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| -rw-r--r-- | R/mkinfit.R | 2 | ||||
| -rw-r--r-- | build.log | 4 | ||||
| -rw-r--r-- | docs/dev/news/index.html | 26 | ||||
| -rw-r--r-- | docs/dev/pkgdown.yml | 2 | ||||
| -rw-r--r-- | docs/dev/reference/D24_2014.html | 32 | ||||
| -rw-r--r-- | docs/dev/reference/Rplot001.png | bin | 19395 -> 1011 bytes | |||
| -rw-r--r-- | docs/dev/reference/mccall81_245T.html | 4 | ||||
| -rw-r--r-- | docs/dev/reference/mkinfit.html | 23 | ||||
| -rw-r--r-- | docs/dev/reference/saem.html | 43 | ||||
| -rw-r--r-- | docs/dev/reference/summary.saem.mmkin.html | 20 | ||||
| -rw-r--r-- | man/mccall81_245T.Rd | 2 | ||||
| -rw-r--r-- | man/mkinfit.Rd | 2 | ||||
| -rw-r--r-- | man/saem.Rd | 8 | ||||
| -rw-r--r-- | man/summary.saem.mmkin.Rd | 2 |
14 files changed, 97 insertions, 73 deletions
diff --git a/R/mkinfit.R b/R/mkinfit.R index c659e446..d7de718b 100644 --- a/R/mkinfit.R +++ b/R/mkinfit.R @@ -169,7 +169,7 @@ utils::globalVariables(c("name", "time", "value")) #' #' Ranke J and Meinecke S (2019) Error Models for the Kinetic Evaluation of Chemical #' Degradation Data. *Environments* 6(12) 124 -#' [doi:10.3390/environments6120124](https://doi.org/10.3390/environments6120124). +#' \doi{10.3390/environments6120124}. #' @examples #' #' # Use shorthand notation for parent only degradation @@ -1,9 +1,11 @@ * checking for file ‘./DESCRIPTION’ ... OK * preparing ‘mkin’: * checking DESCRIPTION meta-information ... OK -* installing the package to build vignettes +* installing the package to process help pages +* saving partial Rd database * creating vignettes ... OK * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories +Removed empty directory ‘mkin/tests/testthat/_snaps’ * building ‘mkin_0.9.50.4.tar.gz’ diff --git a/docs/dev/news/index.html b/docs/dev/news/index.html index e21de4c2..c3597efe 100644 --- a/docs/dev/news/index.html +++ b/docs/dev/news/index.html @@ -145,21 +145,33 @@ <h1 class="page-header" data-toc-text="0.9.50.4"> <a href="#mkin-0-9-50-4-unreleased" class="anchor"></a>mkin 0.9.50.4 (unreleased)<small> Unreleased </small> </h1> +<div id="general-new-features" class="section level2"> +<h2 class="hasAnchor"> +<a href="#general-new-features" class="anchor"></a>General new features</h2> <ul> -<li><p>‘mixed.mmkin’ New container for mmkin objects for plotting with the ‘plot.mixed.mmkin’ method</p></li> <li><p>‘mkinmod’ models gain arguments ‘name’ and ‘dll_dir’ which, in conjunction with a current version of the ‘inline’ package, make it possible to still use the DLL used for fast ODE solutions with ‘deSolve’ after saving and restoring the ‘mkinmod’ object.</p></li> -<li><p>‘f_norm_temp_focus’ generic function to normalise time intervals using the FOCUS method, with methods for numeric vectors and ‘mkindsg’ objects</p></li> <li><p>‘mkindsg’ R6 class for groups of ‘mkinds’ datasets with metadata</p></li> -<li><p>‘D24_2014’ dataset</p></li> +<li><p>‘f_norm_temp_focus’ generic function to normalise time intervals using the FOCUS method, with methods for numeric vectors and ‘mkindsg’ objects</p></li> +<li><p>‘D24_2014’ and ‘dimethenamid_2018’ datasets</p></li> <li><p>‘focus_soil_moisture’ FOCUS default soil moisture data</p></li> -<li><p>‘plot.mixed.mmkin’ method used for ‘nlme.mmkin’ and ‘saem.mmkin’, both inheriting from ‘mixed.mmkin’ (currently virtual)</p></li> -<li><p>‘saem’ generic function to fit saemix models, with a generator ‘saem.mmkin’, summary and plot methods</p></li> -<li><p>‘transform_odeparms’, ‘backtransform_odeparms’: Use logit transformation for solitary fractions like the g parameter of the DFOP model, or formation fractions for a pathway to only one target variable</p></li> <li><p>‘update’ method for ‘mmkin’ objects</p></li> +<li><p>‘transform_odeparms’, ‘backtransform_odeparms’: