From 886c9ef013124aa954d960c655b349b5340ff154 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Mon, 19 Dec 2022 12:31:56 +0100
Subject: Rename template folder, create format

Instead of rmarkdown::pdf_document, mkin::hierarchical_kinetics is used
as a document format in the template. In this way, the template file can
be freed from some R code and yaml options that the average user does
not have to be aware of.
---
 .../rmarkdown/templates/hier/skeleton/skeleton.Rmd | 186 ---------------------
 inst/rmarkdown/templates/hier/template.yaml        |   3 -
 .../hierarchical_kinetics/skeleton/header.tex      |   1 +
 .../hierarchical_kinetics/skeleton/skeleton.Rmd    | 162 ++++++++++++++++++
 .../templates/hierarchical_kinetics/template.yaml  |   3 +
 5 files changed, 166 insertions(+), 189 deletions(-)
 delete mode 100644 inst/rmarkdown/templates/hier/skeleton/skeleton.Rmd
 delete mode 100644 inst/rmarkdown/templates/hier/template.yaml
 create mode 100644 inst/rmarkdown/templates/hierarchical_kinetics/skeleton/header.tex
 create mode 100644 inst/rmarkdown/templates/hierarchical_kinetics/skeleton/skeleton.Rmd
 create mode 100644 inst/rmarkdown/templates/hierarchical_kinetics/template.yaml

(limited to 'inst')

diff --git a/inst/rmarkdown/templates/hier/skeleton/skeleton.Rmd b/inst/rmarkdown/templates/hier/skeleton/skeleton.Rmd
deleted file mode 100644
index df6fa2f9..00000000
--- a/inst/rmarkdown/templates/hier/skeleton/skeleton.Rmd
+++ /dev/null
@@ -1,186 +0,0 @@
----
-title: "Hierarchical kinetic modelling of degradation data"
-author:
-date: Last change on DD MMM YYYY, last compiled on `r format(Sys.time(),
-  "%e %B %Y")`
-output:
-  pdf_document:
-    extra_dependencies: ["float", "listing"]
-toc: yes
-geometry: margin=2cm
----
-
-
-```{r setup, echo = FALSE, cache = FALSE}
-errmods <- c(const = "constant variance", tc = "two-component error")
-
-knitr::opts_chunk$set(
-  comment = "", tidy = FALSE, cache = TRUE, fig.pos = "H", fig.align = "center"
-)
-options(knitr.kable.NA = "")
-
-# Version requirements
-if (getRversion() < "4.1.0")
-  stop("You need R with version > 4.1.0 to compile this document")
-if ((saemix_version <- packageVersion("saemix")) < "3.1") {
-  warning("Your saemix version is ", saemix_version,
-    ", you should preferably use 3.2 to compile this document")
-}
-if ((mkin_version <- packageVersion("mkin")) < "1.2.2") {
-  stop("Your mkin version is ", mkin_version,
-    ", you need at least 1.2.2 to compile this document")
-}
-```
-
-```{r packages, cache = FALSE, message = FALSE, warning = FALSE, echo = FALSE}
-library(mkin)
-library(saemix)
-library(parallel)
-library(knitr)
-```
-
-```{r n_cores, cache = FALSE, echo = FALSE}
-n_cores <- detectCores()
-
-if (Sys.info()["sysname"] == "Windows") {
-  cl <- makePSOCKcluster(n_cores)
-} else {
-  cl <- makeForkCluster(n_cores)
-}
-```
-
-\clearpage
-
-# Introduction
-
-This report shows hierarchical kinetic modelling for ...
-The data were obtained from ...
-
-```{r ds}
-data_path <- system.file("testdata", "lambda-cyhalothrin_soil_efsa_2014.xlsx", package = "mkin")
-ds <- read_spreadsheet(data_path, valid_datasets = c(1:4, 7:13))
-covariates <- attr(ds, "covariates")
-```
-
-The covariate data are shown below.
