From 24eb77216700cf8b2f2bde3abad84c1f83f9e32a Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 9 Jan 2023 06:22:04 +0100 Subject: Prebuilt PDF vignettes, summary_listing --- .../reference/example_analysis/dlls/sforb_sfo2.so | Bin 0 -> 17272 bytes .../example_analysis/example_analysis.Rmd | 314 +++++++++++++++++++++ docs/dev/reference/example_analysis/header.tex | 1 + docs/dev/reference/example_analysis/skeleton.pdf | Bin 0 -> 351780 bytes .../figure-latex/unnamed-chunk-11-1.pdf | Bin 0 -> 30166 bytes .../figure-latex/unnamed-chunk-16-1.pdf | Bin 0 -> 30137 bytes .../figure-latex/unnamed-chunk-6-1.pdf | Bin 0 -> 16408 bytes .../figure-latex/unnamed-chunk-9-1.pdf | Bin 0 -> 16043 bytes docs/dev/reference/hierarchical_kinetics.html | 154 ++++++++++ docs/dev/reference/index.html | 10 +- docs/dev/reference/mkinmod.html | 10 +- docs/dev/reference/summary_listing.html | 147 ++++++++++ 12 files changed, 628 insertions(+), 8 deletions(-) create mode 100755 docs/dev/reference/example_analysis/dlls/sforb_sfo2.so create mode 100644 docs/dev/reference/example_analysis/example_analysis.Rmd create mode 100644 docs/dev/reference/example_analysis/header.tex create mode 100644 docs/dev/reference/example_analysis/skeleton.pdf create mode 100644 docs/dev/reference/example_analysis/skeleton_files/figure-latex/unnamed-chunk-11-1.pdf create mode 100644 docs/dev/reference/example_analysis/skeleton_files/figure-latex/unnamed-chunk-16-1.pdf create mode 100644 docs/dev/reference/example_analysis/skeleton_files/figure-latex/unnamed-chunk-6-1.pdf create mode 100644 docs/dev/reference/example_analysis/skeleton_files/figure-latex/unnamed-chunk-9-1.pdf create mode 100644 docs/dev/reference/hierarchical_kinetics.html create mode 100644 docs/dev/reference/summary_listing.html (limited to 'docs/dev/reference') diff --git a/docs/dev/reference/example_analysis/dlls/sforb_sfo2.so b/docs/dev/reference/example_analysis/dlls/sforb_sfo2.so new file mode 100755 index 00000000..a692256d Binary files /dev/null and b/docs/dev/reference/example_analysis/dlls/sforb_sfo2.so differ diff --git a/docs/dev/reference/example_analysis/example_analysis.Rmd b/docs/dev/reference/example_analysis/example_analysis.Rmd new file mode 100644 index 00000000..38a6bd20 --- /dev/null +++ b/docs/dev/reference/example_analysis/example_analysis.Rmd @@ -0,0 +1,314 @@ +--- +title: "Hierarchical kinetic modelling of degradation data" +author: +date: +output: mkin::hierarchical_kinetics +geometry: margin=2cm +--- + +\clearpage + +# Setup + +```{r packages, cache = FALSE, message = FALSE} +library(mkin) +library(knitr) +library(saemix) +library(parallel) +library(readxl) +``` + +```{r n_cores, cache = 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. The status of the fits +is checked. + +```{r parent-mhmkin-refined} +parent_mhmkin_refined <- update(parent_mhmkin, + no_random_effect = illparms(parent_mhmkin)) +status(parent_mhmkin_refined) |> kable() +``` + +Also, it is checked if the AIC values of the refined fits are actually smaller +than the AIC values of the original fits. + +```{r dependson = "parent-mhmkin-refined"} +(AIC(parent_mhmkin_refined) < AIC(parent_mhmkin)) |> kable() +``` + +From the refined fits, the most suitable model is selected using the AIC. + +```{r parent-best, 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) +parent_best <- parent_mhmkin_refined[[best_degmod_parent, best_errmod_parent]] +``` + +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-best"} +illparms(parent_best) +``` + +The corresponding fit is plotted below. + +```{r dependson = "parent-best"} +plot(parent_best) +``` +The