From df0cff4b829f1abf62f037591a24a8019174dd0a Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 18 Nov 2022 08:37:40 +0100 Subject: Pass error.init to saemix_model, show in parplot Due to an oversight, error.init was not really passed to saemix_model in saem.mmkin. The new initial values were reverted to c(1, 1), in order to avoid changing the test results. Initial values for error model parameters are now shown in parplot.multistart. --- tests/testthat/_snaps/multistart/parplot-for-biphasic-saemix-fit.svg | 2 ++ tests/testthat/_snaps/multistart/parplot-for-sfo-fit.svg | 2 ++ 2 files changed, 4 insertions(+) (limited to 'tests/testthat/_snaps') diff --git a/tests/testthat/_snaps/multistart/parplot-for-biphasic-saemix-fit.svg b/tests/testthat/_snaps/multistart/parplot-for-biphasic-saemix-fit.svg index c0332fd5..7017908e 100644 --- a/tests/testthat/_snaps/multistart/parplot-for-biphasic-saemix-fit.svg +++ b/tests/testthat/_snaps/multistart/parplot-for-biphasic-saemix-fit.svg @@ -173,6 +173,8 @@ + + diff --git a/tests/testthat/_snaps/multistart/parplot-for-sfo-fit.svg b/tests/testthat/_snaps/multistart/parplot-for-sfo-fit.svg index f3373901..18eb7fcc 100644 --- a/tests/testthat/_snaps/multistart/parplot-for-sfo-fit.svg +++ b/tests/testthat/_snaps/multistart/parplot-for-sfo-fit.svg @@ -89,6 +89,8 @@ + + -- cgit v1.2.3 From 5364f037a72863ef5ba81e14ba4417f68fd389f9 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 18 Nov 2022 19:14:47 +0100 Subject: Make mixed model test data permanent to ensure reproducibility To ensure that tests on different platforms work on the same data, the mixed modelling test data previosly generated in tests/testthat/setup_script.R were generated once using the script in inst/dataset/generation/ds_mixed.R, and are now distributed with the package. --- R/ds_mixed.R | 17 ++ _pkgdown.yml | 3 +- data/ds_mixed.rda | Bin 0 -> 6935 bytes inst/dataset_generation/ds_mixed.R | 105 +++++++++++ log/check.log | 4 +- log/test.log | 28 +-- man/ds_mixed.Rd | 24 +++ .../multistart/llhist-for-biphasic-saemix-fit.svg | 62 ------- .../_snaps/multistart/llhist-for-dfop-sfo-fit.svg | 62 +++++++ .../_snaps/multistart/llhist-for-sfo-fit.svg | 30 +-- .../multistart/parplot-for-biphasic-saemix-fit.svg | 201 --------------------- .../_snaps/multistart/parplot-for-dfop-sfo-fit.svg | 201 +++++++++++++++++++++ .../_snaps/multistart/parplot-for-sfo-fit.svg | 90 ++++----- tests/testthat/anova_sfo_saem.txt | 10 +- tests/testthat/print_dfop_saem_1.txt | 23 +++ tests/testthat/print_dfop_saemix_1.txt | 23 --- tests/testthat/print_fits_synth_const.txt | 2 +- tests/testthat/print_mmkin_sfo_1_mixed.txt | 4 +- tests/testthat/print_multistart_biphasic.txt | 4 - tests/testthat/print_multistart_dfop_sfo.txt | 4 + tests/testthat/print_sfo_saem_1_reduced.txt | 12 +- tests/testthat/setup_script.R | 99 +--------- tests/testthat/summary_hfit_sfo_tc.txt | 26 +-- tests/testthat/summary_saem_biphasic_s.txt | 87 --------- tests/testthat/summary_saem_dfop_sfo_s.txt | 87 +++++++++ tests/testthat/test_mixed.R | 32 ++-- tests/testthat/test_multistart.R | 30 ++- tests/testthat/test_plot.R | 22 +-- tests/testthat/test_saemix_parent.R | 40 ++-- 29 files changed, 697 insertions(+), 635 deletions(-) create mode 100644 R/ds_mixed.R create mode 100644 data/ds_mixed.rda create mode 100644 inst/dataset_generation/ds_mixed.R create mode 100644 man/ds_mixed.Rd delete mode 100644 tests/testthat/_snaps/multistart/llhist-for-biphasic-saemix-fit.svg create mode 100644 tests/testthat/_snaps/multistart/llhist-for-dfop-sfo-fit.svg delete mode 100644 tests/testthat/_snaps/multistart/parplot-for-biphasic-saemix-fit.svg create mode 100644 tests/testthat/_snaps/multistart/parplot-for-dfop-sfo-fit.svg create mode 100644 tests/testthat/print_dfop_saem_1.txt delete mode 100644 tests/testthat/print_dfop_saemix_1.txt delete mode 100644 tests/testthat/print_multistart_biphasic.txt create mode 100644 tests/testthat/print_multistart_dfop_sfo.txt delete mode 100644 tests/testthat/summary_saem_biphasic_s.txt create mode 100644 tests/testthat/summary_saem_dfop_sfo_s.txt (limited to 'tests/testthat/_snaps') diff --git a/R/ds_mixed.R b/R/ds_mixed.R new file mode 100644 index 00000000..c5055712 --- /dev/null +++ b/R/ds_mixed.R @@ -0,0 +1,17 @@ +#' Synthetic data for hierarchical kinetic degradation models +#' +#' The R code used to create this data object is installed with this package in +#' the 'dataset_generation' directory. +#' +#' @name ds_mixed +#' @aliases ds_sfo ds_fomc ds_dfop ds_hs ds_dfop_sfo +#' @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") +NULL diff --git a/_pkgdown.yml b/_pkgdown.yml index 8aa44ed4..98ed84f2 