diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2022-09-16 10:51:48 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2022-09-16 10:51:48 +0200 |
| commit | 2a521ab0a4b7d981a2042353e2c60b8a877489b8 (patch) | |
| tree | 5198483a73f37335733cb78cb6507b3ffdbb9fe5 | |
| parent | 03e1598a3c79911a497758fe382461f288bf05e6 (diff) | |
Improve docs and update pkgdown
| -rw-r--r-- | R/multistart.R | 8 | ||||
| -rw-r--r-- | R/parms.mkinfit.R | 19 | ||||
| -rw-r--r-- | _pkgdown.yml | 7 | ||||
| -rw-r--r-- | docs/dev/articles/FOCUS_L.html | 36 | ||||
| -rw-r--r-- | docs/dev/articles/web_only/benchmarks.html | 22 | ||||
| -rw-r--r-- | docs/dev/articles/web_only/dimethenamid_2018.html | 34 | ||||
| -rw-r--r-- | docs/dev/news/index.html | 3 | ||||
| -rw-r--r-- | docs/dev/pkgdown.yml | 2 | ||||
| -rw-r--r-- | docs/dev/reference/aw.html | 202 | ||||
| -rw-r--r-- | docs/dev/reference/dimethenamid_2018.html | 6 | ||||
| -rw-r--r-- | docs/dev/reference/index.html | 22 | ||||
| -rw-r--r-- | docs/dev/reference/mkinfit.html | 17 | ||||
| -rw-r--r-- | docs/dev/reference/multistart.html | 195 | ||||
| -rw-r--r-- | docs/dev/reference/parms.html | 366 | ||||
| -rw-r--r-- | docs/dev/reference/saem.html | 18 | ||||
| -rw-r--r-- | docs/dev/reference/summary.mkinfit.html | 6 | ||||
| -rw-r--r-- | docs/dev/reference/summary.mmkin.html | 2 | ||||
| -rw-r--r-- | docs/dev/reference/summary.saem.mmkin.html | 6 | ||||
| -rw-r--r-- | docs/dev/sitemap.xml | 3 | ||||
| -rw-r--r-- | man/multistart.Rd | 10 | ||||
| -rw-r--r-- | man/parms.Rd | 21 | ||||
| -rw-r--r-- | vignettes/web_only/mkin_benchmarks.rda | bin | 1534 -> 1536 bytes |
22 files changed, 560 insertions, 445 deletions
diff --git a/R/multistart.R b/R/multistart.R index 94292e82..52f279f0 100644 --- a/R/multistart.R +++ b/R/multistart.R @@ -15,7 +15,7 @@ #' used? #' @param cores How many fits should be run in parallel? #' @param \dots Passed to the update function, or to the basic plotting -#' function in the case of the graphical function. +#' function in the case of the graphical functions. #' @param x The multistart object to print #' @param breaks Passed to [hist] #' @param main title of the plot @@ -66,7 +66,7 @@ parms.multistart <- function(object, ...) { #' @rdname multistart #' @importFrom stats median #' @export -parhist <- function(object, lpos = "topleft", ...) { +parhist <- function(object, lpos = "topleft", main = "", ...) { orig <- attr(object, "orig") orig_parms <- parms(orig) start_parms <- orig$mean_dp_start @@ -79,7 +79,7 @@ parhist <- function(object, lpos = "topleft", ...) { start_scaled_parms[names(start_parms)] <- start_parms / median_parms[names(start_parms)] - boxplot(all_scaled_parms, log = "y", ...) + boxplot(all_scaled_parms, log = "y", main = main, ...) points(orig_scaled_parms, col = 2, cex = 2) points(start_scaled_parms, col = 3, cex = 3) legend(lpos, inset = c(0.05, 0.05), bty = "n", @@ -93,7 +93,7 @@ parhist <- function(object, lpos = "topleft", ...) { #' @rdname multistart #' @importFrom KernSmooth bkde #' @export -llhist <- function(object, breaks = "Sturges", main = "", lpos = "topleft", ...) { +llhist <- function(object, breaks = "Sturges", lpos = "topleft", main = "", ...) { ll <- sapply(object, logLik) kde <- KernSmooth::bkde(ll) h <- hist(ll, freq = TRUE, diff --git a/R/parms.mkinfit.R b/R/parms.mkinfit.R index 31ca05bc..83766355 100644 --- a/R/parms.mkinfit.R +++ b/R/parms.mkinfit.R @@ -1,16 +1,15 @@ -#' Extract model parameters from mkinfit models +#' Extract model parameters #' -#' This function always returns degradation model parameters as well as error -#' model parameters, in order to avoid working with a fitted model without -#' considering the error structure that was assumed for the fit. +#' This function returns degradation model parameters as well as error +#' model parameters per default, in order to avoid working with a fitted model +#' without considering the error structure that was assumed for the fit. #' -#' @param object A fitted model object. Methods are implemented for -#' [mkinfit()] objects and for [mmkin()] objects. +#' @param object A fitted model object. #' @param \dots Not used -#' @return For mkinfit objects, a numeric vector of fitted model parameters. -#' For mmkin row objects, a matrix with the parameters with a row for each -#' dataset. If the mmkin object has more than one row, a list of such matrices -#' is returned. +#' @return Depending on the object, a numeric vector of fitted model parameters, +#' a matrix (e.g. for mmkin row objects), or a list of matrices (e.g. for +#' mmkin objects with more than one row). +#' @seealso [saem], [multistart] #' @examples #' # mkinfit objects #' fit <- mkinfit("SFO", FOCUS_2006_C, quiet = TRUE) diff --git a/_pkgdown.yml b/_pkgdown.yml index a68c8d7a..51743488 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -21,21 +21,21 @@ reference: - title: Generics desc: Generic functions introduced by the package contents: + - parms - convergence - illparms - endpoints + - aw - title: Show results desc: Functions working with mkinfit objects contents: - plot.mkinfit - summary.mkinfit - - parms.mkinfit - confint.mkinfit - update.mkinfit - lrtest.mkinfit - loftest - mkinerrmin - - aw - CAKE_export - title: Work with mmkin objects desc: Functions working with aggregated results @@ -59,6 +59,9 @@ reference: - mixed - intervals - intervals.saem.mmkin + - multistart + - llhist + - parhist - title: Datasets and known results contents: - focus_soil_moisture diff --git a/docs/dev/articles/FOCUS_L.html b/docs/dev/articles/FOCUS_L.html index 610d1bdd..43ed0f69 100644 --- a/docs/dev/articles/FOCUS_L.html +++ b/docs/dev/articles/FOCUS_L.html @@ -106,7 +106,7 @@ <h1 data-toc-skip>Example evaluation of FOCUS Laboratory Data L1 to L3</h1> <h4 data-toc-skip class="author">Johannes Ranke</h4> - <h4 data-toc-skip class="date">Last change 18 May 2022 (rebuilt 2022-08-10)</h4> + <h4 data-toc-skip class="date">Last change 18 May 2022 (rebuilt 2022-09-16)</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/FOCUS_L.rmd" class="external-link"><code>vignettes/FOCUS_L.rmd</code></a></small> <div class="hidden name"><code>FOCUS_L.rmd</code></div> @@ -134,15 +134,15 @@ <span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m.L1.SFO</span><span class="op">)</span></span></code></pre></div> <pre><code><span><span class="co">## mkin version used for fitting: 1.1.2 </span></span> <span><span class="co">## R version used for fitting: 4.2.1 </span></span> -<span><span class="co">## Date of fit: Wed Aug 10 15:28:18 2022 </span></span> -<span><span class="co">## Date of summary: Wed Aug 10 15:28:18 2022 </span></span> +<span><span class="co">## Date of fit: Fri Sep 16 10:31:35 2022 </span></span> +<span><span class="co">## Date of summary: Fri Sep 16 10:31:35 2022 </span></span> <span><span class="co">## </span></span> <span><span class="co">## Equations:</span></span> <span><span class="co">## d_parent/dt = - k_parent * parent</span></span> <span><span class="co">## </span></span> <span><span class="co">## Model predictions using solution type analytical </span></span> <span><span class="co">## </span></span> -<span><span class="co">## Fitted using 133 model solutions performed in 0.031 s</span></span> +<span><span class="co">## Fitted using 133 model solutions performed in 0.032 s</span></span> <span><span class="co">## </span></span> <span><span class="co">## Error model: Constant variance </span></span> <span><span class="co">## </span></span> @@ -240,15 +240,15 @@ <span><span class="co">## doubtful</span></span></code></pre> <pre><code><span><span class="co">## mkin version used for fitting: 1.1.2 </span></span> <span><span class="co">## R version used for fitting: 4.2.1 </span></span> -<span><span class="co">## Date of fit: Wed Aug 10 15:28:18 2022 </span></span> -<span><span class="co">## Date of summary: Wed Aug 10 15:28:18 2022 </span></span> +<span><span class="co">## Date of fit: Fri Sep 16 10:31:36 2022 </span></span> +<span><span class="co">## Date of summary: Fri Sep 16 10:31:36 2022 </span></span> <span><span class="co">## </span></span> <span><span class="co">## Equations:</span></span> <span><span class="co">## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent</span></span> <span><span class="co">## </span></span> <span><span class="co">## Model predictions using solution type analytical </span></span> <span><span class="co">## </span></span> -<span><span class="co">## Fitted using 369 model solutions performed in 0.082 s</span></span> +<span><span class="co">## Fitted using 369 model solutions performed in 0.081 s</span></span> <span><span class="co">## </span></span> <span><span class="co">## Error model: Constant variance </span></span> <span><span class="co">## </span></span> @@ -352,15 +352,15 @@ <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m.L2.FOMC</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div> <pre><code><span><span class="co">## mkin version used for fitting: 1.1.2 </span></span> <span><span class="co">## R version used for fitting: 4.2.1 </span></span> -<span><span class="co">## Date of fit: Wed Aug 10 15:28:19 2022 </span></span> -<span><span class="co">## Date of summary: Wed Aug 10 15:28:19 2022 </span></span> +<span><span class="co">## Date of fit: Fri Sep 16 10:31:36 2022 </span></span> +<span><span class="co">## Date of summary: Fri Sep 16 10:31:36 2022 </span></span> <span><span class="co">## </span></span> <span><span class="co">## Equations:</span></span> <span><span class="co">## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent</span></span> <span><span class="co">## </span></span> <span><span class="co">## Model predictions using solution type analytical </span></span> <span><span class="co">## </span></span> -<span><span class="co">## Fitted using 239 model solutions performed in 0.048 s</span></span> +<span><span class="co">## Fitted using 239 model solutions performed in 0.049 s</span></span> <span><span class="co">## </span></span> <span><span class="co">## Error model: Constant variance </span></span> <span><span class="co">## </span></span> @@ -433,8 +433,8 @@ <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m.L2.DFOP</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div> <pre><code><span><span class="co">## mkin version used for fitting: 1.1.2 </span></span> <span><span class="co">## R version used for fitting: 4.2.1 </span></span> -<span><span class="co">## Date of fit: Wed Aug 10 15:28:19 2022 </span></span> -<span><span class="co">## Date of summary: Wed Aug 10 15:28:19 2022 </span></span> +<span><span class="co">## Date of fit: Fri Sep 16 10:31:37 2022 </span></span> +<span><span class="co">## Date of summary: Fri Sep 16 10:31:37 2022 </span></span> <span><span class="co">## </span></span> <span><span class="co">## Equations:</span></span> <span><span class="co">## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *</span></span> @@ -539,8 +539,8 @@ <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">mm.L3</span><span class="op">[[</span><span class="st">"DFOP"</span>, <span class="fl">1</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div> <pre><code><span><span class="co">## mkin version used for fitting: 1.1.2 </span></span> <span><span class="co">## R version used for fitting: 4.2.1 </span></span> -<span><span class="co">## Date of fit: Wed Aug 10 15:28:20 2022 </span></span> -<span><span class="co">## Date of summary: Wed Aug 10 15:28:20 2022 </span></span> +<span><span class="co">## Date of fit: Fri Sep 16 10:31:37 2022 </span></span> +<span><span class="co">## Date of summary: Fri Sep 16 10:31:38 2022 </span></span> <span><span class="co">## </span></span> <span><span class="co">## Equations:</span></span> <span><span class="co">## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *</span></span> @@ -652,8 +652,8 @@ <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">mm.L4</span><span class="op">[[</span><span class="st">"SFO"</span>, <span class="fl">1</span><span class="op">]</span><span class="op">]</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div> <pre><code><span><span class="co">## mkin version used for fitting: 1.1.2 </span></span> <span><span class="co">## R version used for fitting: 4.2.1 </span></span> -<span><span class="co">## Date of fit: Wed Aug 10 15:28:21 2022 </span></span> -<span><span class="co">## Date of summary: Wed Aug 10 15:28:21 2022 </span></span> +<span><span class="co">## Date of fit: Fri Sep 16 10:31:38 2022 </span></span> +<span><span class="co">## Date of summary: Fri Sep 16 10:31:38 2022 </span></span> <span><span class="co">## </span></span> <span><span class="co">## Equations:</span></span> <span><span class="co">## d_parent/dt = - k_parent * parent</span></span> @@ -717,8 +717,8 @@ <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">mm.L4</span><span class="op">[[</span><span class="st">"FOMC"</span>, <span class="fl">1</span><span class="op">]</span><span class="op">]</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div> <pre><code><span><span class="co">## mkin version used for fitting: 1.1.2 </span></span> <span><span class="co">## R version used for fitting: 4.2.1 </span></span> -<span><span class="co">## Date of fit: Wed Aug 10 15:28:21 2022 </span></span> -<span><span class="co">## Date of summary: Wed Aug 10 15:28:21 2022 </span></span> +<span><span class="co">## Date of fit: Fri Sep 16 10:31:38 2022 </span></span> +<span><span class="co">## Date of summary: Fri Sep 16 10:31:38 2022 </span></span> <span><span class="co">## </span></span> <span><span class="co">## Equations:</span></span> <span><span class="co">## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent</span></span> diff --git a/docs/dev/articles/web_only/benchmarks.html b/docs/dev/articles/web_only/benchmarks.html index 3dbf2881..e5bc5a21 100644 --- a/docs/dev/articles/web_only/benchmarks.html +++ b/docs/dev/articles/web_only/benchmarks.html @@ -106,7 +106,7 @@ <h1 data-toc-skip>Benchmark timings for mkin</h1> <h4 data-toc-skip class="author">Johannes Ranke</h4> - <h4 data-toc-skip class="date">Last change 14 July 2022 (rebuilt 2022-08-10)</h4> + <h4 data-toc-skip class="date">Last change 14 July 2022 (rebuilt 2022-09-16)</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/benchmarks.rmd" class="external-link"><code>vignettes/web_only/benchmarks.rmd</code></a></small> <div class="hidden name"><code>benchmarks.rmd</code></div> @@ -337,8 +337,8 @@ <td align="left">Ryzen 7 1700</td> <td align="left">4.2.1</td> <td align="left">1.1.2</td> -<td align="right">1.940</td> -<td align="right">3.619</td> +<td align="right">1.957</td> +<td align="right">3.633</td> </tr> </tbody> </table> @@ -507,9 +507,9 @@ <td align="left">Ryzen 7 1700</td> <td align="left">4.2.1</td> <td align="left">1.1.2</td> -<td align="right">1.490</td> -<td align="right">6.035</td> -<td align="right">2.799</td> +<td align="right">1.503</td> +<td align="right">6.147</td> +<td align="right">2.803</td> </tr> </tbody> </table> @@ -729,12 +729,12 @@ <td align="left">Ryzen 7 1700</td> <td align="left">4.2.1</td> <td align="left">1.1.2</td> -<td align="right">0.857</td> +<td align="right">0.861</td> <td align="right">1.295</td> -<td align="right">1.483</td> -<td align="right">2.989</td> -<td align="right">1.919</td> -<td align="right">2.766</td> +<td align="right">1.507</td> +<td align="right">3.102</td> +<td align="right">1.961</td> +<td align="right">2.852</td> </tr> </tbody> </table> diff --git a/docs/dev/articles/web_only/dimethenamid_2018.html b/docs/dev/articles/web_only/dimethenamid_2018.html index 81b15cb9..60f1ab5a 100644 --- a/docs/dev/articles/web_only/dimethenamid_2018.html +++ b/docs/dev/articles/web_only/dimethenamid_2018.html @@ -106,7 +106,7 @@ <h1 data-toc-skip>Example evaluations of the dimethenamid data from 2018</h1> <h4 data-toc-skip class="author">Johannes Ranke</h4> - <h4 data-toc-skip class="date">Last change 1 July 2022, built on 10 Aug 2022</h4> + <h4 data-toc-skip class="date">Last change 1 July 2022, built on 16 Sep 2022</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/dimethenamid_2018.rmd" class="external-link"><code>vignettes/web_only/dimethenamid_2018.rmd</code></a></small> <div class="hidden name"><code>dimethenamid_2018.rmd</code></div> @@ -457,24 +457,24 @@ attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: -[1] saemix_3.1 npde_3.2 nlme_3.1-158 mkin_1.1.2 knitr_1.39 +[1] nlme_3.1-158 mkin_1.1.2 knitr_1.39 loaded via a namespace (and not attached): - [1] deSolve_1.33 zoo_1.8-10 tidyselect_1.1.2 xfun_0.31 - [5] bslib_0.4.0 purrr_0.3.4 lattice_0.20-45 colorspace_2.0-3 - [9] vctrs_0.4.1 generics_0.1.3 htmltools_0.5.3 yaml_2.3.5 -[13] utf8_1.2.2 rlang_1.0.4 pkgdown_2.0.6 jquerylib_0.1.4 -[17] pillar_1.8.0 glue_1.6.2 DBI_1.1.3 lifecycle_1.0.1 -[21] stringr_1.4.0 munsell_0.5.0 gtable_0.3.0 ragg_1.2.2 -[25] codetools_0.2-18 memoise_2.0.1 evaluate_0.15 fastmap_1.1.0 -[29] lmtest_0.9-40 parallel_4.2.1 fansi_1.0.3 highr_0.9 -[33] scales_1.2.0 cachem_1.0.6 desc_1.4.1 jsonlite_1.8.0 -[37] systemfonts_1.0.4 fs_1.5.2 textshaping_0.3.6 gridExtra_2.3 -[41] ggplot2_3.3.6 digest_0.6.29 stringi_1.7.8 dplyr_1.0.9 -[45] grid_4.2.1 rprojroot_2.0.3 cli_3.3.0 tools_4.2.1 -[49] magrittr_2.0.3 sass_0.4.2 tibble_3.1.8 pkgconfig_2.0.3 -[53] assertthat_0.2.1 rmarkdown_2.14.3 R6_2.5.1 mclust_5.4.10 -[57] compiler_4.2.1 </code></pre> + [1] deSolve_1.33 zoo_1.8-10 tidyselect_1.1.2 xfun_0.31 + [5] bslib_0.4.0 purrr_0.3.4 lattice_0.20-45 colorspace_2.0-3 + [9] vctrs_0.4.1 generics_0.1.3 htmltools_0.5.3 yaml_2.3.5 +[13] utf8_1.2.2 rlang_1.0.4 pkgdown_2.0.6 saemix_3.1 +[17] jquerylib_0.1.4 pillar_1.8.0 glue_1.6.2 DBI_1.1.3 +[21] lifecycle_1.0.1 stringr_1.4.0 munsell_0.5.0 gtable_0.3.0 +[25] ragg_1.2.2 memoise_2.0.1 evaluate_0.15 npde_3.2 +[29] fastmap_1.1.0 lmtest_0.9-40 parallel_4.2.1 fansi_1.0.3 +[33] highr_0.9 KernSmooth_2.23-20 scales_1.2.0 cachem_1.0.6 +[37] desc_1.4.1 jsonlite_1.8.0 systemfonts_1.0.4 fs_1.5.2 +[41] textshaping_0.3.6 gridExtra_2.3 ggplot2_3.3.6 digest_0.6.29 +[45] stringi_1.7.8 dplyr_1.0.9 grid_4.2.1 rprojroot_2.0.3 +[49] cli_3.3.0 tools_4.2.1 magrittr_2.0.3 sass_0.4.2 +[53] tibble_3.1.8 pkgconfig_2.0.3 assertthat_0.2.1 rmarkdown_2.14.3 +[57] mclust_5.4.10 R6_2.5.1 compiler_4.2.1 </code></pre> </div> <div class="section level2"> <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a> diff --git a/docs/dev/news/index.html b/docs/dev/news/index.html index b501ed55..c8863ec6 100644 --- a/docs/dev/news/index.html +++ b/docs/dev/news/index.html @@ -83,7 +83,8 @@ <div class="section level2"> <h2 class="page-header" data-toc-text="1.1.2" id="mkin-112">mkin 1.1.2<a class="anchor" aria-label="anchor" href="#mkin-112"></a></h2> -<ul><li><p>‘R/mhmkin.R’: New method for performing multiple hierarchical mkin fits in one function call, optionally in parallel.