diff options
-rw-r--r-- | R/D24_2014.R | 1 | ||||
-rw-r--r-- | docs/dev/404.html | 2 | ||||
-rw-r--r-- | docs/dev/articles/index.html | 2 | ||||
-rw-r--r-- | docs/dev/authors.html | 2 | ||||
-rw-r--r-- | docs/dev/index.html | 2 | ||||
-rw-r--r-- | docs/dev/news/index.html | 2 | ||||
-rw-r--r-- | docs/dev/pkgdown.yml | 2 | ||||
-rw-r--r-- | docs/dev/reference/D24_2014.html | 20 | ||||
-rw-r--r-- | docs/dev/reference/index.html | 2 | ||||
-rw-r--r-- | docs/dev/reference/saem.html | 41 | ||||
-rw-r--r-- | man/D24_2014.Rd | 1 | ||||
-rw-r--r-- | man/saem.Rd | 2 |
12 files changed, 49 insertions, 30 deletions
diff --git a/R/D24_2014.R b/R/D24_2014.R index bca56dc2..654e1106 100644 --- a/R/D24_2014.R +++ b/R/D24_2014.R @@ -27,4 +27,5 @@ #' m_D24 = mkinmod(D24 = mkinsub("SFO", to = "DCP"), #' DCP = mkinsub("SFO", to = "DCA"), #' DCA = mkinsub("SFO")) +#' print(D24_2014) "D24_2014" diff --git a/docs/dev/404.html b/docs/dev/404.html index 8ca69469..bea38406 100644 --- a/docs/dev/404.html +++ b/docs/dev/404.html @@ -120,7 +120,7 @@ <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> diff --git a/docs/dev/articles/index.html b/docs/dev/articles/index.html index 81d49aa3..6daa6960 100644 --- a/docs/dev/articles/index.html +++ b/docs/dev/articles/index.html @@ -120,7 +120,7 @@ <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> diff --git a/docs/dev/authors.html b/docs/dev/authors.html index 681b964d..d592b39f 100644 --- a/docs/dev/authors.html +++ b/docs/dev/authors.html @@ -120,7 +120,7 @@ <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> diff --git a/docs/dev/index.html b/docs/dev/index.html index b1b64e6d..a4399963 100644 --- a/docs/dev/index.html +++ b/docs/dev/index.html @@ -87,7 +87,7 @@ <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> diff --git a/docs/dev/news/index.html b/docs/dev/news/index.html index 7059189d..e21de4c2 100644 --- a/docs/dev/news/index.html +++ b/docs/dev/news/index.html @@ -120,7 +120,7 @@ <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> diff --git a/docs/dev/pkgdown.yml b/docs/dev/pkgdown.yml index db10e692..a106449f 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: 2020-12-11T14:39Z +last_built: 2020-12-16T17:28Z 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 e4a3216d..5ebf664e 100644 --- a/docs/dev/reference/D24_2014.html +++ b/docs/dev/reference/D24_2014.html @@ -220,7 +220,25 @@ specific pieces of information in the comments.</p> #> 13 365 6.3</div><div class='input'><span class='va'>m_D24</span> <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>D24 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"DCP"</span><span class='op'>)</span>, DCP <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"DCA"</span><span class='op'>)</span>, DCA <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></pre> +</div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></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> +</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: +#> D24 DCP DCA +#> 5 4 4 +#> 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></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/index.html b/docs/dev/reference/index.html index 5c964cf9..d2040184 100644 --- a/docs/dev/reference/index.html +++ b/docs/dev/reference/index.html @@ -120,7 +120,7 @@ <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> diff --git a/docs/dev/reference/saem.html b/docs/dev/reference/saem.html index 73699e19..67468f89 100644 --- a/docs/dev/reference/saem.html +++ b/docs/dev/reference/saem.html @@ -160,7 +160,6 @@ Expectation Maximisation algorithm (SAEM).</p> solution_type <span class='op'>=</span> <span class='st'>"auto"</span>, control <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>displayProgress <span class='op'>=</span> <span class='cn'>FALSE</span>, print <span class='op'>=</span> <span class='cn'>FALSE</span>, save <span class='op'>=</span> <span class='cn'>FALSE</span>, save.graphs <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>, - cores <span class='op'>=</span> <span class='fl'>1</span>, verbose <span class='op'>=</span> <span class='cn'>FALSE</span>, suppressPlot <span class='op'>=</span> <span class='cn'>TRUE</span>, quiet <span class='op'>=</span> <span class='cn'>FALSE</span>, @@ -174,7 +173,6 @@ Expectation Maximisation algorithm (SAEM).</p> <span class='va'>object</span>, solution_type <span class='op'>=</span> <span class='st'>"auto"</span>, transformations <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'>"mkin"</span>, <span class='st'>"saemix"</span><span class='op'>)</span>, - cores <span class='op'>=</span> <span class='fl'>1</span>, verbose <span class='op'>=</span> <span class='cn'>FALSE</span>, <span class='va'>...