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 5 files changed, 193 insertions(+), 1 deletion(-) 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 (limited to 'docs/dev/articles') 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
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  • + 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 + + + + + + + + + + + + + +
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    Short demo of the multistart method

    +

    Johannes Ranke

    + +

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

    + + Source: vignettes/web_only/multistart.rmd + + +
    + + + +

    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")
    +

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    Developed by Johannes Ranke.

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    + +
    +

    +

    Site built with pkgdown 2.0.6.

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    + + + + + + + + diff --git a/docs/dev/articles/web_only/multistart_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/dev/articles/web_only/multistart_files/accessible-code-block-0.0.1/empty-anchor.js new file mode 100644 index 00000000..ca349fd6 --- /dev/null +++ b/docs/dev/articles/web_only/multistart_files/accessible-code-block-0.0.1/empty-anchor.js @@ -0,0 +1,15 @@ +// Hide empty tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) --> +// v0.0.1 +// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020. + +document.addEventListener('DOMContentLoaded', function() { + const codeList = document.getElementsByClassName("sourceCode"); + for (var i = 0; i < codeList.length; i++) { + var linkList = codeList[i].getElementsByTagName('a'); + for (var j = 0; j < linkList.length; j++) { + if (linkList[j].innerHTML === "") { + linkList[j].setAttribute('aria-hidden', 'true'); + } + } + } +}); diff --git a/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-2-1.png b/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-2-1.png new file mode 100644 index 00000000..e30e56f0 Binary files /dev/null and b/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-2-1.png differ diff --git a/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-3-1.png b/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-3-1.png new file mode 100644 index 00000000..3ed0d546 Binary files /dev/null and b/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-3-1.png differ -- cgit v1.2.1