Use logit transformation for solitary fractions like the g parameter of the DFOP model, or formation fractions for a pathway to only one target variable</p></li> +</ul> +</div> +<div id="mixed-effects-models" class="section level2"> +<h2 class="hasAnchor"> +<a href="#mixed-effects-models" class="anchor"></a>Mixed-effects models</h2> +<ul> +<li><p>‘mixed.mmkin’ New container for mmkin objects for plotting with the ‘plot.mixed.mmkin’ method</p></li> +<li><p>‘plot.mixed.mmkin’ method used for ‘nlme.mmkin’ and ‘saem.mmkin’, both inheriting from ‘mixed.mmkin’ (currently virtual)</p></li> <li><p>‘plot’, ‘summary’ and ‘print’ methods for ‘nlme.mmkin’ objects</p></li> -<li><p>‘saemix_model’, ‘saemix_data’: Helper functions to fit nonlinear mixed-effects models for mmkin row objects using the saemix package</p></li> +<li><p>Add the current development version of the saemix package as a second, optional backend for mixed-effects models</p></li> +<li><p>DESCRIPTION: Additional_repositories entry pointing to my drat repository on github for a suitable saemix version</p></li> +<li><p>‘saemix_model’, ‘saemix_data’: Helper functions to fit nonlinear mixed-effects models for mmkin row objects.</p></li> +<li><p>‘saem’ generic function to fit saemix models using ‘saemix_model’ and ‘saemix_data’, with a generator ‘saem.mmkin’, summary and plot methods</p></li> </ul> </div> +</div> <div id="mkin-0-9-50-3-2020-10-08" class="section level1"> <h1 class="page-header" data-toc-text="0.9.50.3"> <a href="#mkin-0-9-50-3-2020-10-08" class="anchor"></a>mkin 0.9.50.3 (2020-10-08)<small> 2020-10-08 </small> diff --git a/docs/dev/pkgdown.yml b/docs/dev/pkgdown.yml index 85a358df..3591cac8 100644 --- a/docs/dev/pkgdown.yml +++ b/docs/dev/pkgdown.yml @@ -10,7 +10,7 @@ articles: web_only/NAFTA_examples: NAFTA_examples.html web_only/benchmarks: benchmarks.html web_only/compiled_models: compiled_models.html -last_built: 2020-12-21T04:57Z +last_built: 2021-01-11T11:41Z urls: reference: https://pkgdown.jrwb.de/mkin/reference article: https://pkgdown.jrwb.de/mkin/articles diff --git a/docs/dev/reference/D24_2014.html b/docs/dev/reference/D24_2014.html index 8160316f..2498c58e 100644 --- a/docs/dev/reference/D24_2014.html +++ b/docs/dev/reference/D24_2014.html @@ -183,22 +183,25 @@ specific pieces of information in the comments.</p> <pre class="examples"><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>D24_2014</span><span class='op'>)</span> </div><div class='output co'>#> <mkindsg> holding 5 mkinds objects #> Title $title: Aerobic soil degradation data on 2,4-D from the EU assessment in 2014 -#> Occurrene of observed compounds $observed_n: +#> Occurrence of observed compounds $observed_n: #> D24 DCP DCA #> 5 4 4 +#> Time normalisation factors $f_time_norm: +#> [1] 1.6062378 0.7118732 0.7156063 0.7156063 0.8977124 #> Meta information $meta: -#> study usda_soil_type study_moisture_ref_type rel_moisture -#> 1 Cohen 1991 Silt loam <NA> NA -#> 2 Liu and Adelfinskaya 2011 Silt loam pF1 0.5 -#> 3 Liu and Adelfinskaya 2011 Loam pF1 0.5 -#> 4 Liu and Adelfinskaya 2011 Loam pF1 0.5 -#> 5 Liu and Adelfinskaya 2011 Loamy sand pF1 0.5 -#> temperature -#> 1 25 -#> 2 20 -#> 3 20 -#> 4 20 -#> 5 20</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>D24_2014</span><span class='op'>$</span><span class='va'>ds</span><span class='op'>[[</span><span class='fl'>1</span><span class='op'>]</span><span class='op'>]</span>, data <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> +#> study usda_soil_type study_moisture_ref_type +#> Mississippi Cohen 1991 Silt loam <NA> +#> Fayette Liu and Adelfinskaya 2011 Silt loam pF1 +#> RefSol 03-G Liu and Adelfinskaya 2011 Loam pF1 +#> Site E1 Liu and Adelfinskaya 2011 Loam pF1 +#> Site I2 Liu and Adelfinskaya 2011 Loamy sand pF1 +#> rel_moisture temperature +#> Mississippi NA 25 +#> Fayette 0.5 20 +#> RefSol 03-G 0.5 20 +#> Site E1 0.5 20 +#> Site I2 0.5 20</div><div class='input'><span class='co'># \dontrun{</span> +<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>D24_2014</span><span class='op'>$</span><span class='va'>ds</span><span class='op'>[[</span><span class='fl'>1</span><span class='op'>]</span><span class='op'>]</span>, data <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> </div><div class='output co'>#> <mkinds> with $title: Mississippi #> Observed compounds $observed: D24 #> Sampling times $sampling_times: @@ -256,7 +259,8 @@ specific pieces of information in the comments.</p> #> d_DCP/dt = + f_D24_to_DCP * ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * #> exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 #> * time))) * D24 - k_DCP * DCP -#> d_DCA/dt = + f_DCP_to_DCA * k_DCP * DCP - k_DCA * DCA</div></pre> +#> d_DCA/dt = + f_DCP_to_DCA * k_DCP * DCP - k_DCA * DCA</div><div class='input'><span class='co'># }</span> +</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> <nav id="toc" data-toggle="toc" class="sticky-top"> diff --git a/docs/dev/reference/Rplot001.png b/docs/dev/reference/Rplot001.png Binary files differindex bca41e2c..17a35806 100644 --- a/docs/dev/reference/Rplot001.png +++ b/docs/dev/reference/Rplot001.png diff --git a/docs/dev/reference/mccall81_245T.html b/docs/dev/reference/mccall81_245T.html index c23bfda2..7179533d 100644 --- a/docs/dev/reference/mccall81_245T.html +++ b/docs/dev/reference/mccall81_245T.html @@ -123,7 +123,7 @@ <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin/"> - <span class="fab fa fab fa-github fa-lg"></span> + <span class="fab fa-github fa-lg"></span> </a> </li> @@ -171,7 +171,7 @@ <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> <p>McCall P, Vrona SA, Kelley SS (1981) Fate of uniformly carbon-14 ring labelled 2,4,5-Trichlorophenoxyacetic acid and 2,4-dichlorophenoxyacetic acid. J Agric Chem 29, 100-107 - <a href='http://dx.doi.org/10.1021/jf00103a026'>http://dx.doi.org/10.1021/jf00103a026</a></p> + doi: <a href='https://doi.org/10.1021/jf00103a026'>10.1021/jf00103a026</a></p> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> <span class='va'>SFO_SFO_SFO</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>T245 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"phenol"</span><span class='op'>)</span>, diff --git a/docs/dev/reference/mkinfit.html b/docs/dev/reference/mkinfit.html index 73c09c1f..6ae7b343 100644 --- a/docs/dev/reference/mkinfit.html +++ b/docs/dev/reference/mkinfit.html @@ -129,7 +129,7 @@ likelihood function." /> <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin/"> - <span class="fab fa fab fa-github fa-lg"></span> + <span class="fab fa-github fa-lg"></span> </a> </li> @@ -413,7 +413,8 @@ internal rate transformation.</p> for measurement error in analytical chemistry. <em>Technometrics</em> 37(2), 176-184.</p> <p>Ranke J and Meinecke S (2019) Error Models for the Kinetic Evaluation of Chemical Degradation Data. <em>Environments</em> 6(12) 124 -<a href='https://doi.org/10.3390/environments6120124'>doi:10.3390/environments6120124</a>.</p> +doi: <a href='https://doi.org/10.3390/environments6120124'>10.3390/environments6120124</a> +.</p> <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> <div class='dont-index'><p><a href='summary.mkinfit.html'>summary.mkinfit</a>, <a href='plot.mkinfit.html'>plot.mkinfit</a>, <a href='parms.html'>parms</a> and <a href='https://rdrr.io/pkg/lmtest/man/lrtest.html'>lrtest</a>.