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 --- vignettes/web_only/multistart.R | 23 ++ vignettes/web_only/multistart.html | 441 +++++++++++++++++++++++++++++++++++++ vignettes/web_only/multistart.rmd | 48 ++++ 3 files changed, 512 insertions(+) create mode 100644 vignettes/web_only/multistart.R create mode 100644 vignettes/web_only/multistart.html create mode 100644 vignettes/web_only/multistart.rmd (limited to 'vignettes/web_only') diff --git a/vignettes/web_only/multistart.R b/vignettes/web_only/multistart.R new file mode 100644 index 00000000..a860757d --- /dev/null +++ b/vignettes/web_only/multistart.R @@ -0,0 +1,23 @@ +## ----------------------------------------------------------------------------- +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) +parhist(f_saem_full_multi, lpos = "bottomright") + +## ----------------------------------------------------------------------------- +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") + diff --git a/vignettes/web_only/multistart.html b/vignettes/web_only/multistart.html new file mode 100644 index 00000000..ab1b768d --- /dev/null +++ b/vignettes/web_only/multistart.html @@ -0,0 +1,441 @@ + + + + + + + + + + + + + + +Short demo of the multistart method + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + +

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")
+

+ + + + +
+ + + + + + + + + + + + + + + diff --git a/vignettes/web_only/multistart.rmd b/vignettes/web_only/multistart.rmd new file mode 100644 index 00000000..5f109f3d --- /dev/null +++ b/vignettes/web_only/multistart.rmd @@ -0,0 +1,48 @@ +--- +title: Short demo of the multistart method +author: Johannes Ranke +date: Last change 16 September 2022 (rebuilt `r Sys.Date()`) +output: + html_document +vignette: > + %\VignetteEngine{knitr::rmarkdown} + %\VignetteIndexEntry{Short demo of the multistart method} + %\VignetteEncoding{UTF-8} +--- + +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. + +```{r} +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. + +```{r} +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. + +```{r} +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") +``` -- cgit v1.2.1