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -67,7 +67,7 @@ reference: - parplot - title: Datasets and known results contents: - - focus_soil_moisture + - ds_mixed - D24_2014 - dimethenamid_2018 - FOCUS_2006_A @@ -82,6 +82,7 @@ reference: - synthetic_data_for_UBA_2014 - experimental_data_for_UBA_2019 - test_data_from_UBA_2014 + - focus_soil_moisture - mkinds - mkindsg - title: NAFTA guidance diff --git a/data/ds_mixed.rda b/data/ds_mixed.rda new file mode 100644 index 00000000..cf9f6463 Binary files /dev/null and b/data/ds_mixed.rda differ diff --git a/inst/dataset_generation/ds_mixed.R b/inst/dataset_generation/ds_mixed.R new file mode 100644 index 00000000..f2ae6e7e --- /dev/null +++ b/inst/dataset_generation/ds_mixed.R @@ -0,0 +1,105 @@ +# 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) diff --git a/log/check.log b/log/check.log index 7aa4610c..31fc31eb 100644 --- a/log/check.log +++ b/log/check.log @@ -5,7 +5,7 @@ * using options ‘--no-tests --as-cran’ * checking for file ‘mkin/DESCRIPTION’ ... OK * checking extension type ... Package -* this is package ‘mkin’ version ‘1.2.0’ +* this is package ‘mkin’ version ‘1.2.1’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... Note_to_CRAN_maintainers Maintainer: ‘Johannes Ranke ’ @@ -41,7 +41,7 @@ Maintainer: ‘Johannes Ranke ’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK -* checking R code for possible problems ... [18s/18s] OK +* checking R code for possible problems ... [17s/17s] OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK diff --git a/log/test.log b/log/test.log index 87d24690..d1de270e 100644 --- a/log/test.log +++ b/log/test.log @@ -5,19 +5,19 @@ ✔ | 5 | Calculation of Akaike weights ✔ | 3 | Export dataset for reading into CAKE ✔ | 12 | Confidence intervals and p-values [1.0s] -✔ | 1 12 | Dimethenamid data from 2018 [31.5s] +✔ | 1 12 | Dimethenamid data from 2018 [32.6s] ──────────────────────────────────────────────────────────────────────────────── Skip ('test_dmta.R:98'): Different backends get consistent results for SFO-SFO3+, dimethenamid data Reason: Fitting this ODE model with saemix takes about 15 minutes on my system ──────────────────────────────────────────────────────────────────────────────── -✔ | 14 | Error model fitting [5.0s] +✔ | 14 | Error model fitting [5.1s] ✔ | 5 | Time step normalisation ✔ | 4 | Calculation of FOCUS chi2 error levels [0.6s] ✔ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [0.8s] ✔ | 4 | Test fitting the decline of metabolites from their maximum [0.4s] ✔ | 1 | Fitting the logistic model [0.2s] -✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [24.4s] -✔ | 1 12 | Nonlinear mixed-effects models [0.3s] +✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [24.6s] +✔ | 1 13 | Nonlinear mixed-effects models [0.4s] ──────────────────────────────────────────────────────────────────────────────── Skip ('test_mixed.R:79'): saemix results are reproducible for biphasic fits Reason: Fitting with saemix takes around 10 minutes when using deSolve @@ -26,32 +26,32 @@ Reason: Fitting with saemix takes around 10 minutes when using deSolve ✔ | 10 | Special cases of mkinfit calls [0.5s] ✔ | 3 | mkinfit features [0.7s] ✔ | 8 | mkinmod model generation and printing [0.2s] -✔ | 3 | Model predictions with mkinpredict [0.3s] -✔ | 9 | Multistart method for saem.mmkin models [36.2s] +✔ | 3 | Model predictions with mkinpredict [0.4s] +✔ | 9 | Multistart method for saem.mmkin models [37.3s] ✔ | 16 | Evaluations according to 2015 NAFTA guidance [2.5s] -✔ | 9 | Nonlinear mixed-effects models with nlme [8.8s] -✔ | 16 | Plotting [10.0s] +✔ | 9 | Nonlinear mixed-effects models with nlme [9.2s] +✔ | 16 | Plotting [10.1s] ✔ | 4 | Residuals extracted from mkinfit models -✔ | 1 36 | saemix parent models [65.8s] +✔ | 1 36 | saemix parent models [71.4s] ──────────────────────────────────────────────────────────────────────────────── Skip ('test_saemix_parent.R:143'): We can also use mkin solution methods for saem Reason: This still takes almost 2.5 minutes although we do not solve ODEs ──────────────────────────────────────────────────────────────────────────────── ✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.4s] ✔ | 11 | Processing of residue series -✔ | 10 | Fitting the SFORB model [3.7s] +✔ | 10 | Fitting the SFORB model [3.9s] ✔ | 1 | Summaries of old mkinfit objects ✔ | 5 | Summary [0.2s] -✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.2s] -✔ | 9 | Hypothesis tests [8.0s] +✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.3s] +✔ | 9 | Hypothesis tests [8.3s] ✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.2s] ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 210.4 s +Duration: 