</p> @@ -432,8 +433,8 @@ Degradation Data. <em>Environments</em> 6(12) 124 <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span> </div><div class='output co'>#> mkin version used for fitting: 0.9.50.4 #> R version used for fitting: 4.0.3 -#> Date of fit: Mon Nov 30 15:48:34 2020 -#> Date of summary: Mon Nov 30 15:48:34 2020 +#> Date of fit: Mon Jan 11 12:41:45 2021 +#> Date of summary: Mon Jan 11 12:41:45 2021 #> #> Equations: #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent @@ -573,10 +574,10 @@ Degradation Data. <em>Environments</em> 6(12) 124 analytical <span class='op'>=</span> <span class='fu'>mkinfit</span><span class='op'>(</span><span class='va'>SFO_SFO</span>, <span class='va'>FOCUS_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span>, solution_type <span class='op'>=</span> <span class='st'>"analytical"</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>}</span> -</div><div class='output co'>#> test relative elapsed -#> 3 analytical 1.000 0.532 -#> 1 deSolve_compiled 1.831 0.974 -#> 2 eigen 2.235 1.189</div><div class='input'><span class='co'># }</span> +</div><div class='output co'>#> <span class='message'>Loading required package: rbenchmark</span></div><div class='output co'>#> test relative elapsed +#> 3 analytical 1.000 0.526 +#> 1 deSolve_compiled 1.903 1.001 +#> 2 eigen 2.308 1.214</div><div class='input'><span class='co'># }</span> <span class='co'># Use stepwise fitting, using optimised parameters from parent only fit, FOMC-SFO</span> <span class='co'># \dontrun{</span> @@ -600,8 +601,8 @@ Degradation Data. <em>Environments</em> 6(12) 124 <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>fit.FOMC_SFO.tc</span>, data <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span> </div><div class='output co'>#> <span class='warning'>Warning: NaNs produced</span></div><div class='output co'>#> <span class='warning'>Warning: NaNs produced</span></div><div class='output co'>#> <span class='warning'>Warning: NaNs produced</span></div><div class='output co'>#> <span class='warning'>Warning: diag(.) had 0 or NA entries; non-finite result is doubtful</span></div><div class='output co'>#> mkin version used for fitting: 0.9.50.4 #> R version used for fitting: 4.0.3 -#> Date of fit: Mon Nov 30 15:48:45 2020 -#> Date of summary: Mon Nov 30 15:48:45 2020 +#> Date of fit: Mon Jan 11 12:41:56 2021 +#> Date of summary: Mon Jan 11 12:41:56 2021 #> #> Equations: #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent @@ -610,7 +611,7 @@ Degradation Data. <em>Environments</em> 6(12) 124 #> #> Model predictions using solution type deSolve #> -#> Fitted using 4273 model solutions performed in 3.191 s +#> Fitted using 4273 model solutions performed in 3.456 s #> #> Error model: Two-component variance function #> diff --git a/docs/dev/reference/saem.html b/docs/dev/reference/saem.html index 1e92e3fb..a832e911 100644 --- a/docs/dev/reference/saem.html +++ b/docs/dev/reference/saem.html @@ -267,33 +267,36 @@ using <a href='mmkin.html'>mmkin</a>.</p> state.ini <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fl'>100</span><span class='op'>)</span>, fixed_initials <span class='op'>=</span> <span class='st'>"parent"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> <span class='va'>f_saem_p0_fixed</span> <span class='op'><-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent_p0_fixed</span><span class='op'>)</span> </div><div class='output co'>#> Running main SAEM algorithm -#> [1] "Mon Dec 21 05:58:33 2020" +#> [1] "Mon Jan 11 12:42:01 2021" #> .... #> Minimisation finished -#> [1] "Mon Dec 21 05:58:34 2020"</div><div class='input'> +#> [1] "Mon Jan 11 12:42:03 2021"</div><div class='input'> <span class='va'>f_mmkin_parent</span> <span class='op'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"FOMC"</span>, <span class='st'>"DFOP"</span><span class='op'>)</span>, <span class='va'>ds</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> <span class='va'>f_saem_sfo</span> <span class='op'><-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"SFO"</span>, <span