</p></li> +<ul><li><p>‘R/multistart.R’: New method for testing multiple start parameters for hierarchical model fits, with diagnostic plotting functions ‘llhist’ and ‘parhist’.</p></li> +<li><p>‘R/mhmkin.R’: New method for performing multiple hierarchical mkin fits in one function call, optionally in parallel.</p></li> <li><p>‘R/saem.R’: Implement and test saemix transformations for FOMC and HS. Also, error out if saemix transformations are requested but not supported.</p></li> <li><p>‘R/saem.R’: ‘logLik’ and ‘update’ methods for ‘saem.mmkin’ objects.</p></li> <li><p>‘R/convergence.R’: New generic to show convergence information with methods for ‘mmkin’ and ‘mhmkin’ objects.</p></li> diff --git a/docs/dev/pkgdown.yml b/docs/dev/pkgdown.yml index 453b4590..1fee5d96 100644 --- a/docs/dev/pkgdown.yml +++ b/docs/dev/pkgdown.yml @@ -11,7 +11,7 @@ articles: benchmarks: web_only/benchmarks.html compiled_models: web_only/compiled_models.html dimethenamid_2018: web_only/dimethenamid_2018.html -last_built: 2022-08-10T14:05Z +last_built: 2022-09-16T08:50Z urls: reference: https://pkgdown.jrwb.de/mkin/reference article: https://pkgdown.jrwb.de/mkin/articles diff --git a/docs/dev/reference/aw.html b/docs/dev/reference/aw.html index 3b06f2a6..57dfa06c 100644 --- a/docs/dev/reference/aw.html +++ b/docs/dev/reference/aw.html @@ -1,69 +1,14 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - 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- -<meta name="robots" content="noindex"> - -<!-- mathjax --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> - -<!--[if lt IE 9]> +by Burnham and Anderson (2004)."><meta name="robots" content="noindex"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - - - </head> - - <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -74,23 +19,21 @@ by Burnham and Anderson (2004)." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.2</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -100,6 +43,9 @@ by Burnham and Anderson (2004)." /> <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> </li> <li> @@ -114,34 +60,27 @@ by Burnham and Anderson (2004)." /> <li> <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> </li> - </ul> -</li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Calculate Akaike weights for model averaging</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/aw.R'><code>R/aw.R</code></a></small> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/aw.R" class="external-link"><code>R/aw.R</code></a></small> <div class="hidden name"><code>aw.Rd</code></div> </div> @@ -151,76 +90,85 @@ expected Kullback-Leibler information as specified by Burnham and Anderson (2004).</p> </div> - <pre class="usage"><span class='fu'>aw</span><span class='op'>(</span><span class='va'>object</span>, <span class='va'>...</span><span class='op'>)</span> - -<span class='co'># S3 method for mkinfit</span> -<span class='fu'>aw</span><span class='op'>(</span><span class='va'>object</span>, <span class='va'>...</span><span class='op'>)</span> - -<span class='co'># S3 method for mmkin</span> -<span class='fu'>aw</span><span class='op'>(</span><span class='va'>object</span>, <span class='va'>...</span><span class='op'>)</span></pre> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">aw</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for mkinfit</span></span> +<span><span class="fu">aw</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for mmkin</span></span> +<span><span class="fu">aw</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for mixed.mmkin</span></span> +<span><span class="fu">aw</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for multistart</span></span> +<span><span class="fu">aw</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> + </div> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>object</th> - <td><p>An <a href='mmkin.html'>mmkin</a> column object, containing two or more -<a href='mkinfit.html'>mkinfit</a> models that have been fitted to the same data, + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>object</dt> +<dd><p>An <a href="mmkin.html">mmkin</a> column object, containing two or more +<a href="mkinfit.html">mkinfit</a> models that have been fitted to the same data, or an mkinfit object. In the latter case, further mkinfit objects fitted to the same data should be specified -as dots arguments.</p></td> - </tr> - <tr> - <th>...</th> - <td><p>Not used in the method for <a href='mmkin.html'>mmkin</a> column objects, -further <a href='mkinfit.html'>mkinfit</a> objects in the method for mkinfit objects.</p></td> - </tr> - </table> +as dots arguments.</p></dd> + - <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> +<dt>...</dt> +<dd><p>Not used in the method for <a href="mmkin.html">mmkin</a> column objects, +further <a href="mkinfit.html">mkinfit</a> objects in the method for mkinfit objects.</p></dd> +</dl></div> + <div id="references"> + <h2>References</h2> <p>Burnham KP and Anderson DR (2004) Multimodel Inference: Understanding AIC and BIC in Model Selection. <em>Sociological Methods & Research</em> <strong>33</strong>(2) 261-304</p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='co'># \dontrun{</span> -<span class='va'>f_sfo</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='va'>FOCUS_2006_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -<span class='va'>f_dfop</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='st'>"DFOP"</span>, <span class='va'>FOCUS_2006_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -<span class='va'>aw_sfo_dfop</span> <span class='op'><-</span> <span class='fu'>aw</span><span class='op'>(</span><span class='va'>f_sfo</span>, <span class='va'>f_dfop</span><span class='op'>)</span> -<span class='fu'><a href='https://rdrr.io/r/base/sum.html'>sum</a></span><span class='op'>(</span><span class='va'>aw_sfo_dfop</span><span class='op'>)</span> -</div><div class='output co'>#> [1] 1</div><div class='input'><span class='va'>aw_sfo_dfop</span> <span class='co'># SFO gets more weight as it has less parameters and a similar fit</span> -</div><div class='output co'>#> [1] 0.5970258 0.4029742</div><div class='input'><span class='va'>f</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='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='st'>"FOCUS D"</span> <span class='op'>=</span> <span class='va'>FOCUS_2006_D</span><span class='op'>)</span>, cores <span class='op'>=</span> <span class='fl'>1</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -<span class='fu'>aw</span><span class='op'>(</span><span class='va'>f</span><span class='op'>)</span> -</div><div class='output co'>#> [1] 0.4808722 0.1945539 0.3245740</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/sum.html'>sum</a></span><span class='op'>(</span><span class='fu'>aw</span><span class='op'>(</span><span class='va'>f</span><span class='op'>)</span><span class='op'>)</span> -</div><div class='output co'>#> [1] 1</div><div class='input'><span class='fu'>aw</span><span class='op'>(</span><span class='va'>f</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'>"DFOP"</span><span class='op'>)</span><span class='op'>]</span><span class='op'>)</span> -</div><div class='output co'>#> [1] 0.5970258 0.4029742</div><div class='input'><span class='co'># }</span> -</div></pre> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span><span class="va">f_sfo</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">FOCUS_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">f_dfop</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"DFOP"</span>, <span