220.0 s ── Skipped tests ────────────────────────────────────────────────────────────── • Fitting this ODE model with saemix takes about 15 minutes on my system (1) • Fitting with saemix takes around 10 minutes when using deSolve (1) • This still takes almost 2.5 minutes although we do not solve ODEs (1) -[ FAIL 0 | WARN 0 | SKIP 3 | PASS 269 ] +[ FAIL 0 | WARN 0 | SKIP 3 | PASS 270 ] diff --git a/man/ds_mixed.Rd b/man/ds_mixed.Rd new file mode 100644 index 00000000..227b8e7f --- /dev/null +++ b/man/ds_mixed.Rd @@ -0,0 +1,24 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/ds_mixed.R +\name{ds_mixed} +\alias{ds_mixed} +\alias{ds_sfo} +\alias{ds_fomc} +\alias{ds_dfop} +\alias{ds_hs} +\alias{ds_dfop_sfo} +\title{Synthetic data for hierarchical kinetic degradation models} +\description{ +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") +} diff --git a/tests/testthat/_snaps/multistart/llhist-for-biphasic-saemix-fit.svg b/tests/testthat/_snaps/multistart/llhist-for-biphasic-saemix-fit.svg deleted file mode 100644 index 6015aed8..00000000 --- a/tests/testthat/_snaps/multistart/llhist-for-biphasic-saemix-fit.svg +++ /dev/null @@ -1,62 +0,0 @@ - - - - - - - - - - - - -Frequency of log likelihoods - - - - - - - --1149.5 --1149.4 --1149.3 --1149.2 --1149.1 --1149.0 - - - - - - -0 -1 -2 -3 -4 - - - - - - - - - - - - - - -original fit - - diff --git a/tests/testthat/_snaps/multistart/llhist-for-dfop-sfo-fit.svg b/tests/testthat/_snaps/multistart/llhist-for-dfop-sfo-fit.svg new file mode 100644 index 00000000..6015aed8 --- /dev/null +++ b/tests/testthat/_snaps/multistart/llhist-for-dfop-sfo-fit.svg @@ -0,0 +1,62 @@ + + + + + + + + + + + + +Frequency of log likelihoods + + + + + + + +-1149.5 +-1149.4 +-1149.3 +-1149.2 +-1149.1 +-1149.0 + + + + + + +0 +1 +2 +3 +4 + + + + + + + + + + + + + + +original fit + + diff --git a/tests/testthat/_snaps/multistart/llhist-for-sfo-fit.svg b/tests/testthat/_snaps/multistart/llhist-for-sfo-fit.svg index 98513d06..028c69de 100644 --- a/tests/testthat/_snaps/multistart/llhist-for-sfo-fit.svg +++ b/tests/testthat/_snaps/multistart/llhist-for-sfo-fit.svg @@ -25,20 +25,22 @@ --649.836 --649.834 --649.832 --649.830 --649.828 +-646.124 +-646.123 +-646.122 +-646.121 +-646.120 - - + + + 0 -1 -2 -3 +1 +2 +3 +4 @@ -46,11 +48,11 @@ - + - - - + + + original fit diff --git a/tests/testthat/_snaps/multistart/parplot-for-biphasic-saemix-fit.svg b/tests/testthat/_snaps/multistart/parplot-for-biphasic-saemix-fit.svg deleted file mode 100644 index 7017908e..00000000 --- a/tests/testthat/_snaps/multistart/parplot-for-biphasic-saemix-fit.svg +++ /dev/null @@ -1,201 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -parent_0 -f_parent_to_m1 -k2 -g -a.1 -b.1 -SD.log_k_m1 -SD.log_k1 -SD.g_qlogis - - - - - -0.5 -1.0 -1.5 -2.0 -Normalised parameters - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -Starting parameters -Original run -Multistart runs - - diff --git a/tests/testthat/_snaps/multistart/parplot-for-dfop-sfo-fit.svg b/tests/testthat/_snaps/multistart/parplot-for-dfop-sfo-fit.svg new file mode 100644 index 00000000..7017908e --- /dev/null +++ b/tests/testthat/_snaps/multistart/parplot-for-dfop-sfo-fit.svg @@ -0,0 +1,201 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +parent_0 +f_parent_to_m1 +k2 +g +a.1 +b.1 +SD.log_k_m1 +SD.log_k1 +SD.g_qlogis + + + + + +0.5 +1.0 +1.5 +2.0 +Normalised parameters + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +Starting parameters +Original run +Multistart runs + + diff --git a/tests/testthat/_snaps/multistart/parplot-for-sfo-fit.svg b/tests/testthat/_snaps/multistart/parplot-for-sfo-fit.svg index 18eb7fcc..a47a585a 100644 --- a/tests/testthat/_snaps/multistart/parplot-for-sfo-fit.svg +++ b/tests/testthat/_snaps/multistart/parplot-for-sfo-fit.svg @@ -25,42 +25,44 @@ - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -87,15 +89,15 @@ - - - - - - - - - + + + + + + + + + diff --git a/tests/testthat/anova_sfo_saem.txt b/tests/testthat/anova_sfo_saem.txt index 9e4bf71f..0ccd6d5c 100644 --- a/tests/testthat/anova_sfo_saem.txt +++ b/tests/testthat/anova_sfo_saem.txt @@ -1,7 +1,7 @@ -Data: 262 observations of 1 variable(s) grouped in 15 datasets +Data: 263 observations of 1 variable(s) grouped in 15 datasets npar AIC BIC Lik Chisq Df Pr(>Chisq) -sfo_saem_1_reduced 5 1310 1313 -650 -sfo_saem_1_reduced_mkin 5 1310 1313 -650 0 0 -sfo_saem_1 6 1312 1316 -650 0 1 1 -sfo_saem_1_mkin 6 1312 1316 -650 0 0 +sfo_saem_1_reduced 5 1302 1306 -646 +sfo_saem_1_reduced_mkin 5 1302 1306 -646 0 0 +sfo_saem_1 6 1304 1308 -646 0 1 1 +sfo_saem_1_mkin 6 1303 1308 -646 1 0 diff --git a/tests/testthat/print_dfop_saem_1.txt b/tests/testthat/print_dfop_saem_1.txt