-
-```{r results = "asis", dependson = "ds", echo = FALSE}
-kable(covariates, caption = "Covariate data for all datasets")
-```
-
-\clearpage
-
-The datasets with the residue time series are shown in the tables below. Please
-refer to the spreadsheet for details like data sources, treatment of values
-below reporting limits and time step normalisation factors.
-
-```{r results = "asis", dependson = "ds", echo = FALSE}
-for (ds_name in names(ds)) {
-  print(
-    kable(mkin_long_to_wide(ds[[ds_name]]),
-      caption = paste("Dataset", ds_name),
-      booktabs = TRUE, row.names = FALSE))
-  cat("\n\\clearpage\n")
-}
-```
-
-# Parent only evaluations
-
-The following code performs separate fits of the candidate degradation models
-to all datasets using constant variance and the two-component error model.
-
-```{r parent-sep, dependson = "ds"}
-parent_deg_mods <- c("SFO", "FOMC", "DFOP", "SFORB")
-parent_sep_const <- mmkin(
-  parent_deg_mods, ds,
-  error_model = "const",
-  cluster = cl, quiet = TRUE)
-parent_sep_tc <- update(parent_sep_const, error_model = "tc")
-```
-
-To select the parent model, the corresponding hierarchical fits are performed below.
-
-```{r parent-mhmkin, dependson = "parent-sep"}
-parent_mhmkin <- mhmkin(list(parent_sep_const, parent_sep_tc), cluster = cl)
-status(parent_mhmkin) |> kable()
-```
-
-All fits terminate without errors (status OK). The check for ill-defined
-parameters shows that not all random effect parameters can be robustly
-quantified.
-
-```{r dependson = "parent_mhmkin"}
-illparms(parent_mhmkin) |> kable()
-```
-
-Therefore, the fits are updated, excluding random effects that were
-ill-defined according to the `illparms` function.
-
-```{r parent-mhmkin-refined}
-parent_mhmkin_refined <- update(parent_mhmkin,
-  no_random_effect = illparms(parent_mhmkin))
-status(parent_mhmkin_refined) |> kable()
-```
-
-The most suitable model is selected based on the AIC.
-
-```{r dependson = "parent-mhmkin"}
-aic_parent <- AIC(parent_mhmkin_refined)
-min_aic <- which(aic_parent == min(aic_parent), arr.ind = TRUE)
-best_degmod_parent <- rownames(aic_parent)[min_aic[1]]
-best_errmod_parent <- colnames(aic_parent)[min_aic[2]]
-anova(parent_mhmkin_refined) |> kable(digits = 1)
-```
-
-Based on the AIC, the combination of the `r best_degmod_parent` degradation
-model with the error model `r errmods[best_errmod_parent]` is identified to
-be most suitable for the degradation of the parent. The check below
-confirms that no ill-defined parameters remain for this combined model.
-
-```{r dependson = "parent-mhmkin"}
-illparms(parent_mhmkin_refined[[best_degmod_parent, best_errmod_parent]])
-```
-
-The corresponding fit is shown below.
-
-```{r parent-best-full, dependson = "parent-mhmkin"}
-plot(parent_mhmkin_refined[[best_degmod_parent, best_errmod_parent]])
-```
-
-Detailed listings of the parent fits are shown in the Appendix.
