c9551 (diff) | |
Prepare release to address failed CRAN check
| -rw-r--r-- | DESCRIPTION | 4 | ||||
| -rw-r--r-- | NEWS.md | 2 | ||||
| -rw-r--r-- | docs/404.html | 2 | ||||
| -rw-r--r-- | docs/articles/index.html | 2 | ||||
| -rw-r--r-- | docs/authors.html | 2 | ||||
| -rw-r--r-- | docs/index.html | 2 | ||||
| -rw-r--r-- | docs/news/index.html | 17 | ||||
| -rw-r--r-- | docs/reference/index.html | 2 | ||||
| -rw-r--r-- | docs/reference/mkinds.html | 2 | ||||
| -rw-r--r-- | docs/reference/mkinfit.html | 44 |
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")), @@ -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'><-</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'>#> 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'>#> mkin version used for fitting: 0.9.49.11 #> R version used for fitting: 3.6.3 -#> Date of fit: Mon Mar 30 21:41:20 2020 -#> Date of summary: Mon Mar 30 21:41:20 2020 +#> Date of fit: Mon Apr 20 18:52:22 2020 +#> Date of summary: Mon Apr 20 18:52:22 2020 #> #> Equations: #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent #> #> Model predictions using solution type analytical #> -#> Fitted using 222 model solutions performed in 0.463 s +#> Fitted using 222 model solutions performed in 0.473 s #> #> Error model: Constant variance #> @@ -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'>#> <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'><-</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'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#> User System verstrichen -#> 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'>#> 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'>#> $ff +#> 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'>#> 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'>#> $ff #> parent_sink parent_m1 m1_sink #> 0.485524 0.514476 1.000000 #> -#> $SFORB -#> logical(0) -#> #> $distimes #> DT50 DT90 #> parent 7.022929 23.32967 @@ -570,13 +567,10 @@ estimators.</p> #> Sum of squared residuals at call 126: 371.2134 #> Sum of squared residuals at call 135: 371.2134 #> Negative log-likelihood at call 145: 97.22429</div><div class='output co'>#> <span class='message'>Optimisation successfully terminated.</span></div><div class='output co'>#> User System verstrichen -#> 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'>#> 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'>#> $ff +#> 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'>#> 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'>#> $ff #> parent_sink parent_m1 m1_sink #> 0.485524 0.514476 1.000000 #> -#> $SFORB -#> logical(0) -#> #> $distimes #> DT50 DT90 #> 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'><-</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'>#> <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'><-</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'>#> <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'>#> 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'>#> <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'><-</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'>#> <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'>#> mkin version used for fitting: 0.9.49.11 #> R version used for fitting: 3.6.3 -#> Date of fit: Mon Mar 30 21:41:36 2020 -#> Date of summary: Mon Mar 30 21:41:36 2020 +#> Date of fit: Mon Apr 20 18:52:37 2020 +#> Date of summary: Mon Apr 20 18:52:37 2020 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -615,7 +609,7 @@ estimators.</p> #> #> Model predictions using solution type deSolve #> -#> Fitted using 422 model solutions performed in 1.144 s +#> Fitted using 422 model solutions performed in 1.087 s #> #> Error model: Constant variance #> @@ -721,10 +715,10 @@ estimators.</p> #> 100 m1 31.04 31.98163 -9.416e-01 #> 100 m1 33.13 31.98163 1.148e+00 #> 120 m1 25.15 28.78984 -3.640e+00 -#> 120 m1 33.31 28.78984 4.520e+00</div><div class='input'><span class='no'>f.obs</span> <span class='kw'><-</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'>#> <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'>#> mkin version used for fitting: 0.9.49.9 +#> 120 m1 33.31 28.78984 4.520e+00</div><div class='input'><span class='no'>f.obs</span> <span class='kw'><-</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'>#> <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'>#> mkin version used for fitting: 0.9.49.11 #> R version used for fitting: 3.6.3 -#> Date of fit: Mon Mar 30 21:41:39 2020 -#> Date of summary: Mon Mar 30 21:41:39 2020 +#> Date of fit: Mon Apr 20 18:52:40 2020 +#> Date of summary: Mon Apr 20 18:52:40 2020 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -732,7 +726,7 @@ estimators.</p> #> #> Model predictions using solution type deSolve #> -#> Fitted using 979 model solutions performed in 2.576 s +#> Fitted using 979 model solutions performed in 2.518 s #> #> Error model: Variance unique to each observed variable #> @@ -853,10 +847,10 @@ estimators.</p> #> 100 m1 31.04 31.98773 -9.477e-01 #> 100 m1 33.13 31.98773 1.142e+00 #> 120 m1 25.15 28.80429 -3.654e+00 -#> 120 m1 33.31 28.80429 4.506e+00</div><div class='input'><span class='no'>f.tc</span> <span class='kw'><-</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'>#> <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'>#> mkin version used for fitting: 0.9.49.9 +#> 120 m1 33.31 28.80429 4.506e+00</div><div class='input'><span class='no'>f.tc</span> <span class='kw'><-</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'>#> <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'>#> mkin version used for fitting: 0.9.49.11 #> R version used for fitting: 3.6.3 -#> Date of fit: Mon Mar 30 21:41:50 2020 -#> Date of summary: Mon Mar 30 21:41:50 2020 +#> Date of fit: Mon Apr 20 18:52:50 2020 +#> Date of summary: Mon Apr 20 18:52:50 2020 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -864,7 +858,7 @@ estimators.</p> #> #> Model predictions using solution type deSolve #> -#> Fitted using 2552 model solutions performed in 10.593 s +#> Fitted using 2552 model solutions performed in 10.186 s #> #> Error model: Two-component variance function #> |