class='op'>]</span><span class='op'>)</span> </div><div class='output co'>#> Running main SAEM algorithm -#> [1] "Mon Dec 21 05:58:36 2020" +#> [1] "Mon Jan 11 12:42:04 2021" #> .... #> Minimisation finished -#> [1] "Mon Dec 21 05:58:37 2020"</div><div class='input'><span class='va'>f_saem_fomc</span> <span class='op'><-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span><span class='op'>)</span> +#> [1] "Mon Jan 11 12:42:06 2021"</div><div class='input'><span class='va'>f_saem_fomc</span> <span class='op'><-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span><span class='op'>)</span> </div><div class='output co'>#> Running main SAEM algorithm -#> [1] "Mon Dec 21 05:58:38 2020" +#> [1] "Mon Jan 11 12:42:06 2021" #> .... #> Minimisation finished -#> [1] "Mon Dec 21 05:58:40 2020"</div><div class='input'><span class='va'>f_saem_dfop</span> <span class='op'><-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"DFOP"</span>, <span class='op'>]</span><span class='op'>)</span> +#> [1] "Mon Jan 11 12:42:08 2021"</div><div class='input'><span class='va'>f_saem_dfop</span> <span class='op'><-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"DFOP"</span>, <span class='op'>]</span><span class='op'>)</span> </div><div class='output co'>#> Running main SAEM algorithm -#> [1] "Mon Dec 21 05:58:40 2020" +#> [1] "Mon Jan 11 12:42:09 2021" #> .... #> Minimisation finished -#> [1] "Mon Dec 21 05:58:43 2020"</div><div class='input'> +#> [1] "Mon Jan 11 12:42:12 2021"</div><div class='input'> <span class='co'># The returned saem.mmkin object contains an SaemixObject, therefore we can use</span> <span class='co'># functions from saemix</span> <span class='kw'><a href='https://rdrr.io/r/base/library.html'>library</a></span><span class='op'>(</span><span class='va'>saemix</span><span class='op'>)</span> </div><div class='output co'>#> <span class='message'>Package saemix, version 3.1.9000</span> #> <span class='message'> please direct bugs, questions and feedback to emmanuelle.comets@inserm.fr</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/compare.saemix.html'>compare.saemix</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='va'>f_saem_sfo</span><span class='op'>$</span><span class='va'>so</span>, <span class='va'>f_saem_fomc</span><span class='op'>$</span><span class='va'>so</span>, <span class='va'>f_saem_dfop</span><span class='op'>$</span><span class='va'>so</span><span class='op'>)</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='error'>Error in compare.saemix(list(f_saem_sfo$so, f_saem_fomc$so, f_saem_dfop$so)): 'compare.saemix' requires at least two models.</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html'>plot</a></span><span class='op'>(</span><span class='va'>f_saem_fomc</span><span class='op'>$</span><span class='va'>so</span>, plot.type <span class='op'>=</span> <span class='st'>"convergence"</span><span class='op'>)</span> +</div><div class='output co'>#> Likelihoods computed by importance sampling </div><div class='output co'>#> AIC BIC +#> 1 624.2484 622.2956 +#> 2 467.7096 464.9757 +#> 3 495.4373 491.9222</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html'>plot</a></span><span class='op'>(</span><span class='va'>f_saem_fomc</span><span class='op'>$</span><span class='va'>so</span>, plot.type <span class='op'>=</span> <span class='st'>"convergence"</span><span class='op'>)</span> </div><div class='output co'>#> Plotting convergence plots</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html'>plot</a></span><span class='op'>(</span><span class='va'>f_saem_fomc</span><span class='op'>$</span><span class='va'>so</span>, plot.type <span class='op'>=</span> <span class='st'>"individual.fit"</span><span class='op'>)</span> </div><div class='img'><img