fitted parameters, together with approximate confidence +intervals are listed below. + +```{r dependson = "parent-best"} +parms(parent_best, ci = TRUE) |> kable(digits = 3) +``` + +To investigate a potential covariate influence on degradation parameters, a +covariate model is added to the hierarchical model for each of the degradation +parameters with well-defined random effects. Also, a version with covariate +models for both of them is fitted. + +```{r parent-best-pH} +parent_best_pH_1 <- update(parent_best, covariates = covariates, + covariate_models = list(log_k_lambda_free ~ pH)) +parent_best_pH_2 <- update(parent_best, covariates = covariates, + covariate_models = list(log_k_lambda_bound_free ~ pH)) +parent_best_pH_3 <- update(parent_best, covariates = covariates, + covariate_models = list(log_k_lambda_free ~ pH, log_k_lambda_bound_free ~ pH)) +``` + +The resulting models are compared. + +```{r dependson = "parent-best-pH"} +anova(parent_best, parent_best_pH_1, parent_best_pH_2, parent_best_pH_3) |> + kable(digits = 1) +``` + +The model fit with the lowest AIC is the one with a pH correlation of the +desorption rate constant `k_lambda_bound_free`. Plot and parameter listing +of this fit are shown below. Also, it is confirmed that no ill-defined +variance parameters are found. + +```{r dependson = "parent-best-pH"} +plot(parent_best_pH_2) +``` + +```{r dependson = "parent-best-pH"} +illparms(parent_best_pH_2) +parms(parent_best_pH_2, ci = TRUE) |> kable(digits = 3) +``` + +\clearpage + +# Pathway fits + +As an example of a pathway fit, a model with SFORB for the parent compound and +parallel formation of two metabolites is set up. + +```{r path-1-degmod} +if (!dir.exists("dlls")) dir.create("dlls") + +m_sforb_sfo2 = mkinmod( + lambda = mkinsub("SFORB", to = c("c_V", "c_XV")), + c_V = mkinsub("SFO"), + c_XV = mkinsub("SFO"), + name = "sforb_sfo2", + dll_dir = "dlls", + overwrite = TRUE, quiet = TRUE +) +``` + +Separate evaluations of all datasets are performed with constant variance +and using two-component error. + +```{r path-1-sep, dependson = c("path-1-degmod", "ds")} +sforb_sep_const <- mmkin(list(sforb_path = m_sforb_sfo2), ds, + cluster = cl, quiet = TRUE) +sforb_sep_tc <- update(sforb_sep_const, error_model = "tc") +``` + +The separate fits with constant variance are plotted. + +```{r dependson = "path-1-sep", fig.height = 9} +plot(mixed(sforb_sep_const)) +``` + +The two corresponding hierarchical fits, with the random effects for the parent +degradation parameters excluded as discussed above, and including the covariate +model that was identified for the parent degradation, are attempted below. + +```{r path-1, dependson = "path-1-sep"} +path_1 <- mhmkin(list(sforb_sep_const, sforb_sep_tc), + no_random_effect = c("lambda_free_0", "log_k_lambda_free_bound"), + covariates = covariates, covariate_models = list(log_k_lambda_bound_free ~ pH), + cluster = cl) +``` + +```{r dependson = "path-1"} +status(path_1) |> kable() +``` + +The status information shows that both fits were successfully completed. + +```{r dependson = "path-1"} +anova(path_1) |> kable(digits = 1) +``` +Model comparison shows that the two-component error model provides a much +better fit. + +```{r dependson = "path-1"} +illparms(path_1[["sforb_path", "tc"]]) +``` + +Two ill-defined variance components are found. Therefore, the fit is +repeated with the corresponding random effects removed. + +```{r path-1-refined, dependson = "path-1"} +path_1_refined <- update(path_1[["sforb_path", "tc"]], + no_random_effect = c("lambda_free_0", "log_k_lambda_free_bound", + "log_k_c_XV", "f_lambda_ilr_2")) +``` + +The empty output of the illparms function indicates that there are no +ill-defined parameters remaining in the refined fit. + +```{r dependson = "path-1-refined"} +illparms(path_1_refined) +``` + +Below, the refined fit is plotted and the fitted parameters are shown together +with their 95% confidence intervals. + +```{r dependson = "path-1-refined", fig.height = 9} +plot(path_1_refined) +``` + +```{r dependson = "path-1-refined", fig.height = 9} +parms(path_1_refined, ci = TRUE) |> kable(digits = 3) +``` + +\clearpage + +# Appendix + +## Listings of initial 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) + } +} +``` + +## Listings of 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) + } +} +``` + +## Listings of pathway fits + +```{r listings-path-1, results = "asis", echo = FALSE, dependson = "path-1-refined"} +tex_listing(path_1[["sforb_path", "const"]], + caption = "Hierarchical fit of SFORB-SFO2 with constant variance") +tex_listing(path_1[["sforb_path", "tc"]], + caption = "Hierarchical fit of SFORB-SFO2 with two-component error") +tex_listing(path_1_refined, + caption = "Refined hierarchical fit of SFORB-SFO2 with two-component error") +``` + +## Session info + +```{r echo = FALSE, cache = FALSE} +parallel::stopCluster(cl) +sessionInfo() +``` + diff --git a/docs/dev/reference/example_analysis/header.tex b/docs/dev/reference/example_analysis/header.tex new file mode 100644 index 00000000..a2b7ce83 --- /dev/null +++ b/docs/dev/reference/example_analysis/header.tex @@ -0,0 +1 @@ +\definecolor{shadecolor}{RGB}{248,248,248} diff --git a/docs/dev/reference/example_analysis/skeleton.pdf b/docs/dev/reference/example_analysis/skeleton.pdf new file mode 100644 index 00000000..53c5fb31 Binary files /dev/null and b/docs/dev/reference/example_analysis/skeleton.pdf differ diff --git a/docs/dev/reference/example_analysis/skeleton_files/figure-latex/unnamed-chunk-11-1.pdf b/docs/dev/reference/example_analysis/skeleton_files/figure-latex/unnamed-chunk-11-1.pdf new file mode 100644 index 00000000..ab685d92 Binary files /dev/null and b/docs/dev/reference/example_analysis/skeleton_files/figure-latex/unnamed-chunk-11-1.pdf differ diff --git a/docs/dev/reference/example_analysis/skeleton_files/figure-latex/unnamed-chunk-16-1.pdf b/docs/dev/reference/example_analysis/skeleton_files/figure-latex/unnamed-chunk-16-1.pdf new file mode 100644 index 00000000..5d88063b Binary files /dev/null and b/docs/dev/reference/example_analysis/skeleton_files/figure-latex/unnamed-chunk-16-1.pdf differ diff --git a/docs/dev/reference/example_analysis/skeleton_files/figure-latex/unnamed-chunk-6-1.pdf b/docs/dev/reference/example_analysis/skeleton_files/figure-latex/unnamed-chunk-6-1.pdf new file mode 100644 index 00000000..5e0d7b6f Binary files /dev/null and b/docs/dev/reference/example_analysis/skeleton_files/figure-latex/unnamed-chunk-6-1.pdf differ diff --git a/docs/dev/reference/example_analysis/skeleton_files/figure-latex/unnamed-chunk-9-1.pdf b/docs/dev/reference/example_analysis/skeleton_files/figure-latex/unnamed-chunk-9-1.pdf new file mode 100644 index 00000000..eecd06a8 Binary files /dev/null and b/docs/dev/reference/example_analysis/skeleton_files/figure-latex/unnamed-chunk-9-1.pdf differ diff --git a/docs/dev/reference/hierarchical_kinetics.html b/docs/dev/reference/hierarchical_kinetics.html new file mode 100644 index 00000000..bedb8753 --- /dev/null +++ b/docs/dev/reference/hierarchical_kinetics.html @@ -0,0 +1,154 @@ + +Hierarchical kinetics template — hierarchical_kinetics • mkin + + +
+
+ + + +
+
+
+