new file mode 100644 index 00000000..bdc40065 --- /dev/null +++ b/tests/testthat/print_dfop_saem_1.txt @@ -0,0 +1,23 @@ +Kinetic nonlinear mixed-effects model fit by SAEM +Structural model: +d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * + time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time))) + * parent + +Data: +270 observations of 1 variable(s) grouped in 15 datasets + +Likelihood computed by importance sampling + AIC BIC logLik + 1409 1415 -696 + +Fitted parameters: + estimate lower upper +parent_0 99.92 98.77 101.06 +log_k1 -2.72 -2.95 -2.50 +log_k2 -4.14 -4.27 -4.01 +g_qlogis -0.35 -0.53 -0.16 +a.1 0.92 0.68 1.16 +b.1 0.05 0.04 0.06 +SD.log_k1 0.37 0.23 0.51 +SD.log_k2 0.23 0.14 0.31 diff --git a/tests/testthat/print_dfop_saemix_1.txt b/tests/testthat/print_dfop_saemix_1.txt deleted file mode 100644 index 1d399a52..00000000 --- a/tests/testthat/print_dfop_saemix_1.txt +++ /dev/null @@ -1,23 +0,0 @@ -Kinetic nonlinear mixed-effects model fit by SAEM -Structural model: -d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * - time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time))) - * parent - -Data: -270 observations of 1 variable(s) grouped in 15 datasets - -Likelihood computed by importance sampling - AIC BIC logLik - 1409 1415 -696 - -Fitted parameters: - estimate lower upper -parent_0 100.00 99.00 100.00 -log_k1 -2.70 -3.00 -2.50 -log_k2 -4.10 -4.30 -4.00 -g_qlogis -0.35 -0.53 -0.16 -a.1 0.92 0.68 1.20 -b.1 0.05 0.04 0.06 -SD.log_k1 0.37 0.23 0.51 -SD.log_k2 0.23 0.14 0.31 diff --git a/tests/testthat/print_fits_synth_const.txt b/tests/testthat/print_fits_synth_const.txt index 2ea1f133..b4bbe6ca 100644 --- a/tests/testthat/print_fits_synth_const.txt +++ b/tests/testthat/print_fits_synth_const.txt @@ -4,7 +4,7 @@ Status of individual fits: dataset model 1 2 3 4 5 6 SFO OK OK OK OK OK OK - FOMC C C OK OK OK OK + FOMC C OK OK OK OK C C: Optimisation did not converge: false convergence (8) diff --git a/tests/testthat/print_mmkin_sfo_1_mixed.txt b/tests/testthat/print_mmkin_sfo_1_mixed.txt index 33e5bf5c..c12cfe2b 100644 --- a/tests/testthat/print_mmkin_sfo_1_mixed.txt +++ b/tests/testthat/print_mmkin_sfo_1_mixed.txt @@ -3,7 +3,7 @@ Structural model: d_parent/dt = - k_parent * parent Data: -262 observations of 1 variable(s) grouped in 15 datasets +263 observations of 1 variable(s) grouped in 15 datasets object Status of individual fits: @@ -16,4 +16,4 @@ OK: No warnings Mean fitted parameters: parent_0 log_k_parent - 99.9 -3.3 + 100.0 -3.4 diff --git a/tests/testthat/print_multistart_biphasic.txt b/tests/testthat/print_multistart_biphasic.txt deleted file mode 100644 index b4344f22..00000000 --- a/tests/testthat/print_multistart_biphasic.txt +++ /dev/null @@ -1,4 +0,0 @@ - object with 8 fits: -OK - 8 -OK: Fit terminated successfully diff --git a/tests/testthat/print_multistart_dfop_sfo.txt b/tests/testthat/print_multistart_dfop_sfo.txt new file mode 100644 index 00000000..b4344f22 --- /dev/null +++ b/tests/testthat/print_multistart_dfop_sfo.txt @@ -0,0 +1,4 @@ + object with 8 fits: +OK + 8 +OK: Fit terminated successfully diff --git a/tests/testthat/print_sfo_saem_1_reduced.txt b/tests/testthat/print_sfo_saem_1_reduced.txt index bac8848e..1c7fb588 100644 --- a/tests/testthat/print_sfo_saem_1_reduced.txt +++ b/tests/testthat/print_sfo_saem_1_reduced.txt @@ -3,16 +3,16 @@ Structural model: d_parent/dt = - k_parent * parent Data: -262 observations of 1 variable(s) grouped in 15 datasets +263 observations of 1 variable(s) grouped in 15 datasets Likelihood computed by importance sampling AIC BIC logLik - 1310 1313 -650 + 1302 1306 -646 Fitted parameters: estimate lower upper -parent_0 1e+02 99.08 1e+02 -k_parent 4e-02 0.03 4e-02 -a.1 9e-01 0.75 1e+00 +parent_0 1e+02 99.03 1e+02 +k_parent 3e-02 0.03 4e-02 +a.1 9e-01 0.71 1e+00 b.1 5e-02 0.04 5e-02 -SD.k_parent 3e-01 0.20 4e-01 +SD.k_parent 2e-01 0.14 3e-01 diff --git a/tests/testthat/setup_script.R b/tests/testthat/setup_script.R index 362038c3..c554800d 100644 --- a/tests/testthat/setup_script.R +++ b/tests/testthat/setup_script.R @@ -81,112 +81,27 @@ fit_obs_1 <- mkinfit(m_synth_SFO_lin, SFO_lin_a, error_model = "obs", quiet = TR fit_tc_1 <- mkinfit(m_synth_SFO_lin, SFO_lin_a, error_model = "tc", quiet = TRUE, error_model_algorithm = "threestep") -# Mixed models data and fits -sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120) -n <- n_biphasic <- 15 -log_sd <- 0.3 -err_1 = list(const = 1, prop = 0.05) -tc <- function(value) sigma_twocomp(value, err_1$const, err_1$prop) -const <- function(value) 2 - -set.seed(123456) -SFO <- mkinmod(parent = mkinsub("SFO")) -k_parent = rlnorm(n, log(0.03), log_sd) -set.seed(123456) -ds_sfo <- lapply(1:n, function(i) { - ds_mean <- mkinpredict(SFO, c(k_parent = k_parent[i]), - c(parent = 100), sampling_times) - add_err(ds_mean, tc, n = 1)[[1]] -}) - -set.seed(123456) -FOMC <- mkinmod(parent = mkinsub("FOMC")) -fomc_pop <- list(parent_0 = 100, alpha = 2, beta = 8) -fomc_parms <- as.matrix(data.frame( - alpha = rlnorm(n, log(fomc_pop$alpha), 0.4), - beta = rlnorm(n, log(fomc_pop$beta), 0.2))) -set.seed(123456) -ds_fomc <- lapply(1:3, function(i) { - ds_mean <- mkinpredict(FOMC, fomc_parms[i, ], - c(parent = 100), sampling_times) - add_err(ds_mean, tc, n = 1)[[1]] -}) - -set.seed(123456) -DFOP <- mkinmod(parent = mkinsub("DFOP")) -dfop_pop <- list(parent_0 = 100, k1 = 0.06, k2 = 0.015, g = 0.4) -dfop_parms <- as.matrix(data.frame( - k1 = rlnorm(n, log(dfop_pop$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$parent_0), sampling_times) - add_err(ds_mean, tc, n = 1)[[1]] -}) - -set.seed(123456) -HS <- mkinmod(parent = mkinsub("HS")) -hs_pop <- list(parent_0 = 100, k1 = 0.08, k2 = 0.01, tb = 15) -hs_parms <- as.matrix(data.frame( - k1 = rlnorm(n, log(hs_pop$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(1:10, function(i) { - ds_mean <- mkinpredict(HS, hs_parms[i, ], - c(parent = hs_pop$parent_0), sampling_times) - add_err(ds_mean, const, n = 1)[[1]] -}) - -set.seed(123456) -DFOP_SFO <- mkinmod( - parent = mkinsub("DFOP", "m1"), - m1 = mkinsub("SFO"), - quiet = TRUE) -dfop_sfo_pop <- list(parent_0 = 100, - k_m1 = 0.007, f_parent_to_m1 = 0.5, - k1 = 0.1, k2 = 0.02, g = 0.5) -syn_biphasic_parms <- as.matrix(data.frame( - k1 = rlnorm(n_biphasic, log(dfop_sfo_pop$k1), log_sd), - k2 = rlnorm(n_biphasic, log(dfop_sfo_pop$k2), log_sd), - g = plogis(rnorm(n_biphasic, qlogis(dfop_sfo_pop$g), log_sd)), - f_parent_to_m1 = plogis(rnorm(n_biphasic, - qlogis(dfop_sfo_pop$f_parent_to_m1), log_sd)), - k_m1 = rlnorm(n_biphasic, log(dfop_sfo_pop$k_m1), log_sd))) -ds_biphasic_mean <- lapply(1:n_biphasic, - function(i) { - mkinpredict(DFOP_SFO, syn_biphasic_parms[i, ], - c(parent = 100, m1 = 0), sampling_times) - } -) -set.seed(123456) -ds_biphasic <- lapply(ds_biphasic_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]] -}) - # Mixed model fits mmkin_sfo_1 <- mmkin("SFO", ds_sfo, quiet = TRUE, error_model = "tc", cores = n_cores) mmkin_dfop_1 <- mmkin("DFOP", ds_dfop, quiet = TRUE, cores = n_cores, error_model = "tc") -mmkin_biphasic <- mmkin(list("DFOP-SFO" = DFOP_SFO), ds_biphasic, quiet = TRUE, cores = n_cores, +DFOP_SFO <- mkinmod(parent = mkinsub("DFOP", "m1"), + m1 = mkinsub("SFO"), quiet = TRUE) +mmkin_dfop_sfo <- mmkin(list("DFOP-SFO" = DFOP_SFO), ds_dfop_sfo, quiet = TRUE, cores = n_cores, control = list(eval.max = 500, iter.max = 400), error_model = "tc") # nlme dfop_nlme_1 <- suppressWarnings(nlme(mmkin_dfop_1)) -nlme_biphasic <- suppressWarnings(nlme(mmkin_biphasic)) +nlme_dfop_sfo <- suppressWarnings(nlme(mmkin_dfop_sfo)) # saemix sfo_saem_1 <- saem(mmkin_sfo_1, quiet = TRUE, transformations = "saemix") sfo_saem_1_reduced <- update(sfo_saem_1, no_random_effect = "parent_0") -dfop_saemix_1 <- saem(mmkin_dfop_1, quiet = TRUE, transformations = "mkin", +dfop_saem_1 <- saem(mmkin_dfop_1, quiet = TRUE, transformations = "mkin", no_random_effect = c("parent_0", "g_qlogis")) -saem_biphasic_m <- saem(mmkin_biphasic, transformations = "mkin", quiet = TRUE) -saem_biphasic_s <- saem(mmkin_biphasic, transformations = "saemix", quiet = TRUE) +saem_dfop_sfo_m <- saem(mmkin_dfop_sfo, transformations = "mkin", quiet = TRUE) +saem_dfop_sfo_s <- saem(mmkin_dfop_sfo, transformations = "saemix", quiet = TRUE) diff --git a/tests/testthat/summary_hfit_sfo_tc.txt b/tests/testthat/summary_hfit_sfo_tc.txt index 41743091..bb5bf6fb 100644 --- a/tests/testthat/summary_hfit_sfo_tc.txt +++ b/tests/testthat/summary_hfit_sfo_tc.txt @@ -8,7 +8,7 @@ Equations: d_parent/dt = - k_parent * parent Data: -106 observations of 1 variable(s) grouped in 6 datasets +104 observations of 1 variable(s) grouped in 6 datasets Model predictions using solution type analytical @@ -28,15 +28,15 @@ Results: Likelihood computed by importance sampling AIC BIC logLik - 533 531 -261 + 524 523 -257 Optimised parameters: - est. lower upper -parent_0 101.02 99.58 102.46 -log_k_parent -3.32 -3.53 -3.11 -a.1 0.91 0.64 1.17 -b.1 0.05 0.04 0.06 -SD.log_k_parent 0.27 0.11 0.42 + est. lower upper +parent_0 100.68 99.27 102.08 +log_k_parent -3.38 -3.55 -3.21 +a.1 0.87 0.59 1.14 +b.1 0.05 0.04 0.06 +SD.log_k_parent 0.21 0.09 0.33 Correlation: pr_0 @@ -44,18 +44,18 @@ log_k_parent 0.1 Random effects: est. lower upper -SD.log_k_parent 0.3 0.1 0.4 +SD.log_k_parent 0.2 0.09 0.3 Variance model: est. lower upper -a.1 0.91 0.64 