src='saem-1.png' alt='' width='700' height='433' /></div><div class='output co'>#> Plotting individual fits</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html'>plot</a></span><span class='op'>(</span><span class='va'>f_saem_fomc</span><span class='op'>$</span><span class='va'>so</span>, plot.type <span class='op'>=</span> <span class='st'>"npde"</span><span class='op'>)</span> </div><div class='img'><img src='saem-2.png' alt='' width='700' height='433' /></div><div class='output co'>#> Simulating data using nsim = 1000 simulated datasets @@ -330,11 +333,13 @@ using <a href='mmkin.html'>mmkin</a>.</p> <span class='va'>f_mmkin_parent_tc</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span><span class='op'>(</span><span class='va'>f_mmkin_parent</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span><span class='op'>)</span> <span class='va'>f_saem_fomc_tc</span> <span class='op'><-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent_tc</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span><span class='op'>)</span> </div><div class='output co'>#> Running main SAEM algorithm -#> [1] "Mon Dec 21 05:58:46 2020" +#> [1] "Mon Jan 11 12:42:14 2021" #> .... #> Minimisation finished -#> [1] "Mon Dec 21 05:58:51 2020"</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/compare.saemix.html'>compare.saemix</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='va'>f_saem_fomc</span><span class='op'>$</span><span class='va'>so</span>, <span class='va'>f_saem_fomc_tc</span><span class='op'>$</span><span class='va'>so</span><span class='op'>)</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='error'>Error in compare.saemix(list(f_saem_fomc$so, f_saem_fomc_tc$so)): 'compare.saemix' requires at least two models.</span></div><div class='input'> +#> [1] "Mon Jan 11 12:42:19 2021"</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/compare.saemix.html'>compare.saemix</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='va'>f_saem_fomc</span><span class='op'>$</span><span class='va'>so</span>, <span class='va'>f_saem_fomc_tc</span><span class='op'>$</span><span class='va'>so</span><span class='op'>)</span><span class='op'>)</span> +</div><div class='output co'>#> Likelihoods computed by importance sampling </div><div class='output co'>#> AIC BIC +#> 1 467.7096 464.9757 +#> 2 469.5208 466.3963</div><div class='input'> <span class='va'>sfo_sfo</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"A1"</span><span class='op'>)</span>, A1 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span><span class='op'>)</span> </div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'><span class='va'>fomc_sfo</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"FOMC"</span>, <span class='st'>"A1"</span><span class='op'>)</span>, @@ -352,15 +357,15 @@ using <a href='mmkin.html'>mmkin</a>.</p> <span class='co'># four minutes</span> <span class='va'>f_saem_sfo_sfo</span> <span class='op'><-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin</span><span class='op'>[</span><span class='st'>"SFO-SFO"</span>, <span class='op'>]</span><span class='op'>)</span> </div><div class='output co'>#> Running main SAEM algorithm -#> [1] "Mon Dec 21 05:58:53 2020" +#> [1] "Mon Jan 11 12:42:22 2021" #> .... #> Minimisation finished -#> [1] "Mon Dec 21 05:58:58 2020"</div><div class='input'><span class='va'>f_saem_dfop_sfo</span> <span class='op'><-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin</span><span class='op'>[</span><span class='st'>"DFOP-SFO"</span>, <span class='op'>]</span><span class='op'>)</span> +#> [1] "Mon Jan 11 12:42:27 2021"</div><div class='input'><span class='va'>f_saem_dfop_sfo</span> <span class='op'><-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin</span><span class='op'>[</span><span