class="va">FOCUS_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">aw_sfo_dfop</span> <span class="op"><-</span> <span class="fu">aw</span><span class="op">(</span><span class="va">f_sfo</span>, <span class="va">f_dfop</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum</a></span><span class="op">(</span><span class="va">aw_sfo_dfop</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [1] 1</span> +<span class="r-in"><span><span class="va">aw_sfo_dfop</span> <span class="co"># SFO gets more weight as it has less parameters and a similar fit</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [1] 0.5970258 0.4029742</span> +<span class="r-in"><span><span class="va">f</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" class="external-link">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="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="st">"FOCUS D"</span> <span class="op">=</span> <span class="va">FOCUS_2006_D</span><span class="op">)</span>, cores <span class="op">=</span> <span class="fl">1</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu">aw</span><span class="op">(</span><span class="va">f</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [1] 0.4808722 0.1945539 0.3245740</span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum</a></span><span class="op">(</span><span class="fu">aw</span><span class="op">(</span><span class="va">f</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [1] 1</span> +<span class="r-in"><span><span class="fu">aw</span><span class="op">(</span><span class="va">f</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"DFOP"</span><span class="op">)</span><span class="op">]</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [1] 0.5970258 0.4029742</span> +<span class="r-in"><span><span class="co"># }</span></span></span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/dev/reference/dimethenamid_2018.html b/docs/dev/reference/dimethenamid_2018.html index 7a356284..2454a609 100644 --- a/docs/dev/reference/dimethenamid_2018.html +++ b/docs/dev/reference/dimethenamid_2018.html @@ -203,8 +203,8 @@ specific pieces of information in the comments.</p> <span class="r-out co"><span class="r-pr">#></span> saemix version used for fitting: 3.1 </span> <span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.1.2 </span> <span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.1 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Wed Aug 10 15:24:12 2022 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Wed Aug 10 15:24:12 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Fri Sep 16 10:29:07 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Fri Sep 16 10:29:07 2022 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_DMTA/dt = - k_DMTA * DMTA</span> @@ -217,7 +217,7 @@ specific pieces of information in the comments.</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type deSolve </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted in 791.863 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted in 797.539 s</span> <span class="r-out co"><span class="r-pr">#></span> Using 300, 100 iterations and 9 chains</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Variance model: Two-component variance function </span> diff --git a/docs/dev/reference/index.html b/docs/dev/reference/index.html index 98f170b6..3372a69a 100644 --- a/docs/dev/reference/index.html +++ b/docs/dev/reference/index.html @@ -107,6 +107,10 @@ degradation models and one or more error models</p></td> <p class="section-desc"></p><p>Generic functions introduced by the package</p> </th> </tr></tbody><tbody><tr><td> + <p><code><a href="parms.html">parms()</a></code> </p> + </td> + <td><p>Extract model parameters</p></td> + </tr><tr><td> <p><code><a href="convergence.html">convergence()</a></code> <code><a href="convergence.html">print(<i><convergence.mmkin></i>)</a></code> </p> </td> <td><p>Method to get convergence information</p></td> @@ -119,6 +123,10 @@ degradation models and one or more error models</p></td> </td> <td><p>Function to calculate endpoints for further use from kinetic models fitted with mkinfit</p></td> + </tr><tr><td> + <p><code><a href="aw.html">aw()</a></code> </p> + </td> + <td><p>Calculate Akaike weights for model averaging</p></td> </tr></tbody><tbody><tr><th colspan="2"> <h2 id="show-results">Show results <a href="#show-results" class="anchor" aria-hidden="true"></a></h2> <p class="section-desc"></p><p>Functions working with mkinfit objects</p> @@ -132,10 +140,6 @@ with mkinfit</p></td> </td> <td><p>Summary method for class "mkinfit"</p></td> </tr><tr><td> - <p><code><a href="parms.html">parms()</a></code> </p> - </td> - <td><p>Extract model parameters from mkinfit models</p></td> - </tr><tr><td> <p><code><a href="confint.mkinfit.html">confint(<i><mkinfit></i>)</a></code> </p> </td> <td><p>Confidence intervals for parameters of mkinfit objects</p></td> @@ -156,10 +160,6 @@ with mkinfit</p></td> </td> <td><p>Calculate the minimum error to assume in order to pass the variance test</p></td> </tr><tr><td> - <p><code><a href="aw.html">aw()</a></code> </p> - </td> - <td><p>Calculate Akaike weights for model averaging</p></td> - </tr><tr><td> <p><code><a href="CAKE_export.html">CAKE_export()</a></code> </p> </td> <td><p>Export a list of datasets format to a CAKE study file</p></td> @@ -193,7 +193,7 @@ of an mmkin object</p></td> </td> <td><p>Create an nlme model for an mmkin row object</p></td> </tr><tr><td> - <p><code><a href="saem.html">saem()</a></code> <code><a href="saem.html">print(<i><saem.mmkin></i>)</a></code> <code><a href="saem.html">saemix_model()</a></code> <code><a href="saem.html">saemix_data()</a></code> </p> + <p><code><a href="saem.html">saem()</a></code> <code><a href="saem.html">print(<i><saem.mmkin></i>)</a></code> <code><a href="saem.html">saemix_model()</a></code> <code><a href="saem.html">saemix_data()</a></code> <code><a href="saem.html">parms(<i><saem.mmkin></i>)</a></code> </p> </td> <td><p>Fit nonlinear mixed models with SAEM</p></td> </tr><tr><td> @@ -233,6 +233,10 @@ degradation models and one or more error models</p></td> <p><code><a href="intervals.saem.mmkin.html">intervals(<i><saem.mmkin></i>)</a></code> </p> </td> <td><p>Confidence intervals for parameters in saem.mmkin objects</p></td> + </tr><tr><td> + <p><code><a href="multistart.html">multistart()</a></code> <code><a href="multistart.html">print(<i><multistart></i>)</a></code> <code><a href="multistart.html">parms(<i><multistart></i>)</a></code> <code><a href="multistart.html">parhist()</a></code> <code><a href="multistart.html">llhist()</a></code> </p> + </td> + <td><p>Perform a hierarchical model fit with multiple starting values</p></td> </tr></tbody><tbody><tr><th colspan="2"> <h2 id="datasets-and-known-results">Datasets and known results <a href="#datasets-and-known-results" class="anchor" aria-hidden="true"></a></h2> <p class="section-desc"></p> diff --git a/docs/dev/reference/mkinfit.html b/docs/dev/reference/mkinfit.html index a00a0458..bcc86ded 100644 --- a/docs/dev/reference/mkinfit.html +++ b/docs/dev/reference/mkinfit.html @@ -380,8 +380,8 @@ Degradation Data. <em>Environments</em> 6(12) 124 <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.1.2 </span> <span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.1 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Wed Aug 10 15:24:16 2022 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Wed Aug 10 15:24:16 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Fri Sep 16 10:29:10 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Fri Sep 16 10:29:10 2022 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent</span> @@ -528,10 +528,11 @@ Degradation Data. <em>Environments</em> 6(12) 124 <span class="r-in"><span> 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>,</span></span> <span class="r-in"><span> solution_type <span class="op">=</span> <span class="st">"analytical"</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="op">}</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Loading required package: rbenchmark</span> <span class="r-out co"><span class="r-pr">#></span> test relative elapsed</span> -<span class="r-out co"><span class="r-pr">#></span> 3 analytical 1.000 0.605</span> -<span class="r-out co"><span class="r-pr">#></span> 1 deSolve_compiled 1.448 0.876</span> -<span class="r-out co"><span class="r-pr">#></span> 2 eigen 2.479 1.500</span> +<span class="r-out co"><span class="r-pr">#></span> 3 analytical 1.000 0.577</span> +<span class="r-out co"><span class="r-pr">#></span> 1 deSolve_compiled 1.537 0.887</span> +<span class="r-out co"><span class="r-pr">#></span> 2 