1.17 +a.1 0.87 0.59 1.14 b.1 0.05 0.04 0.06 Backtransformed parameters: est. lower upper -parent_0 1e+02 1e+02 1e+02 -k_parent 4e-02 3e-02 4e-02 +parent_0 1e+02 99.27 1e+02 +k_parent 3e-02 0.03 4e-02 Estimated disappearance times: DT50 DT90 -parent 19 64 +parent 20 68 diff --git a/tests/testthat/summary_saem_biphasic_s.txt b/tests/testthat/summary_saem_biphasic_s.txt deleted file mode 100644 index 7c337843..00000000 --- a/tests/testthat/summary_saem_biphasic_s.txt +++ /dev/null @@ -1,87 +0,0 @@ -saemix version used for fitting: Dummy 0.0 for testing -mkin version used for pre-fitting: Dummy 0.0 for testing -R version used for fitting: Dummy R version for testing -Date of fit: Dummy date for testing -Date of summary: Dummy date for testing - -Equations: -d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * - time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time))) - * parent -d_m1/dt = + f_parent_to_m1 * ((k1 * g * exp(-k1 * time) + k2 * (1 - g) - * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) * - exp(-k2 * time))) * parent - k_m1 * m1 - -Data: -510 observations of 2 variable(s) grouped in 15 datasets - -Model predictions using solution type analytical - -Fitted in test time 0 s -Using 300, 100 iterations and 4 chains - -Variance model: Two-component variance function - -Mean of starting values for individual parameters: - parent_0 k_m1 f_parent_to_m1 k1 k2 - 1e+02 7e-03 5e-01 1e-01 2e-02 - g - 5e-01 - -Fixed degradation parameter values: -None - -Results: - -Likelihood computed by importance sampling - AIC BIC logLik - 2334 2344 -1153 - -Optimised parameters: - est. lower upper -parent_0 1e+02 1e+02 1e+02 -k_m1 7e-03 6e-03 7e-03 -f_parent_to_m1 5e-01 4e-01 5e-01 -k1 1e-01 9e-02 1e-01 -k2 2e-02 2e-02 3e-02 -g 5e-01 5e-01 5e-01 -a.1 9e-01 8e-01 1e+00 -b.1 5e-02 5e-02 6e-02 -SD.parent_0 3e-02 -5e+01 5e+01 -SD.k_m1 2e-01 1e-01 3e-01 -SD.f_parent_to_m1 3e-01 2e-01 4e-01 -SD.k1 4e-01 2e-01 5e-01 -SD.k2 3e-01 2e-01 5e-01 -SD.g 2e-01 6e-02 4e-01 - -Correlation: - pr_0 k_m1 f___ k1 k2 -k_m1 -0.2 -f_parent_to_m1 -0.3 0.1 -k1 0.1 0.0 0.0 -k2 0.0 0.0 0.0 0.1 -g 0.1 -0.1 0.0 -0.2 -0.2 - -Random effects: - est. lower upper -SD.parent_0 0.03 -49.24 49.3 -SD.k_m1 0.23 0.13 0.3 -SD.f_parent_to_m1 0.30 0.19 0.4 -SD.k1 0.40 0.25 0.5 -SD.k2 0.34 0.21 0.5 -SD.g 0.21 0.06 0.4 - -Variance model: - est. lower upper -a.1 0.93 0.79 1.06 -b.1 0.05 0.05 0.06 - -Resulting formation fractions: - ff -parent_m1 0.5 -parent_sink 0.5 - -Estimated disappearance times: - DT50 DT90 DT50back DT50_k1 DT50_k2 -parent 13 73 22 6 32 -m1 105 348 NA NA NA diff --git a/tests/testthat/summary_saem_dfop_sfo_s.txt b/tests/testthat/summary_saem_dfop_sfo_s.txt new file mode 100644 index 00000000..7c337843 --- /dev/null +++ b/tests/testthat/summary_saem_dfop_sfo_s.txt @@ -0,0 +1,87 @@ +saemix version used for fitting: Dummy 0.0 for testing +mkin version used for pre-fitting: Dummy 0.0 for testing +R version used for fitting: Dummy R version for testing +Date of fit: Dummy date for testing +Date of summary: Dummy date for testing + +Equations: +d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * + time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time))) + * parent +d_m1/dt = + f_parent_to_m1 * ((k1 * g * exp(-k1 * time) + k2 * (1 - g) + * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) * + exp(-k2 * time))) * parent - k_m1 * m1 + +Data: +510 observations of 2 variable(s) grouped in 15 datasets + +Model predictions using solution type analytical + +Fitted in test time 0 s +Using 300, 100 iterations and 4 chains + +Variance model: Two-component variance function + +Mean of starting values for individual parameters: + parent_0 k_m1 f_parent_to_m1 k1 k2 + 1e+02 7e-03 5e-01 1e-01 2e-02 + g + 5e-01 + +Fixed degradation parameter values: +None + +Results: + +Likelihood computed by importance sampling + AIC BIC logLik + 2334 2344 -1153 + +Optimised parameters: + est. lower upper +parent_0 1e+02 1e+02 1e+02 +k_m1 7e-03 6e-03 7e-03 +f_parent_to_m1 5e-01 4e-01 5e-01 +k1 1e-01 9e-02 1e-01 +k2 2e-02 2e-02 3e-02 +g 5e-01 5e-01 5e-01 +a.1 9e-01 8e-01 1e+00 +b.1 5e-02 5e-02 6e-02 +SD.parent_0 3e-02 -5e+01 5e+01 +SD.k_m1 2e-01 1e-01 3e-01 +SD.f_parent_to_m1 3e-01 2e-01 4e-01 +SD.k1 4e-01 2e-01 5e-01 +SD.k2 3e-01 2e-01 5e-01 +SD.g 2e-01 6e-02 4e-01 + +Correlation: + pr_0 k_m1 f___ k1 k2 +k_m1 -0.2 +f_parent_to_m1 -0.3 0.1 +k1 0.1 0.0 0.0 +k2 0.0 0.0 0.0 0.1 +g 0.1 -0.1 0.0 -0.2 -0.2 + +Random effects: + est. lower upper +SD.parent_0 0.03 -49.24 49.3 +SD.k_m1 0.23 0.13 0.3 +SD.f_parent_to_m1 0.30 0.19 0.4 +SD.k1 0.40 0.25 0.5 +SD.k2 0.34 0.21 0.5 +SD.g 0.21 0.06 0.4 + +Variance model: + est. lower upper +a.1 0.93 0.79 1.06 +b.1 