class='st'>"DFOP-SFO"</span>, <span class='op'>]</span><span class='op'>)</span> </div><div class='output co'>#> Running main SAEM algorithm -#> [1] "Mon Dec 21 05:58:59 2020" +#> [1] "Mon Jan 11 12:42:28 2021" #> .... #> Minimisation finished -#> [1] "Mon Dec 21 05:59:08 2020"</div><div class='input'><span class='co'># We can use print, plot and summary methods to check the results</span> +#> [1] "Mon Jan 11 12:42:37 2021"</div><div class='input'><span class='co'># We can use print, plot and summary methods to check the results</span> <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>f_saem_dfop_sfo</span><span class='op'>)</span> </div><div class='output co'>#> Kinetic nonlinear mixed-effects model fit by SAEM #> Structural model: @@ -403,8 +408,8 @@ using <a href='mmkin.html'>mmkin</a>.</p> </div><div class='output co'>#> saemix version used for fitting: 3.1.9000 #> mkin version used for pre-fitting: 0.9.50.4 #> R version used for fitting: 4.0.3 -#> Date of fit: Mon Dec 21 05:59:09 2020 -#> Date of summary: Mon Dec 21 05:59:09 2020 +#> Date of fit: Mon Jan 11 12:42:38 2021 +#> Date of summary: Mon Jan 11 12:42:38 2021 #> #> Equations: #> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -419,7 +424,7 @@ using <a href='mmkin.html'>mmkin</a>.</p> #> #> Model predictions using solution type analytical #> -#> Fitted in 9.836 s using 300, 100 iterations +#> Fitted in 10.092 s using 300, 100 iterations #> #> Variance model: Constant variance #> diff --git a/docs/dev/reference/summary.saem.mmkin.html b/docs/dev/reference/summary.saem.mmkin.html index 1a82f7ef..722415fb 100644 --- a/docs/dev/reference/summary.saem.mmkin.html +++ b/docs/dev/reference/summary.saem.mmkin.html @@ -125,7 +125,7 @@ endpoints such as formation fractions and DT50 values. Optionally <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin/"> - <span class="fab fa fab fa-github fa-lg"></span> + <span class="fab fa-github fa-lg"></span> </a> </li> @@ -260,15 +260,15 @@ saemix authors for the parts inherited from saemix.</p> quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span>, cores <span class='op'>=</span> <span class='fl'>5</span><span class='op'>)</span> <span class='va'>f_saem_dfop_sfo</span> <span class='op'><-</span> <span class='fu'><a href='saem.html'>saem</a></span><span class='op'>(</span><span class='va'>f_mmkin_dfop_sfo</span><span class='op'>)</span> </div><div class='output co'>#> Running main SAEM algorithm -#> [1] "Mon Nov 30 16:01:26 2020" +#> [1] "Mon Jan 11 12:42:40 2021" #> .... #> Minimisation finished -#> [1] "Mon Nov 30 16:01:39 2020"</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>f_saem_dfop_sfo</span>, data <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> +#> [1] "Mon Jan 11 12:42:53 2021"</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>f_saem_dfop_sfo</span>, data <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> </div><div class='output co'>#> saemix version used for fitting: 3.1.9000 #> mkin version used for pre-fitting: 0.9.50.4 #> R version used for fitting: 4.0.3 -#> Date of fit: Mon Nov 30 16:01:40 2020 -#> Date of summary: Mon Nov 30 16:01:40 2020 +#> Date of fit: Mon Jan 11 12:42:54 2021 +#> Date of summary: Mon Jan 11 12:42:54 2021 #> #> Equations: #> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -283,15 +283,15 @@ saemix authors for the parts inherited from saemix.</p> #> #> Model predictions using solution type analytical #> -#> Fitted in 14.5 s using 300, 100 iterations +#> Fitted in 13.298 s using 300, 100 iterations #> #> Variance model: Two-component variance function #> #> Mean of starting values for individual parameters: #> parent_0 log_k_m1 f_parent_qlogis log_k1 log_k2 -#> 101.65644697 -4.05368181 -0.94310703 -2.35943247 -4.07006293 +#> 101.65645 -4.05368 -0.94311 -2.35943 -4.07006 #> g_qlogis -#> -0.01132621 +#> -0.01133 #> #> Fixed degradation parameter values: #> None @@ -302,7 +302,7 @@ saemix authors for the parts inherited from saemix.