Hierarchical kinetics template

+ Source: R/hierarchical_kinetics.R + +
+ +
+

R markdown format for setting up hierarchical kinetics based on a template +provided with the mkin package.

+
+ +
+ 
hierarchical_kinetics(..., keep_tex = FALSE)
+
+ +
+

Arguments

+
...
+

Arguments to rmarkdown::pdf_document

+ + +
keep_tex
+

Keep the intermediate tex file used in the conversion to PDF

+ +
+
+

Value

+ + +

R Markdown output format to pass to +render

+ + +
+ +
+

Examples

+ 

+# \dontrun{
+library(rmarkdown)
+draft("example_analysis.rmd", template = "hierarchical_kinetics", package = "mkin")
+# }
+
+
+
+
+ +
+ + +
+

Developed by Johannes Ranke.

+
+ +
+

Site built with pkgdown 2.0.7.

+
+ +
+ + + + + + + + diff --git a/docs/dev/reference/index.html b/docs/dev/reference/index.html index 794126cf..525551fd 100644 --- a/docs/dev/reference/index.html +++ b/docs/dev/reference/index.html @@ -195,6 +195,10 @@ of an mmkin object

Create and work with nonlinear hierarchical models

+

hierarchical_kinetics()

+ +

Hierarchical kinetics template

+

read_spreadsheet()

Read datasets and relevant meta information from a spreadsheet file

@@ -356,9 +360,9 @@ degradation models and one or more error models

-

tex_listing()

+

summary_listing() tex_listing() html_listing()

-

Wrap the output of a summary function in tex listing environment

+

Display the output of a summary function according to the output format

f_time_norm_focus()

@@ -493,7 +497,7 @@ kinetic models fitted with mkinfit

-

Site built with pkgdown 2.0.6.

+

Site built with pkgdown 2.0.7.

diff --git a/docs/dev/reference/mkinmod.html b/docs/dev/reference/mkinmod.html index 251215a7..145dee83 100644 --- a/docs/dev/reference/mkinmod.html +++ b/docs/dev/reference/mkinmod.html @@ -132,7 +132,7 @@ the source compartment. Additionally, mkinsub() has an argument to, specifying names of variables to which a transfer is to be assumed in the model. If the argument use_of_ff is set to "min" -(default) and the model for the compartment is "SFO" or "SFORB", an +and the model for the compartment is "SFO" or "SFORB", an additional mkinsub() argument can be sink = FALSE, effectively fixing the flux to sink to zero. In print.mkinmod, this argument is currently not used.

@@ -247,7 +247,7 @@ in the FOCUS and NAFTA guidance documents are used.

For kinetic models with more than one observed variable, a symbolic solution of the system of differential equations is included in the resulting mkinmod object in some cases, speeding up the solution.

-

If a C compiler is found by pkgbuild::has_compiler() and there +

If a C compiler is found by pkgbuild::has_compiler() and there is more than one observed variable in the specification, C code is generated for evaluating the differential equations, compiled using inline::cfunction() and added to the resulting mkinmod object.

@@ -310,7 +310,7 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media

parent = mkinsub("SFO", "m1", full_name = "Test compound"), m1 = mkinsub("SFO", full_name = "Metabolite M1"), name = "SFO_SFO", dll_dir = DLL_dir, unload = TRUE, overwrite = TRUE) -#> Copied DLL from /tmp/RtmpbZbZ8Y/file8c6a9f402f42.so to /home/jranke/.local/share/mkin/SFO_SFO.so +#> Copied DLL from /tmp/RtmpelWAOB/fileb43c31a25a86.so to /home/jranke/.local/share/mkin/SFO_SFO.so # Now we can save the model and restore it in a new session saveRDS(SFO_SFO.2, file = "~/SFO_SFO.rds") # Terminate the R session here if you would like to check, and then do @@ -363,7 +363,7 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media

#> }) #> return(predicted) #> } -#> <environment: 0x55556029f678> +#> <environment: 0x55555f013820> # If we have several parallel metabolites # (compare tests/testthat/test_synthetic_data_for_UBA_2014.R) @@ -392,7 +392,7 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media

-

Site built with pkgdown 2.0.6.

+

Site built with pkgdown 2.0.7.

diff --git a/docs/dev/reference/summary_listing.html b/docs/dev/reference/summary_listing.html new file mode 100644 index 00000000..876412cc --- /dev/null +++ b/docs/dev/reference/summary_listing.html @@ -0,0 +1,147 @@ + +Display the output of a summary function according to the output format — summary_listing • mkin + + +
+
+ + + +
+
+
+

Display the output of a summary function according to the output format

+ Source: R/summary_listing.R + +
+ +
+

This function is intended for use in a R markdown code chunk with the chunk +option results = "asis".

+
+ +
+ 
summary_listing(object, caption = NULL, label = NULL, clearpage = TRUE)
+
+tex_listing(object, caption = NULL, label = NULL, clearpage = TRUE)
+
+html_listing(object, caption = NULL)
+
+ +
+

Arguments

+
object
+

The object for which the summary is to be listed

+ + +
caption
+

An optional caption

+ + +
label
+

An optional label, ignored in html output

+ + +
clearpage
+

Should a new page be started after the listing? Ignored in html output

+ +
+ +
+ +
+ + +
+ + + + + + + + -- cgit v1.2.1