</span> <span class='op'>)</span> @@ -262,27 +260,27 @@ 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] "Fri Dec 11 15:37:47 2020" +#> [1] "Wed Dec 16 18:27:30 2020" #> .... #> Minimisation finished -#> [1] "Fri Dec 11 15:37:49 2020"</div><div class='input'> +#> [1] "Wed Dec 16 18:27:31 2020"</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] "Fri Dec 11 15:37:51 2020" +#> [1] "Wed Dec 16 18:27:33 2020" #> .... #> Minimisation finished -#> [1] "Fri Dec 11 15:37:52 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] "Wed Dec 16 18:27:35 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> </div><div class='output co'>#> Running main SAEM algorithm -#> [1] "Fri Dec 11 15:37:52 2020" +#> [1] "Wed Dec 16 18:27:35 2020" #> .... #> Minimisation finished -#> [1] "Fri Dec 11 15:37:55 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] "Wed Dec 16 18:27:37 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> </div><div class='output co'>#> Running main SAEM algorithm -#> [1] "Fri Dec 11 15:37:55 2020" +#> [1] "Wed Dec 16 18:27:37 2020" #> .... #> Minimisation finished -#> [1] "Fri Dec 11 15:37:58 2020"</div><div class='input'> +#> [1] "Wed Dec 16 18:27:40 2020"</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> @@ -328,10 +326,10 @@ 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] "Fri Dec 11 15:38:01 2020" +#> [1] "Wed Dec 16 18:27:43 2020" #> .... #> Minimisation finished -#> [1] "Fri Dec 11 15:38:06 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'>$</span><span class='va'>so</span><span class='op'>)</span><span class='op'>)</span> +#> [1] "Wed Dec 16 18:27:48 2020"</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/compare.saemix.html'>compare.saemix</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='va'>f_saem_fomc</span><span class='op'>$</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'>#> 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'> @@ -352,15 +350,15 @@ 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] "Fri Dec 11 15:38:09 2020" +#> [1] "Wed Dec 16 18:27:50 2020" #> .... #> Minimisation finished -#> [1] "Fri Dec 11 15:38:14 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] "Wed Dec 16 18:27:55 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> </div><div class='output co'>#> Running main SAEM algorithm -#> [1] "Fri Dec 11 15:38:15 2020" +#> [1] "Wed Dec 16 18:27:56 2020" #> .... #> Minimisation finished -#> [1] "Fri Dec 11 15:38:24 2020"</div><div class='input'><span class='co'># We can use print, plot and summary methods to check the results</span> +#> [1] "Wed Dec 16 18:28:05 2020"</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: @@ -375,6 +373,8 @@ using <a href='mmkin.html'>mmkin</a>.</p> #> 170 observations of 2 variable(s) grouped in 5 datasets #> #> Likelihood computed by importance sampling +#> +#> LL by is "-407.78 (df=13)" #> AIC BIC logLik #> 841.6 836.5 -407.8 #> @@ -400,11 +400,12 @@ using <a href='mmkin.html'>mmkin</a>.</p> #> SD.log_k2 1.90634 0.70934 3.1033 #> SD.g_qlogis 0.44771 -0.86417 1.7596</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_dfop_sfo</span><span class='op'>)</span> </div><div class='img'><img src='saem-5.png' alt='' width='700' height='433' /></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 +</div><div class='output co'>#> +#> LL by is "-407.78 (df=13)"</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: Fri Dec 11 15:38:25 2020 -#> Date of summary: Fri Dec 11 15:38:25 2020 +#> Date of fit: Wed Dec 16 18:28:06 2020 +#> Date of summary: Wed Dec 16 18:28:06 2020 #> #> Equations: #> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -419,7 +420,7 @@ using <a href='mmkin.html'>mmkin</a>.</p> #> #> Model predictions using solution type analytical #> -#> Fitted in 10.096 s using 300, 100 iterations +#> Fitted in 9.889 s using 300, 100 iterations #> #> Variance model: Constant variance #> diff --git a/man/D24_2014.Rd b/man/D24_2014.Rd index d0ab516a..90fde27b 100644 --- a/man/D24_2014.Rd +++ b/man/D24_2014.Rd @@ -40,5 +40,6 @@ print(D24_2014$ds[[1]], data = TRUE) m_D24 = mkinmod(D24 = mkinsub("SFO", to = "DCP"), DCP = mkinsub("SFO", to = "DCA"), DCA = mkinsub("SFO")) +print(D24_2014) } \keyword{datasets} diff --git a/man/saem.Rd b/man/saem.Rd index 1fdfb2c4..dba948bb 100644 --- a/man/saem.Rd +++ b/man/saem.Rd @@ -16,7 +16,6 @@ saem(object, ...) solution_type = "auto", control = list(displayProgress = FALSE, print = FALSE, save = FALSE, save.graphs = FALSE), - cores = 1, verbose = FALSE, suppressPlot = TRUE, quiet = FALSE, @@ -29,7 +28,6 @@ saemix_model( object, solution_type = "auto", transformations = c("mkin", "saemix"), - cores = 1, verbose = FALSE, ... ) |