Synthetic data for hierarchical kinetic degradation models

Date: Thu, 17 Nov 2022 14:54:20 +0100 Subject: Complete update of online docs for v1.2.0 --- docs/news/index.html | 27 +++++++++++++++++++-------- 1 file changed, 19 insertions(+), 8 deletions(-) (limited to 'docs/news') diff --git a/docs/news/index.html b/docs/news/index.html index faaab288..90768141 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -17,7 +17,7 @@ @@ -44,11 +44,14 @@ Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models

@@ -82,13 +88,18 @@

- -

‘R/mhmkin.R’: New method for performing multiple hierarchical mkin fits in one function call, optionally in parallel.
‘R/saem.R’: Implement and test saemix transformations for FOMC and HS. Also, error out if saemix transformations are requested but not supported.
‘R/saem.R’: ‘logLik’ and ‘update’ methods for ‘saem.mmkin’ objects.
‘R/convergence.R’: New generic to show convergence information with methods for ‘mmkin’ and ‘mhmkin’ objects.

‘R/saem.R’: ‘logLik’, ‘update’ and ‘anova’ methods for ‘saem.mmkin’ objects.
‘R/saem.R’: Automatic estimation of start parameters for random effects for the case of mkin transformations, nicely improving convergence and reducing problems with iterative ODE solutions.
‘R/status.R’: New generic to show status information for fit array objects with methods for ‘mmkin’, ‘mhmkin’ and ‘multistart’ objects.
‘R/mhmkin.R’: New method for performing multiple hierarchical mkin fits in one function call, optionally in parallel.
‘R/mhmkin.R’: ‘anova.mhmkin’ for conveniently comparing the resulting fits.
‘R/illparms.R’: New generic to show ill-defined parameters with methods for ‘mkinfit’, ‘mmkin’, ‘saem.mmkin’ and ‘mhmkin’ objects.
‘R/multistart.R’: New method for testing multiple start parameters for hierarchical model fits, with function ‘llhist’ and new generic ‘parplot’ for diagnostics, and new generics ‘which.best’ and ‘best’ for extracting the fit with the highest likelihood
‘R/summary.mmkin.R’: Summary method for mmkin objects.
‘R/saem.R’: Implement and test saemix transformations for FOMC and HS. Also, error out if saemix transformations are requested but not supported.
‘R/read_spreadsheet.R’: Conveniently read in data from a spreadsheet file.
‘R/tex_listings.R’: Conveniently include summaries of fit objects in R markdown documents that are compiled to LaTeX.

-- cgit v1.2.3 From 317fd7514e638780c09ed6349a165a854ba2deea Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 18 Nov 2022 19:23:56 +0100 Subject: Update docs --- docs/404.html | 2 +- docs/articles/index.html | 2 +- docs/authors.html | 6 +- docs/index.html | 2 +- docs/news/index.html | 10 +- docs/pkgdown.yml | 2 +- docs/reference/Rplot001.png | Bin 14083 -> 22432 bytes docs/reference/Rplot002.png | Bin 13699 -> 16953 bytes docs/reference/ds_mixed-1.png | Bin 0 -> 219939 bytes docs/reference/ds_mixed.html | 240 ++++++++++++++++++++++++++++++++++++++++++ docs/reference/index.html | 10 +- docs/reference/parplot.html | 8 +- docs/reference/saem.html | 12 +-- docs/sitemap.xml | 3 + 14 files changed, 279 insertions(+), 18 deletions(-) create mode 100644 docs/reference/ds_mixed-1.png create mode 100644 docs/reference/ds_mixed.html (limited to 'docs/news') diff --git a/docs/404.html b/docs/404.html index 36135992..8e7e8f45 100644 --- a/docs/404.html +++ b/docs/404.html @@ -32,7 +32,7 @@

diff --git a/docs/articles/index.html b/docs/articles/index.html index 292a72a4..f4f6d557 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -17,7 +17,7 @@ diff --git a/docs/authors.html b/docs/authors.html index 6560ab17..7afe3000 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -17,7 +17,7 @@ @@ -115,13 +115,13 @@

Ranke J (2022). mkin: Kinetic Evaluation of Chemical Degradation Data. -R package version 1.2.0, https://pkgdown.jrwb.de/mkin/. +R package version 1.2.1, https://pkgdown.jrwb.de/mkin/.