0.05 0.05 0.06 + +Resulting formation fractions: + ff +parent_m1 0.5 +parent_sink 0.5 + +Estimated disappearance times: + DT50 DT90 DT50back DT50_k1 DT50_k2 +parent 13 73 22 6 32 +m1 105 348 NA NA NA diff --git a/tests/testthat/test_mixed.R b/tests/testthat/test_mixed.R index 2d53c6dd..ab8dfc27 100644 --- a/tests/testthat/test_mixed.R +++ b/tests/testthat/test_mixed.R @@ -1,22 +1,23 @@ context("Nonlinear mixed-effects models") + # Round error model parameters as they are not rounded in print methods dfop_nlme_1$modelStruct$varStruct$const <- signif(dfop_nlme_1$modelStruct$varStruct$const, 3) dfop_nlme_1$modelStruct$varStruct$prop <- signif(dfop_nlme_1$modelStruct$varStruct$prop, 4) +dfop_sfo_pop <- attr(ds_dfop_sfo, "pop") + test_that("Print methods work", { expect_known_output(print(fits[, 2:3], digits = 2), "print_mmkin_parent.txt") expect_known_output(print(mixed(mmkin_sfo_1), digits = 2), "print_mmkin_sfo_1_mixed.txt") expect_known_output(print(dfop_nlme_1, digits = 1), "print_dfop_nlme_1.txt") + expect_known_output(print(sfo_saem_1_reduced, digits = 1), "print_sfo_saem_1_reduced.txt") - # In order to address the platform dependence of the results, we round to two - # significant digits before printing - dfop_saemix_1_print <- dfop_saemix_1 - dfop_saemix_1_print$so@results@conf.int[c("estimate", "lower", "upper")] <- - signif(dfop_saemix_1_print$so@results@conf.int[c("estimate", "lower", "upper")], 2) - expect_known_output(print(dfop_saemix_1_print, digits = 1), "print_dfop_saemix_1.txt") + skip_on_cran() # The following test is platform dependent and fails on + # win-builder with current (18 Nov 2022) R-devel and on the Fedora CRAN check systems + expect_known_output(print(dfop_saem_1, digits = 1), "print_dfop_saem_1.txt") }) test_that("nlme results are reproducible to some degree", { @@ -36,17 +37,16 @@ test_that("nlme results are reproducible to some degree", { # k1 and k2 just fail the first test (lower bound of the ci), so we need to exclude it dfop_no_k1_k2 <- c("parent_0", "k_m1", "f_parent_to_m1", "g") dfop_sfo_pop_no_k1_k2 <- as.numeric(dfop_sfo_pop[dfop_no_k1_k2]) - dfop_sfo_pop <- as.numeric(dfop_sfo_pop) # to remove names - ci_dfop_sfo_n <- summary(nlme_biphasic)$confint_back + ci_dfop_sfo_n <- summary(nlme_dfop_sfo)$confint_back expect_true(all(ci_dfop_sfo_n[dfop_no_k1_k2, "lower"] < dfop_sfo_pop_no_k1_k2)) - expect_true(all(ci_dfop_sfo_n[, "upper"] > dfop_sfo_pop)) + expect_true(all(ci_dfop_sfo_n[, "upper"] > as.numeric(dfop_sfo_pop))) }) test_that("saemix results are reproducible for biphasic fits", { - test_summary <- summary(saem_biphasic_s) + test_summary <- summary(saem_dfop_sfo_s) test_summary$saemixversion <- "Dummy 0.0 for testing" test_summary$mkinversion <- "Dummy 0.0 for testing" test_summary$Rversion <- "Dummy R version for testing" @@ -54,33 +54,33 @@ test_that("saemix results are reproducible for biphasic fits", { test_summary$date.summary <- "Dummy date for testing" test_summary$time <- c(elapsed = "test time 0") - expect_known_output(print(test_summary, digits = 1), "summary_saem_biphasic_s.txt") + expect_known_output(print(test_summary, digits = 1), "summary_saem_dfop_sfo_s.txt") dfop_sfo_pop <- as.numeric(dfop_sfo_pop) no_k1 <- c(1, 2, 3, 5, 6) no_k2 <- c(1, 2, 3, 4, 6) no_k1_k2 <- c(1, 2, 3, 6) - ci_dfop_sfo_s_s <- summary(saem_biphasic_s)$confint_back + ci_dfop_sfo_s_s <- summary(saem_dfop_sfo_s)$confint_back expect_true(all(ci_dfop_sfo_s_s[, "lower"] < dfop_sfo_pop)) expect_true(all(ci_dfop_sfo_s_s[, "upper"] > dfop_sfo_pop)) # k2 is not fitted well - ci_dfop_sfo_s_m <- summary(saem_biphasic_m)$confint_back + ci_dfop_sfo_s_m <- summary(saem_dfop_sfo_m)$confint_back expect_true(all(ci_dfop_sfo_s_m[no_k2, "lower"] < dfop_sfo_pop[no_k2])) expect_true(all(ci_dfop_sfo_s_m[no_k1, "upper"] > dfop_sfo_pop[no_k1])) # I tried to only do few iterations in routine tests as this is so slow # but then deSolve fails at some point (presumably at the switch between # the two types of iterations) - #saem_biphasic_2 <- saem(mmkin_biphasic, solution_type = "deSolve", + #saem_dfop_sfo_2 <- saem(mmkin_biphasic, solution_type = "deSolve", # control = list(nbiter.saemix = c(10, 5), nbiter.burn = 5), quiet = TRUE) skip("Fitting with saemix takes around 10 minutes when using deSolve") - saem_biphasic_2 <- saem(mmkin_biphasic, solution_type = "deSolve", quiet = TRUE) + saem_dfop_sfo_2 <- saem(mmkin_dfop_sfo, solution_type = "deSolve", quiet = TRUE) # As with the analytical solution, k1 and k2 are not fitted well - ci_dfop_sfo_s_d <- summary(saem_biphasic_2)$confint_back + ci_dfop_sfo_s_d <- summary(saem_dfop_sfo_2)$confint_back