eigen 2.551 1.472</span> <span class="r-in"><span><span class="co"># }</span></span></span> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="co"># Use stepwise fitting, using optimised parameters from parent only fit, FOMC-SFO</span></span></span> @@ -560,8 +561,8 @@ Degradation Data. <em>Environments</em> 6(12) 124 <span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>diag(.) had 0 or NA entries; non-finite result is doubtful</span> <span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.1.2 </span> <span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.1 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Wed Aug 10 15:24:27 2022 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Wed Aug 10 15:24:27 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Fri Sep 16 10:29:21 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Fri Sep 16 10:29:21 2022 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent</span> @@ -570,7 +571,7 @@ Degradation Data. <em>Environments</em> 6(12) 124 <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type deSolve </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted using 3729 model solutions performed in 2.475 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted using 3729 model solutions performed in 2.48 s</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Error model: Two-component variance function </span> <span class="r-out co"><span class="r-pr">#></span> </span> diff --git a/docs/dev/reference/multistart.html b/docs/dev/reference/multistart.html new file mode 100644 index 00000000..9f2d297e --- /dev/null +++ b/docs/dev/reference/multistart.html @@ -0,0 +1,195 @@ +<!DOCTYPE html> +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Perform a hierarchical model fit with multiple starting values — multistart • mkin</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link 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src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Perform a hierarchical model fit with multiple starting values — multistart"><meta property="og:description" content="The purpose of this method is to check if a certain algorithm for fitting +nonlinear hierarchical models (also known as nonlinear mixed-effects models) +will reliably yield results that are sufficiently similar to each other, if +started with a certain range of reasonable starting parameters. It is +inspired by the article on practical identifiabiliy in the frame of nonlinear +mixed-effects models by Duchesne et al (2021)."><meta name="robots" content="noindex"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + + + <div class="container template-reference-topic"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> + <span class="sr-only">Toggle navigation</span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">mkin</a> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.2</span> + </span> + </div> + + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"><li> + <a href="../reference/index.html">Functions and data</a> +</li> +<li class="dropdown"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> + Articles + + <span class="caret"></span> + </a> + <ul class="dropdown-menu" role="menu"><li> + <a href="../articles/mkin.html">Introduction to mkin</a> + </li> + <li> + <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a> + </li> + <li> + <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> + </li> + <li> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + </li> + <li> + <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + </li> + <li> + <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + </li> + <li> + <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + </li> + </ul></li> +<li> + <a href="../news/index.html">News</a> +</li> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> + <span class="fab fa-github fa-lg"></span> + + </a> +</li> + </ul></div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + + </header><div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>Perform a hierarchical model fit with multiple starting values</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/multistart.R" class="external-link"><code>R/multistart.R</code></a></small> + <div class="hidden name"><code>multistart.Rd</code></div> + </div> + + <div class="ref-description"> + <p>The purpose of this method is to check if a certain algorithm for fitting +nonlinear hierarchical models (also known as nonlinear mixed-effects models) +will reliably yield results that are sufficiently similar to each other, if +started with a certain range of reasonable starting parameters. It is +inspired by the article on practical identifiabiliy in the frame of nonlinear +mixed-effects models by Duchesne et al (2021).</p> + </div> + + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">multistart</span><span class="op">(</span><span class="va">object</span>, n <span class="op">=</span> <span class="fl">50</span>, cores <span class="op">=</span> <span class="fl">1</span>, <span class="va">...</span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for saem.mmkin</span></span> +<span><span class="fu">multistart</span><span class="op">(</span><span class="va">object</span>, n <span class="op">=</span> <span class="fl">50</span>, cores <span class="op">=</span> <span class="fl">1</span>, <span class="va">...</span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for multistart</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for multistart</span></span> +<span><span class="fu"><a href="parms.html">parms</a></span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span> +<span></span> +<span><span class="fu">parhist</span><span class="op">(</span><span class="va">object</span>, lpos <span class="op">=</span> <span class="st">"topleft"</span>, main <span class="op">=</span> <span class="st">""</span>, <span class="va">...</span><span class="op">)</span></span> +<span></span> +<span><span class="fu">llhist</span><span class="op">(</span><span class="va">object</span>, breaks <span class="op">=</span> <span class="st">"Sturges"</span>, lpos <span class="op">=</span> <span class="st">"topleft"</span>, main <span class="op">=</span> <span class="st">""</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>object</dt> +<dd><p>The fit object to work with</p></dd> + + +<dt>n</dt> +<dd><p>How many different combinations of starting parameters should be +used?</p></dd> + + +<dt>cores</dt> +<dd><p>How many fits should be run in parallel?</p></dd> + + +<dt>...</dt> +<dd><p>Passed to the update function, or to the basic plotting +function in the case of the graphical functions.</p></dd> + + +<dt>x</dt> +<dd><p>The multistart object to print</p></dd> + + +<dt>lpos</dt> +<dd><p>Positioning of the legend.</p></dd> + + +<dt>main</dt> +<dd><p>title of the plot</p></dd> + + +<dt>breaks</dt> +<dd><p>Passed to <a href="https://rdrr.io/r/graphics/hist.html" class="external-link">hist</a></p></dd> + +</dl></div> + <div id="value"> + <h2>Value</h2> + + +<p>A list of <a href="saem.html">saem.mmkin</a> objects, with class attributes +'multistart.saem.mmkin' and 'multistart'.</p> + </div> + <div id="details"> + <h2>Details</h2> + <p>Currently, parallel execution of the fits is only supported using +<a href="https://rdrr.io/r/parallel/mclapply.html" class="external-link">parallel::mclapply</a>, i.e. not available on Windows.</p> + </div> + <div id="references"> + <h2>References</h2> + <p>Duchesne R, Guillemin A, Gandrillon O, Crauste F. Practical +identifiability in the frame of nonlinear mixed effects models: the example +of the in vitro erythropoiesis. BMC Bioinformatics. 2021 Oct 4;22(1):478. +doi: 10.1186/s12859-021-04373-4.</p> + </div> + + </div> + <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> +</div> + + + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> +</div> + + </footer></div> + + + + + + + </body></html> + diff --git a/docs/dev/reference/parms.html b/docs/dev/reference/parms.html index 9f6f4225..ded4567a 100644 --- a/docs/dev/reference/parms.html +++ b/docs/dev/reference/parms.html @@ -1,69 +1,14 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<meta http-equiv="X-UA-Compatible" content="IE=edge"> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> - 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+<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - - </head> - - <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -74,23 +19,21 @@ considering the error structure that was assumed for the fit." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.2</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - 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</ul> -</li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1>Extract model parameters from mkinfit models</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/parms.mkinfit.R'><code>R/parms.mkinfit.R</code></a></small> + <h1>Extract model parameters</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/parms.mkinfit.R" class="external-link"><code>R/parms.mkinfit.R</code></a></small> <div class="hidden name"><code>parms.Rd</code></div> </div> <div class="ref-description"> - <p>This function always returns degradation model parameters as well as error -model parameters, in order to avoid working with a fitted model without -considering the error structure that was assumed for the fit.</p> + <p>This function returns degradation model parameters as well as error +model parameters per default, in order to avoid working with a fitted model +without considering the error structure that was assumed for the fit.</p> + </div> + + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">parms</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for mkinfit</span></span> +<span><span class="fu">parms</span><span class="op">(</span><span class="va">object</span>, transformed <span class="op">=</span> <span class="cn">FALSE</span>, errparms <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for mmkin</span></span> +<span><span class="fu">parms</span><span class="op">(</span><span class="va">object</span>, transformed <span class="op">=</span> <span class="cn">FALSE</span>, errparms <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> </div> - <pre class="usage"><span class='fu'>parms</span><span class='op'>(</span><span class='va'>object</span>, <span class='va'>...</span><span class='op'>)</span> + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>object</dt> +<dd><p>A fitted model object.</p></dd> + + +<dt>...</dt> +<dd><p>Not used</p></dd> -<span class='co'># S3 method for mkinfit</span> -<span class='fu'>parms</span><span class='op'>(</span><span class='va'>object</span>, transformed <span class='op'>=</span> <span class='cn'>FALSE</span>, <span class='va'>...</span><span class='op'>)</span> -<span class='co'># S3 method for mmkin</span> -<span class='fu'>parms</span><span class='op'>(</span><span class='va'>object</span>, transformed <span class='op'>=</span> <span class='cn'>FALSE</span>, <span class='va'>...</span><span class='op'>)</span></pre> +<dt>transformed</dt> +<dd><p>Should the parameters be returned as used internally +during the optimisation?</p></dd> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>object</th> - <td><p>A fitted model object. Methods are implemented for -<code><a href='mkinfit.html'>mkinfit()</a></code> objects and for <code><a href='mmkin.html'>mmkin()</a></code> objects.</p></td> - </tr> - <tr> - <th>...</th> - <td><p>Not used</p></td> - </tr> - <tr> - <th>transformed</th> - <td><p>Should the parameters be returned -as used internally during the optimisation?</p></td> - </tr> - </table> - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> +<dt>errparms</dt> +<dd><p>Should the error model parameters be returned +in addition to the degradation parameters?</p></dd> - <p>For mkinfit objects, a numeric vector of fitted model parameters. -For mmkin row objects, a matrix with the parameters with a -row for each dataset. If the mmkin object has more than one row, a list of -such matrices is returned.</p> +</dl></div> + <div id="value"> + <h2>Value</h2> + - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='co'># mkinfit objects</span> -<span class='va'>fit</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='va'>FOCUS_2006_C</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -<span class='fu'>parms</span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span> -</div><div class='output co'>#> parent_0 k_parent sigma -#> 82.4921598 0.3060633 4.6730124 </div><div class='input'><span class='fu'>parms</span><span class='op'>(</span><span class='va'>fit</span>, transformed <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -</div><div class='output co'>#> parent_0 log_k_parent sigma -#> 82.492160 -1.183963 4.673012 </div><div class='input'> -<span class='co'># mmkin objects</span> -<span class='va'>ds</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span><span class='op'>(</span><span class='va'>experimental_data_for_UBA_2019</span><span class='op'>[</span><span class='fl'>6</span><span class='op'>:</span><span class='fl'>10</span><span class='op'>]</span>, - <span class='kw'>function</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span> <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</span><span class='va'>data</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'>"name"</span>, <span class='st'>"time"</span>, <span class='st'>"value"</span><span class='op'>)</span><span class='op'>]</span><span class='op'>)</span><span class='op'>)</span> -<span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>ds</span><span class='op'>)</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"Dataset"</span>, <span class='fl'>6</span><span class='op'>:</span><span class='fl'>10</span><span class='op'>)</span> -<span class='co'># \dontrun{</span> -<span class='va'>fits</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>, cores <span class='op'>=</span> <span class='fl'>1</span><span class='op'>)</span> -<span class='fu'>parms</span><span class='op'>(</span><span class='va'>fits</span><span class='op'>[</span><span class='st'>"SFO"</span>, <span class='op'>]</span><span class='op'>)</span> -</div><div class='output co'>#> Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10 -#> parent_0 88.52275400 82.666781678 86.8547308 91.7779306 82.14809450 -#> k_parent 0.05794659 0.009647805 0.2102974 0.1232258 0.00720421 -#> sigma 5.15274487 7.040168584 3.6769645 6.4669234 6.50457673</div><div class='input'><span class='fu'>parms</span><span class='op'>(</span><span class='va'>fits</span><span class='op'>[</span>, <span class='fl'>2</span><span class='op'>]</span><span class='op'>)</span> -</div><div class='output co'>#> $SFO -#> Dataset 7 -#> parent_0 82.666781678 -#> k_parent 0.009647805 -#> sigma 7.040168584 -#> -#> $FOMC -#> Dataset 7 -#> parent_0 92.6837649 -#> alpha 0.4967832 -#> beta 14.1451255 -#> sigma 1.9167519 -#> -#> $DFOP -#> Dataset 7 -#> parent_0 91.058971589 -#> k1 0.044946770 -#> k2 0.002868336 -#> g 0.526942415 -#> sigma 2.221302196 -#> </div><div class='input'><span class='fu'>parms</span><span class='op'>(</span><span class='va'>fits</span><span class='op'>)</span> -</div><div class='output co'>#> $SFO -#> Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10 -#> parent_0 88.52275400 82.666781678 86.8547308 91.7779306 82.14809450 -#> k_parent 0.05794659 0.009647805 0.2102974 0.1232258 0.00720421 -#> sigma 5.15274487 7.040168584 3.6769645 6.4669234 6.50457673 -#> -#> $FOMC -#> Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10 -#> parent_0 95.558575 92.6837649 90.719787 98.383939 94.8481459 -#> alpha 1.338667 0.4967832 1.639099 1.074460 0.2805272 -#> beta 13.033315 14.1451255 5.007077 4.397126 6.9052224 -#> sigma 1.847671 1.9167519 1.066063 3.146056 1.6222778 -#> -#> $DFOP -#> Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10 -#> parent_0 96.55213663 91.058971589 90.34509493 98.14858820 94.311323734 -#> k1 0.21954588 0.044946770 0.41232288 0.31697588 0.080663857 -#> k2 0.02957934 0.002868336 0.07581766 0.03260384 0.003425417 -#> g 0.44845068 0.526942415 0.66091967 0.65322767 0.342652880 -#> sigma 1.35690468 2.221302196 1.34169076 2.87159846 1.942067831 -#> </div><div class='input'><span class='fu'>parms</span><span class='op'>(</span><span class='va'>fits</span>, transformed <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -</div><div class='output co'>#> $SFO -#> Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10 -#> parent_0 88.522754 82.666782 86.854731 91.777931 82.148094 -#> log_k_parent -2.848234 -4.641025 -1.559232 -2.093737 -4.933090 -#> sigma 5.152745 7.040169 3.676964 6.466923 6.504577 -#> -#> $FOMC -#> Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10 -#> parent_0 95.5585751 92.6837649 90.7197870 98.38393897 94.848146 -#> log_alpha 0.2916741 -0.6996015 0.4941466 0.07181816 -1.271085 -#> log_beta 2.5675088 2.6493701 1.6108523 1.48095106 1.932278 -#> sigma 1.8476712 1.9167519 1.0660627 3.14605557 1.622278 -#> -#> $DFOP -#> Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10 -#> parent_0 96.5521366 91.0589716 90.3450949 98.1485882 94.3113237 -#> log_k1 -1.5161940 -3.1022764 -0.8859486 -1.1489296 -2.5174647 -#> log_k2 -3.5206791 -5.8540232 -2.5794240 -3.4233253 -5.6765322 -#> g_qlogis -0.2069326 0.1078741 0.6673953 0.6332573 -0.6514943 -#> sigma 1.3569047 2.2213022 1.3416908 2.8715985 1.9420678 -#> </div><div class='input'><span class='co'># }</span> -</div></pre> +<p>Depending on the object, a numeric vector of fitted model parameters, +a matrix (e.g. for mmkin row objects), or a list of matrices (e.g. for +mmkin objects with more than one row).