Short demo of the multistart method

From fd205e13061de8abc595d266f3b0c7650773d442 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 16 Sep 2022 21:06:54 +0200 Subject: Improve multistart documentation, bugfix - Split out llhist and parhist documentation - Add example code for multistart - Create a multistart vignette, because the example code fails when run by pkgdown - Fix multistart for the case of mkin transformations in the saem fit --- docs/dev/articles/index.html | 7 +- docs/dev/articles/web_only/multistart.html | 172 +++++++++++++++++++++ .../accessible-code-block-0.0.1/empty-anchor.js | 15 ++ .../figure-html/unnamed-chunk-2-1.png | Bin 0 -> 52067 bytes .../figure-html/unnamed-chunk-3-1.png | Bin 0 -> 50142 bytes docs/dev/authors.html | 5 +- docs/dev/index.html | 5 +- docs/dev/news/index.html | 5 +- docs/dev/pkgdown.yml | 3 +- docs/dev/reference/index.html | 15 +- docs/dev/reference/llhist.html | 147 ++++++++++++++++++ docs/dev/reference/multistart.html | 64 +++++--- docs/dev/reference/parhist.html | 156 +++++++++++++++++++ docs/dev/sitemap.xml | 9 ++ 14 files changed, 576 insertions(+), 27 deletions(-) create mode 100644 docs/dev/articles/web_only/multistart.html create mode 100644 docs/dev/articles/web_only/multistart_files/accessible-code-block-0.0.1/empty-anchor.js create mode 100644 docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-2-1.png create mode 100644 docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-3-1.png create mode 100644 docs/dev/reference/llhist.html create mode 100644 docs/dev/reference/parhist.html (limited to 'docs/dev') diff --git a/docs/dev/articles/index.html b/docs/dev/articles/index.html index 526708a4..551e9c98 100644 --- a/docs/dev/articles/index.html +++ b/docs/dev/articles/index.html @@ -44,11 +44,14 @@ Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models

- Example evaluation of FOCUS Example Dataset Z + Short demo of the multistart method

Performance benefit by using compiled model definitions in mkin

+ Example evaluation of FOCUS Example Dataset Z +

Calculation of time weighted average concentrations with mkin

@@ -102,6 +105,8 @@

Example evaluations of the dimethenamid data from 2018

Short demo of the multistart method

diff --git a/docs/dev/articles/web_only/multistart.html b/docs/dev/articles/web_only/multistart.html new file mode 100644 index 00000000..a119a0d6 --- /dev/null +++ b/docs/dev/articles/web_only/multistart.html @@ -0,0 +1,172 @@ + + + + + + + +Short demo of the multistart method • mkin + + + + + + + + + + + + + +

+ + + + +

This is a vignette, because the multistart method does not seem to work in pkgdown example code and I wanted to show the plots in the online docs. The dimethenamid data from 2018 from seven soils is used as example data.

+library(mkin)
+dmta_ds <- lapply(1:7, function(i) {
+  ds_i <- dimethenamid_2018$ds[[i]]$data
+  ds_i[ds_i$name == "DMTAP", "name"] <-  "DMTA"
+  ds_i$time <- ds_i$time * dimethenamid_2018$f_time_norm[i]
+  ds_i
+})
+names(dmta_ds) <- sapply(dimethenamid_2018$ds, function(ds) ds$title)
+dmta_ds[["Elliot"]] <- rbind(dmta_ds[["Elliot 1"]], dmta_ds[["Elliot 2"]])
+dmta_ds[["Elliot 1"]] <- dmta_ds[["Elliot 2"]] <- NULL

First, we check the DFOP model with the two-component error model and random effects for all degradation parameters.

+f_mmkin <- mmkin("DFOP", dmta_ds, error_model = "tc", cores = 7, quiet = TRUE)
+f_saem_full <- saem(f_mmkin)
+f_saem_full_multi <- multistart(f_saem_full, n = 16, cores = 16)
+parhist(f_saem_full_multi, lpos = "bottomright")

We see that not all variability parameters are identifiable, most problematic is the variance of k2. So we reduce the parameter distribution model by removing the intersoil variability for this parameter.

+f_saem_reduced <- update(f_saem_full, covariance.model = diag(c(1, 1, 0, 1)))
+f_saem_reduced_multi <- multistart(f_saem_reduced, n = 16, cores = 16)
+parhist(f_saem_reduced_multi, lpos = "bottomright")

+ + + +

+ + + + +

- Example evaluation of FOCUS Example Dataset Z + Short demo of the multistart method

Performance benefit by using compiled model definitions in mkin

+ Example evaluation of FOCUS Example Dataset Z +

Calculation of time weighted average concentrations with mkin

diff --git a/docs/dev/index.html b/docs/dev/index.html index 7d3abbb2..5257b590 100644 --- a/docs/dev/index.html +++ b/docs/dev/index.html @@ -74,11 +74,14 @@ Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models

- Example evaluation of FOCUS Example Dataset Z + Short demo of the multistart method

Performance benefit by using compiled model definitions in mkin

+ Example evaluation of FOCUS Example Dataset Z +

Calculation of time weighted average concentrations with mkin

diff --git a/docs/dev/news/index.html b/docs/dev/news/index.html index c8863ec6..029b6999 100644 --- a/docs/dev/news/index.html +++ b/docs/dev/news/index.html @@ -44,11 +44,14 @@ Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models

- Example evaluation of FOCUS Example Dataset Z + Short demo of the multistart method