-
-\clearpage
-
-# Appendix
-
-## Summaries of saem fits
-
-### Parent fits
-
-```{r listings-parent, results = "asis", echo = FALSE}
-for (deg_mod in parent_deg_mods) {
-  for (err_mod in c("const", "tc")) {
-    caption <- paste("Hierarchical", deg_mod, "fit with", errmods[err_mod])
-    tex_listing(parent_mhmkin[[deg_mod, err_mod]], caption)
-  }
-}
-```
-
-### Refined parent fits
-
-```{r listings-pathway, results = "asis", echo = FALSE}
-for (deg_mod in parent_deg_mods) {
-  for (err_mod in c("const", "tc")) {
-    caption <- paste("Refined hierarchical", deg_mod, "fit with", errmods[err_mod])
-    tex_listing(parent_mhmkin_refined[[deg_mod, err_mod]], caption)
-  }
-}
-```
-
-## Session info
-
-```{r, echo = FALSE}
-parallel::stopCluster(cl)
-sessionInfo()
-```
-
diff --git a/inst/rmarkdown/templates/hier/template.yaml b/inst/rmarkdown/templates/hier/template.yaml
deleted file mode 100644
index d8ab6a4d..00000000
--- a/inst/rmarkdown/templates/hier/template.yaml
+++ /dev/null
@@ -1,3 +0,0 @@
-name: Hierarchical kinetics
-description: Hierarchical kinetic modelling of degradation data
-create_dir: true
diff --git a/inst/rmarkdown/templates/hierarchical_kinetics/skeleton/header.tex b/inst/rmarkdown/templates/hierarchical_kinetics/skeleton/header.tex
new file mode 100644
index 00000000..a2b7ce83
--- /dev/null
+++ b/inst/rmarkdown/templates/hierarchical_kinetics/skeleton/header.tex
@@ -0,0 +1 @@
+\definecolor{shadecolor}{RGB}{248,248,248}
diff --git a/inst/rmarkdown/templates/hierarchical_kinetics/skeleton/skeleton.Rmd b/inst/rmarkdown/templates/hierarchical_kinetics/skeleton/skeleton.Rmd
new file mode 100644
index 00000000..74fae164
--- /dev/null
+++ b/inst/rmarkdown/templates/hierarchical_kinetics/skeleton/skeleton.Rmd
@@ -0,0 +1,162 @@
+---
+title: "Hierarchical kinetic modelling of degradation data"
+author:
+date:
+output: mkin::hierarchical_kinetics
+geometry: margin=2cm
+---
+
+```{r packages, cache = FALSE, message = FALSE}
+library(mkin)
+library(knitr)
+library(saemix)
+library(parallel)
+library(readxl)
+```
+
+```{r n_cores, cache = FALSE, echo = FALSE}
+n_cores <- detectCores()
+
+if (Sys.info()["sysname"] == "Windows") {
+  cl <- makePSOCKcluster(n_cores)
+} else {
+  cl <- makeForkCluster(n_cores)
+}
+```
+
+\clearpage
+
+# Introduction
+
+This report shows hierarchical kinetic modelling for ...
+The data were obtained from ...
+
+```{r ds}
+data_path <- system.file("testdata", "lambda-cyhalothrin_soil_efsa_2014.xlsx", package = "mkin")
+ds <- read_spreadsheet(data_path, valid_datasets = c(1:4, 7:13))
+covariates <- attr(ds, "covariates")
+```
+
+The covariate data are shown below.
+
+```{r results = "asis", dependson = "ds", echo = FALSE}
+kable(covariates, caption = "Covariate data for all datasets")
+```
+
+\clearpage
+
+The datasets with the residue time series are shown in the tables below. Please
+refer to the spreadsheet for details like data sources, treatment of values
+below reporting limits and time step normalisation factors.
+
+```{r results = "asis", dependson = "ds", echo = FALSE}
+for (ds_name in names(ds)) {
+  print(
+    kable(mkin_long_to_wide(ds[[ds_name]]),
+      caption = paste("Dataset", ds_name),
+      booktabs = TRUE, row.names = FALSE))
+  cat("\n\\clearpage\n")
+}
+```
+
+# Parent only evaluations
+
+The following code performs separate fits of the candidate degradation models
+to all datasets using constant variance and the two-component error model.