</p> + </div> + <div id="see-also"> + <h2>See also</h2> + <div class="dont-index"><p><a href="saem.html">saem</a>, <a href="multistart.html">multistart</a></p></div> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># mkinfit objects</span></span></span> +<span class="r-in"><span><span class="va">fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">FOCUS_2006_C</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu">parms</span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 k_parent sigma </span> +<span class="r-out co"><span class="r-pr">#></span> 82.4921598 0.3060633 4.6730124 </span> +<span class="r-in"><span><span class="fu">parms</span><span class="op">(</span><span class="va">fit</span>, transformed <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 log_k_parent sigma </span> +<span class="r-out co"><span class="r-pr">#></span> 82.492160 -1.183963 4.673012 </span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># mmkin objects</span></span></span> +<span class="r-in"><span><span class="va">ds</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="va">experimental_data_for_UBA_2019</span><span class="op">[</span><span class="fl">6</span><span class="op">:</span><span class="fl">10</span><span class="op">]</span>,</span></span> +<span class="r-in"><span> <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">x</span><span class="op">$</span><span class="va">data</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"name"</span>, <span class="st">"time"</span>, <span class="st">"value"</span><span class="op">)</span><span class="op">]</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">ds</span><span class="op">)</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste</a></span><span class="op">(</span><span class="st">"Dataset"</span>, <span class="fl">6</span><span class="op">:</span><span class="fl">10</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span><span class="va">fits</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" class="external-link">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>, cores <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu">parms</span><span class="op">(</span><span class="va">fits</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="op">]</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 88.52275400 82.666781678 86.8547308 91.7779306 82.14809450</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent 0.05794659 0.009647805 0.2102974 0.1232258 0.00720421</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 5.15274487 7.040168584 3.6769645 6.4669234 6.50457673</span> +<span class="r-in"><span><span class="fu">parms</span><span class="op">(</span><span class="va">fits</span><span class="op">[</span>, <span class="fl">2</span><span class="op">]</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> $SFO</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 82.666781678</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent 0.009647805</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 7.040168584</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $FOMC</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 92.6837649</span> +<span class="r-out co"><span class="r-pr">#></span> alpha 0.4967832</span> +<span class="r-out co"><span class="r-pr">#></span> beta 14.1451255</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 1.9167519</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $DFOP</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 91.058971589</span> +<span class="r-out co"><span class="r-pr">#></span> k1 0.044946770</span> +<span class="r-out co"><span class="r-pr">#></span> k2 0.002868336</span> +<span class="r-out co"><span class="r-pr">#></span> g 0.526942415</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 2.221302196</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-in"><span><span class="fu">parms</span><span class="op">(</span><span class="va">fits</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> $SFO</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 88.52275400 82.666781678 86.8547308 91.7779306 82.14809450</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent 0.05794659 0.009647805 0.2102974 0.1232258 0.00720421</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 5.15274487 7.040168584 3.6769645 6.4669234 6.50457673</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $FOMC</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 95.558575 92.6837649 90.719787 98.383939 94.8481459</span> +<span class="r-out co"><span class="r-pr">#></span> alpha 1.338667 0.4967832 1.639099 1.074460 0.2805272</span> +<span class="r-out co"><span class="r-pr">#></span> beta 13.033315 14.1451255 5.007077 4.397126 6.9052224</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 1.847671 1.9167519 1.066063 3.146056 1.6222778</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $DFOP</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 96.55213663 91.058971589 90.34509493 98.14858820 94.311323734</span> +<span class="r-out co"><span class="r-pr">#></span> k1 0.21954588 0.044946770 0.41232288 0.31697588 0.080663857</span> +<span class="r-out co"><span class="r-pr">#></span> k2 0.02957934 0.002868336 0.07581766 0.03260384 0.003425417</span> +<span class="r-out co"><span class="r-pr">#></span> g 0.44845068 0.526942415 0.66091967 0.65322767 0.342652880</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 1.35690468 2.221302196 1.34169076 2.87159846 1.942067831</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-in"><span><span class="fu">parms</span><span class="op">(</span><span class="va">fits</span>, transformed <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> $SFO</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 88.522754 82.666782 86.854731 91.777931 82.148094</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_parent -2.848234 -4.641025 -1.559232 -2.093737 -4.933090</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 5.152745 7.040169 3.676964 6.466923 6.504577</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $FOMC</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 95.5585751 92.6837649 90.7197870 98.38393897 94.848146</span> +<span class="r-out co"><span class="r-pr">#></span> log_alpha 0.2916741 -0.6996015 0.4941466 0.07181816 -1.271085</span> +<span class="r-out co"><span class="r-pr">#></span> log_beta 2.5675088 2.6493701 1.6108523 1.48095106 1.932278</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 1.8476712 1.9167519 1.0660627 3.14605557 1.622278</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $DFOP</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 96.5521366 91.0589716 90.3450949 98.1485882 94.3113237</span> +<span class="r-out co"><span class="r-pr">#></span> log_k1 -1.5161940 -3.1022764 -0.8859486 -1.1489296 -2.5174647</span> +<span class="r-out co"><span class="r-pr">#></span> log_k2 -3.5206791 -5.8540232 -2.5794240 -3.4233253 -5.6765322</span> +<span class="r-out co"><span class="r-pr">#></span> g_qlogis -0.2069326 0.1078741 0.6673953 0.6332573 -0.6514943</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 1.3569047 2.2213022 1.3416908 2.8715985 1.9420678</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-in"><span><span class="co"># }</span></span></span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/dev/reference/saem.html b/docs/dev/reference/saem.html index b55f29a8..ce3d428c 100644 --- a/docs/dev/reference/saem.html +++ b/docs/dev/reference/saem.html @@ -124,7 +124,10 @@ Expectation Maximisation algorithm (SAEM).</p> <span> <span class="va">...</span></span> <span><span class="op">)</span></span> <span></span> -<span><span class="fu">saemix_data</span><span class="op">(</span><span class="va">object</span>, verbose <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> +<span><span class="fu">saemix_data</span><span class="op">(</span><span class="va">object</span>, verbose <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for saem.mmkin</span></span> +<span><span class="fu"><a href="parms.html">parms</a></span><span class="op">(</span><span class="va">object</span>, ci <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> </div> <div id="arguments"> @@ -199,6 +202,11 @@ and the end of the optimisation process?</p></dd> <dt>digits</dt> <dd><p>Number of digits to use for printing</p></dd> + +<dt>ci</dt> +<dd><p>Should a matrix with estimates and confidence interval boundaries +be returned? If FALSE (default), a vector of estimates is returned.</p></dd> + </dl></div> <div id="value"> <h2>Value</h2> @@ -304,7 +312,7 @@ using <a href="mmkin.html">mmkin</a>.