@Manual{,
   title = {mkin: Kinetic Evaluation of Chemical Degradation Data},
   author = {Johannes Ranke},
   year = {2022},
-  note = {R package version 1.2.0},
+  note = {R package version 1.2.1},
   url = {https://pkgdown.jrwb.de/mkin/},
 }

diff --git a/docs/index.html b/docs/index.html index 9048bc38..bb14906d 100644 --- a/docs/index.html +++ b/docs/index.html @@ -44,7 +44,7 @@ diff --git a/docs/news/index.html b/docs/news/index.html index 90768141..6b9a7d51 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -17,7 +17,7 @@ @@ -87,6 +87,14 @@ Source: NEWS.md +

+ +

‘tests/testthat/setup_script.R’: Excluded another ill-defined random effect for the DFOP fit with ‘saem’, in an attempt to avoid a platform dependence that surfaced on Fedora systems on the CRAN check farm
‘tests/testthat/test_mixed.R’: Round parameters found by saemix to two significant digits before printing, to also help to avoid platform dependence of tests
‘R/saem.R’: Fix a bug that prevented that ‘error.ini’ is passed to ‘saemix_model’, and set default to c(1, 1) to avoid changing test results
‘R/parplot.R’: Show initial values for error model parameters
‘R/loglik.mkinfit.R’: Add ‘nobs’ attribute to the resulting ‘logLik’ object, in order to make test_AIC.R succeed on current R-devel

‘R/saem.R’: ‘logLik’, ‘update’ and ‘anova’ methods for ‘saem.mmkin’ objects.

Synthetic data for hierarchical kinetic degradation models — ds_mixed • mkin

+ + + +

+ + +

The R code used to create this data object is installed with this package in +the 'dataset_generation' directory.