</p> #> AIC BIC logLik #> 830 824.5 -401 #> -#> Optimised, transformed parameters with symmetric confidence intervals: +#> Optimised parameters: #> est. lower upper #> parent_0 101.4423 97.862 105.0224 #> log_k_m1 -4.0703 -4.191 -3.9495 @@ -333,7 +333,7 @@ saemix authors for the parts inherited from saemix.</p> #> a.1 0.65859 0.49250 0.82469 #> b.1 0.06411 0.05006 0.07817 #> -#> Backtransformed parameters with asymmetric confidence intervals: +#> Backtransformed parameters: #> est. lower upper #> parent_0 101.44231 97.86220 105.02241 #> k_m1 0.01707 0.01513 0.01926 diff --git a/man/mccall81_245T.Rd b/man/mccall81_245T.Rd index 44a0c2cf..e7eaed94 100644 --- a/man/mccall81_245T.Rd +++ b/man/mccall81_245T.Rd @@ -25,7 +25,7 @@ }
\source{
McCall P, Vrona SA, Kelley SS (1981) Fate of uniformly carbon-14 ring labelled 2,4,5-Trichlorophenoxyacetic acid and 2,4-dichlorophenoxyacetic acid. J Agric Chem 29, 100-107
- \url{http://dx.doi.org/10.1021/jf00103a026}
+ \doi{10.1021/jf00103a026}
}
\examples{
SFO_SFO_SFO <- mkinmod(T245 = list(type = "SFO", to = "phenol"),
diff --git a/man/mkinfit.Rd b/man/mkinfit.Rd index 768b85d3..b5b24449 100644 --- a/man/mkinfit.Rd +++ b/man/mkinfit.Rd @@ -286,7 +286,7 @@ for measurement error in analytical chemistry. \emph{Technometrics} 37(2), 176-1 Ranke J and Meinecke S (2019) Error Models for the Kinetic Evaluation of Chemical Degradation Data. \emph{Environments} 6(12) 124 -\href{https://doi.org/10.3390/environments6120124}{doi:10.3390/environments6120124}. +\doi{10.3390/environments6120124}. } \seealso{ \link{summary.mkinfit}, \link{plot.mkinfit}, \link{parms} and \link{lrtest}. diff --git a/man/saem.Rd b/man/saem.Rd index 969e9a22..775a8e7b 100644 --- a/man/saem.Rd +++ b/man/saem.Rd @@ -57,7 +57,7 @@ automatic choice is not desired} \item{control}{Passed to \link[saemix:saemix]{saemix::saemix}} \item{verbose}{Should we print information about created objects of -type \link[saemix:SaemixModel]{saemix::SaemixModel} and \link[saemix:SaemixData]{saemix::SaemixData}?} +type \link[saemix:SaemixModel-class]{saemix::SaemixModel} and \link[saemix:SaemixData-class]{saemix::SaemixData}?} \item{suppressPlot}{Should we suppress any plotting that is done by the saemix function?} @@ -71,12 +71,12 @@ and the end of the optimisation process?} } \value{ An S3 object of class 'saem.mmkin', containing the fitted -\link[saemix:SaemixObject]{saemix::SaemixObject} as a list component named 'so'. The +\link[saemix:SaemixObject-class]{saemix::SaemixObject} as a list component named 'so'. The object also inherits from 'mixed.mmkin'. -An \link[saemix:SaemixModel]{saemix::SaemixModel} object. +An \link[saemix:SaemixModel-class]{saemix::SaemixModel} object. -An \link[saemix:SaemixData]{saemix::SaemixData} object. +An \link[saemix:SaemixData-class]{saemix::SaemixData} object. } \description{ This function uses \code{\link[saemix:saemix]{saemix::saemix()}} as a backend for fitting nonlinear mixed diff --git a/man/summary.saem.mmkin.Rd b/man/summary.saem.mmkin.Rd index 4f83489c..67cb3cbb 100644 --- a/man/summary.saem.mmkin.Rd +++ b/man/summary.saem.mmkin.Rd @@ -27,7 +27,7 @@ included.} \item{digits}{Number of digits to use for printing} } \value{ -The summary function returns a list based on the \link[saemix:SaemixObject]{saemix::SaemixObject} +The summary function returns a list based on the \link[saemix:SaemixObject-class]{saemix::SaemixObject} obtained in the fit, with at least the following additional components \item{saemixversion, mkinversion, Rversion}{The saemix, mkin and R versions used} \item{date.fit, date.summary}{The dates where the fit and the summary were |