</p> <span class="r-msg co"><span class="r-pr">#></span> Likelihoods calculated by importance sampling</span> <span class="r-out co"><span class="r-pr">#></span> AIC BIC</span> <span class="r-out co"><span class="r-pr">#></span> 1 467.8664 465.1324</span> -<span class="r-out co"><span class="r-pr">#></span> 2 469.9096 466.7851</span> +<span class="r-out co"><span class="r-pr">#></span> 2 469.8018 466.6773</span> <span class="r-in"><span></span></span> <span class="r-in"><span><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>,</span></span> <span class="r-in"><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></span></span> @@ -365,8 +373,8 @@ using <a href="mmkin.html">mmkin</a>.</p> <span class="r-out co"><span class="r-pr">#></span> saemix version used for fitting: 3.1 </span> <span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.1.2 </span> <span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.1 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Wed Aug 10 15:27:26 2022 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Wed Aug 10 15:27:26 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Fri Sep 16 10:30:47 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Fri Sep 16 10:30:47 2022 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *</span> @@ -381,7 +389,7 @@ using <a href="mmkin.html">mmkin</a>.</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type analytical </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted in 9.438 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted in 9.651 s</span> <span class="r-out co"><span class="r-pr">#></span> Using 300, 100 iterations and 10 chains</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Variance model: Constant variance </span> diff --git a/docs/dev/reference/summary.mkinfit.html b/docs/dev/reference/summary.mkinfit.html index 3a31bfe7..c58fffbb 100644 --- a/docs/dev/reference/summary.mkinfit.html +++ b/docs/dev/reference/summary.mkinfit.html @@ -209,15 +209,15 @@ EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, <span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">FOCUS_2006_A</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.1.2 </span> <span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.1 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Wed Aug 10 15:27:28 2022 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Wed Aug 10 15:27:28 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Fri Sep 16 10:30:48 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Fri Sep 16 10:30:48 2022 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - k_parent * parent</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type analytical </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted using 131 model solutions performed in 0.029 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted using 131 model solutions performed in 0.028 s</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Error model: Constant variance </span> <span class="r-out co"><span class="r-pr">#></span> </span> diff --git a/docs/dev/reference/summary.mmkin.html b/docs/dev/reference/summary.mmkin.html index e916ba24..e440e4a9 100644 --- a/docs/dev/reference/summary.mmkin.html +++ b/docs/dev/reference/summary.mmkin.html @@ -129,7 +129,7 @@ and gives an overview of ill-defined parameters calculated by <a href="illparms. <span class="r-in"><span> quiet <span class="op">=</span> <span class="cn">TRUE</span>, cores <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></span> <span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fits</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> Error model: Constant variance </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted in 0.802 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted in 0.81 s</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Convergence:</span> <span class="r-out co"><span class="r-pr">#></span> dataset</span> diff --git a/docs/dev/reference/summary.saem.mmkin.html b/docs/dev/reference/summary.saem.mmkin.html index 6cab9c5f..1a6da753 100644 --- a/docs/dev/reference/summary.saem.mmkin.html +++ b/docs/dev/reference/summary.saem.mmkin.html @@ -289,8 +289,8 @@ saemix authors for the parts inherited from saemix.</p> <span class="r-out co"><span class="r-pr">#></span> saemix version used for fitting: 3.1 </span> <span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.1.2 </span> <span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.1 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Wed Aug 10 15:28:15 2022 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Wed Aug 10 15:28:15 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Fri Sep 16 10:31:33 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Fri Sep 16 10:31:33 2022 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *</span> @@ -305,7 +305,7 @@ saemix authors for the parts inherited from saemix.</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type analytical </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted in 27.674 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted in 27.615 s</span> <span class="r-out co"><span class="r-pr">#></span> Using 300, 100 iterations and 10 chains</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Variance model: Two-component variance function </span> diff --git a/docs/dev/sitemap.xml b/docs/dev/sitemap.xml index fde124d6..da4ada00 100644 --- a/docs/dev/sitemap.xml +++ b/docs/dev/sitemap.xml @@ -208,6 +208,9 @@ <loc>https://pkgdown.jrwb.de/mkin/reference/mmkin.html</loc> </url> <url> + <loc>https://pkgdown.jrwb.de/mkin/reference/multistart.html</loc> + </url> + <url> <loc>https://pkgdown.jrwb.de/mkin/reference/nafta.html</loc> </url> <url> diff --git a/man/multistart.Rd b/man/multistart.Rd index 4dd95503..cb971557 100644 --- a/man/multistart.Rd +++ b/man/multistart.Rd @@ -17,9 +17,9 @@ multistart(object, n = 50, cores = 1, ...) \method{parms}{multistart}(object, ...) -parhist(object, lpos = "topleft", ...) +parhist(object, lpos = "topleft", main = "", ...) -llhist(object, breaks = "Sturges", main = "", lpos = "topleft", ...) +llhist(object, breaks = "Sturges", lpos = "topleft", main = "", ...) } \arguments{ \item{object}{The fit object to work with} @@ -30,15 +30,15 @@ used?} \item{cores}{How many fits should be run in parallel?} \item{\dots}{Passed to the update function, or to the basic plotting -function in the case of the graphical function.} +function in the case of the graphical functions.} \item{x}{The multistart object to print} \item{lpos}{Positioning of the legend.} -\item{breaks}{Passed to \link{hist}} - \item{main}{title of the plot} + +\item{breaks}{Passed to \link{hist}} } \value{ A list of \link{saem.mmkin} objects, with class attributes diff --git a/man/parms.Rd b/man/parms.Rd index 293bdaab..acae2d91 100644 --- a/man/parms.Rd +++ b/man/parms.Rd @@ -4,7 +4,7 @@ \alias{parms} \alias{parms.mkinfit} \alias{parms.mmkin} -\title{Extract model parameters from mkinfit models} +\title{Extract model parameters} \usage{ parms(object, ...) @@ -13,8 +13,7 @@ parms(object, ...) \method{parms}{mmkin}(object, transformed = FALSE, errparms = TRUE, ...) } \arguments{ -\item{object}{A fitted model object. Methods are implemented for -\code{\link[=mkinfit]{mkinfit()}} objects and for \code{\link[=mmkin]{mmkin()}} objects.} +\item{object}{A fitted model object.} \item{\dots}{Not used} @@ -25,15 +24,14 @@ during the optimisation?} in addition to the degradation parameters?} } \value{ -For mkinfit objects, a numeric vector of fitted model parameters. -For mmkin row objects, a matrix with the parameters with a row for each -dataset. If the mmkin object has more than one row, a list of such matrices -is returned. +Depending on the object, a numeric vector of fitted model parameters, +a matrix (e.g. for mmkin row objects), or a list of matrices (e.g. for +mmkin objects with more than one row). } \description{ -This function always returns degradation model parameters as well as error -model parameters, in order to avoid working with a fitted model without -considering the error structure that was assumed for the fit. +This function returns degradation model parameters as well as error +model parameters per default, in order to avoid working with a fitted model +without considering the error structure that was assumed for the fit. } \examples{ # mkinfit objects @@ -53,3 +51,6 @@ parms(fits) parms(fits, transformed = TRUE) } } +\seealso{ +\link{saem}, \link{multistart} +} diff --git a/vignettes/web_only/mkin_benchmarks.rda b/vignettes/web_only/mkin_benchmarks.rda Binary files differindex 05297c01..06d62afd 100644 --- a/vignettes/web_only/mkin_benchmarks.rda +++ b/vignettes/web_only/mkin_benchmarks.rda |