Performance benefit by using compiled model definitions in mkin

+ Example evaluation of FOCUS Example Dataset Z +

Calculation of time weighted average concentrations with mkin

diff --git a/docs/dev/pkgdown.yml b/docs/dev/pkgdown.yml index 1fee5d96..6cd0f89b 100644 --- a/docs/dev/pkgdown.yml +++ b/docs/dev/pkgdown.yml @@ -11,7 +11,8 @@ articles: benchmarks: web_only/benchmarks.html compiled_models: web_only/compiled_models.html dimethenamid_2018: web_only/dimethenamid_2018.html -last_built: 2022-09-16T08:50Z + multistart: web_only/multistart.html +last_built: 2022-09-16T19:00Z urls: reference: https://pkgdown.jrwb.de/mkin/reference article: https://pkgdown.jrwb.de/mkin/articles diff --git a/docs/dev/reference/index.html b/docs/dev/reference/index.html index 3372a69a..b7a5de92 100644 --- a/docs/dev/reference/index.html +++ b/docs/dev/reference/index.html @@ -44,11 +44,14 @@ Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models

- Example evaluation of FOCUS Example Dataset Z + Short demo of the multistart method

Performance benefit by using compiled model definitions in mkin

+ Example evaluation of FOCUS Example Dataset Z +

Calculation of time weighted average concentrations with mkin

@@ -234,9 +237,17 @@ degradation models and one or more error models

Confidence intervals for parameters in saem.mmkin objects

multistart() print(<multistart>) parms(<multistart>) parhist() llhist()

multistart() print(<multistart>) parms(<multistart>)

Perform a hierarchical model fit with multiple starting values

+ +

llhist()

+ +

Plot the distribution of log likelihoods from multistart objects

+ +

parhist()

+ +

Plot parameter distributions from multistart objects

Datasets and known results

diff --git a/docs/dev/reference/llhist.html b/docs/dev/reference/llhist.html new file mode 100644 index 00000000..2eb77a82 --- /dev/null +++ b/docs/dev/reference/llhist.html @@ -0,0 +1,147 @@ + +Plot the distribution of log likelihoods from multistart objects — llhist • mkin + + +

+ + + +

+ + +

Produces a histogram of log-likelihoods, and an overlayed kernel density +estimate. In addition, the likelihood of the original fit is shown as +a red vertical line.

+ +

llhist(object, breaks = "Sturges", lpos = "topleft", main = "", ...)

+ +

Arguments

object: The multistart object
breaks: Passed to hist
lpos: Positioning of the legend.
main: Title of the plot
...: Passed to hist

Value

@@ -160,6 +146,11 @@ function in the case of the graphical functions.

Details

Currently, parallel execution of the fits is only supported using parallel::mclapply, i.e. not available on Windows.

In case the online version of this help page contains error messages +in the example code and no plots, this is due to the multistart method +not working when called by pkgdown. Please refer to the +online vignette +in this case.

References

@@ -168,7 +159,40 @@ 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.

Examples

# \dontrun{
+library(mkin)
+dmta_ds <- lapply(1:7, function(i) {
+  ds_i <- dimethenamid_2018$ds[[i]]$data
+  ds_i[ds_i$name == "DMTAP", "name"] <-  "DMTA"
+  ds_i$time <- ds_i$time * dimethenamid_2018$f_time_norm[i]
+  ds_i
+})
+names(dmta_ds) <- sapply(dimethenamid_2018$ds, function(ds) ds$title)
+dmta_ds[["Elliot"]] <- rbind(dmta_ds[["Elliot 1"]], dmta_ds[["Elliot 2"]])
+dmta_ds[["Elliot 1"]] <- dmta_ds[["Elliot 2"]] <- NULL
+
+f_mmkin <- mmkin("DFOP", dmta_ds, error_model = "tc", cores = 7, quiet = TRUE)
+f_saem_full <- saem(f_mmkin)
+f_saem_full_multi <- multistart(f_saem_full, n = 16, cores = 16)
+#> Warning: all scheduled cores encountered errors in user code
+parhist(f_saem_full_multi, lpos = "bottomright")
+#> Error in UseMethod("parms", object): no applicable method for 'parms' applied to an object of class "try-error"
+
+f_saem_reduced <- update(f_saem_full, covariance.model = diag(c(1, 1, 0, 1)))
+f_saem_reduced_multi <- multistart(f_saem_reduced, n = 16, cores = 16)
+#> Warning: all scheduled cores encountered errors in user code
+parhist(f_saem_reduced_multi, lpos = "bottomright")
+#> Error in UseMethod("parms", object): no applicable method for 'parms' applied to an object of class "try-error"
+# }
+

diff --git a/docs/dev/reference/parhist.html b/docs/dev/reference/parhist.html new file mode 100644 index 00000000..a2fd717b --- /dev/null +++ b/docs/dev/reference/parhist.html @@ -0,0 +1,156 @@ + +Plot parameter distributions from multistart objects — parhist • mkin + + +

+ + + +

+ + +

Produces a boxplot with all parameters from the multiple runs, scaled using +their medians. If parameter transformations were done by mkin (default in +saem), then the parameters found by saem are on the transformed scale, and +scaling is simply done by subtracting the median. If parameter +transformations were done by saemix, scaling is done by dividing by the +median, as in the paper by Duchesne et al. (2021).

+ +

parhist(object, lpos = "topleft", main = "", ...)

+ +

Arguments

object: The multistart object
lpos: Positioning of the legend.
main: Title of the plot
...: Passed to boxplot

References

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.

Johannes Ranke

Last change 16 September 2022 (rebuilt 2022-09-16)

Datasets and known results

Plot the distribution of log likelihoods from multistart objects

Arguments

See also

Value

Details

References

See also

Examples