+ + + +

Examples

# \dontrun{
+  sfo_mmkin <- mmkin("SFO", ds_sfo, quiet = TRUE, error_model = "tc", cores = 15)
+  sfo_saem <- saem(sfo_mmkin, no_random_effect = "parent_0")
+  plot(sfo_saem)
+
+# }
+
+# This is the code used to generate the datasets
+cat(readLines(system.file("dataset_generation/ds_mixed.R", package = "mkin")), sep = "\n")
+#> # Synthetic data for hierarchical kinetic models
+#> # Refactored version of the code previously in tests/testthat/setup_script.R
+#> # The number of datasets was 3 for FOMC, and 10 for HS in that script, now it
+#> # is always 15 for consistency
+#> 
+#> library(mkin)  # We use mkinmod and mkinpredict
+#> sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120)
+#> n <- 15
+#> log_sd <- 0.3
+#> err_1 = list(const = 1, prop = 0.05)
+#> tc <- function(value) sigma_twocomp(value, err_1$const, err_1$prop)
+#> const <- function(value) 2
+#> 
+#> set.seed(123456)
+#> SFO <- mkinmod(parent = mkinsub("SFO"))
+#> sfo_pop <- list(parent_0 = 100, k_parent = 0.03)
+#> sfo_parms <- as.matrix(data.frame(
+#>     k_parent = rlnorm(n, log(sfo_pop$k_parent), log_sd)))
+#> set.seed(123456)
+#> ds_sfo <- lapply(1:n, function(i) {
+#>   ds_mean <- mkinpredict(SFO, sfo_parms[i, ],
+#>     c(parent = sfo_pop$parent_0), sampling_times)
+#>   add_err(ds_mean, tc, n = 1)[[1]]
+#> })
+#> attr(ds_sfo, "pop") <- sfo_pop
+#> attr(ds_sfo, "parms") <- sfo_parms
+#> 
+#> set.seed(123456)
+#> FOMC <- mkinmod(parent = mkinsub("FOMC"))
+#> fomc_pop <- list(parent_0 = 100, alpha = 2, beta = 8)
+#> fomc_parms <- as.matrix(data.frame(
+#>     alpha = rlnorm(n, log(fomc_pop$alpha), 0.4),
+#>     beta = rlnorm(n, log(fomc_pop$beta), 0.2)))
+#> set.seed(123456)
+#> ds_fomc <- lapply(1:n, function(i) {
+#>   ds_mean <- mkinpredict(FOMC, fomc_parms[i, ],
+#>     c(parent = fomc_pop$parent_0), sampling_times)
+#>   add_err(ds_mean, tc, n = 1)[[1]]
+#> })
+#> attr(ds_fomc, "pop") <- fomc_pop
+#> attr(ds_fomc, "parms") <- fomc_parms
+#> 
+#> set.seed(123456)
+#> DFOP <- mkinmod(parent = mkinsub("DFOP"))
+#> dfop_pop <- list(parent_0 = 100, k1 = 0.06, k2 = 0.015, g = 0.4)
+#> dfop_parms <- as.matrix(data.frame(
+#>   k1 = rlnorm(n, log(dfop_pop$k1), log_sd),
+#>   k2 = rlnorm(n, log(dfop_pop$k2), log_sd),
+#>   g = plogis(rnorm(n, qlogis(dfop_pop$g), log_sd))))
+#> set.seed(123456)
+#> ds_dfop <- lapply(1:n, function(i) {
+#>   ds_mean <- mkinpredict(DFOP, dfop_parms[i, ],
+#>     c(parent = dfop_pop$parent_0), sampling_times)
+#>   add_err(ds_mean, tc, n = 1)[[1]]
+#> })
+#> attr(ds_dfop, "pop") <- dfop_pop
+#> attr(ds_dfop, "parms") <- dfop_parms
+#> 
+#> set.seed(123456)
+#> HS <- mkinmod(parent = mkinsub("HS"))
+#> hs_pop <- list(parent_0 = 100, k1 = 0.08, k2 = 0.01, tb = 15)
+#> hs_parms <- as.matrix(data.frame(
+#>   k1 = rlnorm(n, log(hs_pop$k1), log_sd),
+#>   k2 = rlnorm(n, log(hs_pop$k2), log_sd),
+#>   tb = rlnorm(n, log(hs_pop$tb), 0.1)))
+#> set.seed(123456)
+#> ds_hs <- lapply(1:n, function(i) {
+#>   ds_mean <- mkinpredict(HS, hs_parms[i, ],
+#>     c(parent = hs_pop$parent_0), sampling_times)
+#>   add_err(ds_mean, const, n = 1)[[1]]
+#> })
+#> attr(ds_hs, "pop") <- hs_pop
+#> attr(ds_hs, "parms") <- hs_parms
+#> 
+#> set.seed(123456)
+#> DFOP_SFO <- mkinmod(
+#>   parent = mkinsub("DFOP", "m1"),
+#>   m1 = mkinsub("SFO"),
+#>   quiet = TRUE)
+#> dfop_sfo_pop <- list(parent_0 = 100,
+#>   k_m1 = 0.007, f_parent_to_m1 = 0.5,
+#>   k1 = 0.1, k2 = 0.02, g = 0.5)
+#> dfop_sfo_parms <- as.matrix(data.frame(
+#>   k1 = rlnorm(n, log(dfop_sfo_pop$k1), log_sd),
+#>   k2 = rlnorm(n, log(dfop_sfo_pop$k2), log_sd),
+#>   g = plogis(rnorm(n, qlogis(dfop_sfo_pop$g), log_sd)),
+#>   f_parent_to_m1 = plogis(rnorm(n,
+#>       qlogis(dfop_sfo_pop$f_parent_to_m1), log_sd)),
+#>   k_m1 = rlnorm(n, log(dfop_sfo_pop$k_m1), log_sd)))
+#> ds_dfop_sfo_mean <- lapply(1:n,
+#>   function(i) {
+#>     mkinpredict(DFOP_SFO, dfop_sfo_parms[i, ],
+#>       c(parent = dfop_sfo_pop$parent_0, m1 = 0), sampling_times)
+#>   }
+#> )
+#> set.seed(123456)
+#> ds_dfop_sfo <- lapply(ds_dfop_sfo_mean, function(ds) {
+#>   add_err(ds,
+#>     sdfunc = function(value) sqrt(err_1$const^2 + value^2 * err_1$prop^2),
+#>     n = 1, secondary = "m1")[[1]]
+#> })
+#> attr(ds_dfop_sfo, "pop") <- dfop_sfo_pop
+#> attr(ds_dfop_sfo, "parms") <- dfop_sfo_parms
+#> 
+#> #save(ds_sfo, ds_fomc, ds_dfop, ds_hs, ds_dfop_sfo, file = "data/ds_mixed.rda", version = 2)
+

+ +

+ + +

@@ -268,9 +268,9 @@ degradation models and one or more error models

focus_soil_moisture

ds_mixed ds_sfo ds_fomc ds_dfop ds_hs ds_dfop_sfo

FOCUS default values for soil moisture contents at field capacity, MWHC and 1/3 bar

Synthetic data for hierarchical kinetic degradation models

D24_2014

@@ -327,6 +327,10 @@ degradation models and one or more error models

test_data_from_UBA_2014

Three experimental datasets from two water sediment systems and one soil

+ +

focus_soil_moisture

+ +

FOCUS default values for soil moisture contents at field capacity, MWHC and 1/3 bar

print(<mkinds>)

diff --git a/docs/reference/parplot.html b/docs/reference/parplot.html index f4f3c811..ab02cbb3 100644 --- a/docs/reference/parplot.html +++ b/docs/reference/parplot.html @@ -19,7 +19,7 @@ or by their medians as proposed in the paper by Duchesne et al. (2021).">

mkin 1.1.2

mkin 1.2.0 (2022-11-17)

mkin 1.1.1 (2022-07-12)

mkin 1.2.1 (unreleased)

mkin 1.2.0 (2022-11-17)

Synthetic data for hierarchical kinetic degradation models

Examples