+
+```{r parent-sep, dependson = "ds"}
+parent_deg_mods <- c("SFO", "FOMC", "DFOP", "SFORB")
+errmods <- c(const = "constant variance", tc = "two-component error")
+parent_sep_const <- mmkin(
+  parent_deg_mods, ds,
+  error_model = "const",
+  cluster = cl, quiet = TRUE)
+parent_sep_tc <- update(parent_sep_const, error_model = "tc")
+```
+
+To select the parent model, the corresponding hierarchical fits are performed below.
+
+```{r parent-mhmkin, dependson = "parent-sep"}
+parent_mhmkin <- mhmkin(list(parent_sep_const, parent_sep_tc), cluster = cl)
+status(parent_mhmkin) |> kable()
+```
+
+All fits terminate without errors (status OK). The check for ill-defined
+parameters shows that not all random effect parameters can be robustly
+quantified.
+
+```{r dependson = "parent_mhmkin"}
+illparms(parent_mhmkin) |> kable()
+```
+
+Therefore, the fits are updated, excluding random effects that were
+ill-defined according to the `illparms` function.
+
+```{r parent-mhmkin-refined}
+parent_mhmkin_refined <- update(parent_mhmkin,
+  no_random_effect = illparms(parent_mhmkin))
+status(parent_mhmkin_refined) |> kable()
+```
+
+The most suitable model is selected based on the AIC.
+
+```{r, dependson = "parent-mhmkin"}
+aic_parent <- AIC(parent_mhmkin_refined)
+min_aic <- which(aic_parent == min(aic_parent), arr.ind = TRUE)
+best_degmod_parent <- rownames(aic_parent)[min_aic[1]]
+best_errmod_parent <- colnames(aic_parent)[min_aic[2]]
+anova(parent_mhmkin_refined) |> kable(digits = 1)
+```
+
+Based on the AIC, the combination of the `r best_degmod_parent` degradation
+model with the error model `r errmods[best_errmod_parent]` is identified to
+be most suitable for the degradation of the parent. The check below
+confirms that no ill-defined parameters remain for this combined model.
+
+```{r dependson = "parent-mhmkin"}
+illparms(parent_mhmkin_refined[[best_degmod_parent, best_errmod_parent]])
+```
+
+The corresponding fit is shown below.
+
+```{r parent-best-full, dependson = "parent-mhmkin"}
+plot(parent_mhmkin_refined[[best_degmod_parent, best_errmod_parent]])
+```
+
+Detailed listings of the parent fits are shown in the Appendix.
+
+\clearpage
+
+# Appendix
+
+## Summaries of saem fits
+
+### Parent fits
+
+```{r listings-parent, results = "asis", echo = FALSE, dependson = "parent_mhmkin"}
+for (deg_mod in parent_deg_mods) {
+  for (err_mod in c("const", "tc")) {
+    caption <- paste("Hierarchical", deg_mod, "fit with", errmods[err_mod])
+    tex_listing(parent_mhmkin[[deg_mod, err_mod]], caption)
+  }
+}
+```
+
+### Refined parent fits
+
+```{r listings-parent-refined, results = "asis", echo = FALSE, dependson = "parent_mhmkin_refined"}
+for (deg_mod in parent_deg_mods) {
+  for (err_mod in c("const", "tc")) {
+    caption <- paste("Refined hierarchical", deg_mod, "fit with", errmods[err_mod])
+    tex_listing(parent_mhmkin_refined[[deg_mod, err_mod]], caption)
+  }
+}
+```
+
+## Session info
+
+```{r, echo = FALSE, cache = FALSE}
+parallel::stopCluster(cl)
+sessionInfo()
+```
+
diff --git a/inst/rmarkdown/templates/hierarchical_kinetics/template.yaml b/inst/rmarkdown/templates/hierarchical_kinetics/template.yaml
new file mode 100644
index 00000000..d8ab6a4d
--- /dev/null
+++ b/inst/rmarkdown/templates/hierarchical_kinetics/template.yaml
@@ -0,0 +1,3 @@
+name: Hierarchical kinetics
+description: Hierarchical kinetic modelling of degradation data
+create_dir: true
-- 
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