expect_true(all(ci_dfop_sfo_s_d[no_k2, "lower"] < dfop_sfo_pop[no_k2])) expect_true(all(ci_dfop_sfo_s_d[no_k1, "upper"] > dfop_sfo_pop[no_k1])) }) diff --git a/tests/testthat/test_multistart.R b/tests/testthat/test_multistart.R index 502cee98..3a511e06 100644 --- a/tests/testthat/test_multistart.R +++ b/tests/testthat/test_multistart.R @@ -9,26 +9,22 @@ test_that("multistart works for saem.mmkin models", { best(saem_sfo_s_multi), test = TRUE ) - # On winbuilder, sfo_saem_1 gives an AIC of 1310.8, while we get 1311.7 - # locally (using saemix 3.2, which likely makes the difference due to the - # error parameter patch) on Linux and Windows. The other, well-determined - # fits both give 1309.7. - expect_equal(round(anova_sfo, 1)["sfo_saem_1_reduced", "AIC"], 1309.7) - expect_equal(round(anova_sfo, 1)["best(saem_sfo_s_multi)", "AIC"], 1309.7) - expect_true(anova_sfo[3, "Pr(>Chisq)"] > 0.2) # Local: 1, CRAN: 0.4 + expect_equal(round(anova_sfo, 1)["sfo_saem_1_reduced", "AIC"], 1302.2) + expect_equal(round(anova_sfo, 1)["best(saem_sfo_s_multi)", "AIC"], 1302.2) + expect_true(anova_sfo[3, "Pr(>Chisq)"] > 0.2) # Local: 1, win-builder: 0.4 set.seed(123456) - saem_biphasic_m_multi <- multistart(saem_biphasic_m, n = 8, + saem_dfop_sfo_m_multi <- multistart(saem_dfop_sfo_m, n = 8, cores = n_cores) - expect_known_output(print(saem_biphasic_m_multi), - file = "print_multistart_biphasic.txt") + expect_known_output(print(saem_dfop_sfo_m_multi), + file = "print_multistart_dfop_sfo.txt") - anova_biphasic <- anova(saem_biphasic_m, - best(saem_biphasic_m_multi)) + anova_dfop_sfo <- anova(saem_dfop_sfo_m, + best(saem_dfop_sfo_m_multi)) # With the new starting parameters we do not improve # with multistart any more - expect_equal(anova_biphasic[2, "AIC"], anova_biphasic[1, "AIC"], + expect_equal(anova_dfop_sfo[2, "AIC"], anova_dfop_sfo[1, "AIC"], tolerance = 1e-4) skip_on_travis() # Plots are platform dependent @@ -37,10 +33,10 @@ test_that("multistart works for saem.mmkin models", { vdiffr::expect_doppelganger("llhist for sfo fit", llhist_sfo) vdiffr::expect_doppelganger("parplot for sfo fit", parplot_sfo) - llhist_biphasic <- function() llhist(saem_biphasic_m_multi) - parplot_biphasic <- function() parplot(saem_biphasic_m_multi, + llhist_dfop_sfo <- function() llhist(saem_dfop_sfo_m_multi) + parplot_dfop_sfo <- function() parplot(saem_dfop_sfo_m_multi, ylim = c(0.5, 2)) - vdiffr::expect_doppelganger("llhist for biphasic saemix fit", llhist_biphasic) - vdiffr::expect_doppelganger("parplot for biphasic saemix fit", parplot_biphasic) + vdiffr::expect_doppelganger("llhist for dfop sfo fit", llhist_dfop_sfo) + vdiffr::expect_doppelganger("parplot for dfop sfo fit", parplot_dfop_sfo) }) diff --git a/tests/testthat/test_plot.R b/tests/testthat/test_plot.R index 13058c00..01b0c1ee 100644 --- a/tests/testthat/test_plot.R +++ b/tests/testthat/test_plot.R @@ -44,24 +44,24 @@ test_that("Plotting mkinfit, mmkin and mixed model objects is reproducible", { f_uba_dfop_sfo_saem <- saem(f_uba_mmkin["DFOP-SFO", ], quiet = TRUE, transformations = "saemix") - plot_biphasic_mmkin <- function() plot(f_uba_dfop_sfo_mixed, pop_curve = TRUE) - vdiffr::expect_doppelganger("mixed model fit for mmkin object", plot_biphasic_mmkin) + plot_dfop_sfo_mmkin <- function() plot(f_uba_dfop_sfo_mixed, pop_curve = TRUE) + vdiffr::expect_doppelganger("mixed model fit for mmkin object", plot_dfop_sfo_mmkin) - plot_biphasic_saem_s <- function() plot(f_uba_dfop_sfo_saem) - vdiffr::expect_doppelganger("mixed model fit for saem object with saemix transformations", plot_biphasic_saem_s) + plot_dfop_sfo_saem_s <- function() plot(f_uba_dfop_sfo_saem) + vdiffr::expect_doppelganger("mixed model fit for saem object with saemix transformations", plot_dfop_sfo_saem_s) skip_on_travis() - plot_biphasic_nlme <- function() plot(dfop_nlme_1) - vdiffr::expect_doppelganger("mixed model fit for nlme object", plot_biphasic_nlme) + plot_dfop_sfo_nlme <- function() plot(dfop_nlme_1) + vdiffr::expect_doppelganger("mixed model fit for nlme object", plot_dfop_sfo_nlme) - #plot_biphasic_mmkin <- function() plot(mixed(mmkin_biphasic)) + #plot_dfop_sfo_mmkin <- function() plot(mixed(mmkin_dfop_sfo)) # Biphasic fits with lots of data and fits have lots of potential for differences - plot_biphasic_nlme <- function() plot(nlme_biphasic) - #plot_biphasic_saem_s <- function() plot(saem_biphasic_s) - plot_biphasic_saem_m <- function() plot(saem_biphasic_m) + plot_dfop_sfo_nlme <- function() plot(nlme_dfop_sfo) + #plot_dfop_sfo_saem_s <- function() plot(saem_dfop_sfo_s) + plot_dfop_sfo_saem_m <- function() plot(saem_dfop_sfo_m) - vdiffr::expect_doppelganger("mixed model fit for saem object with mkin transformations", plot_biphasic_saem_m) + vdiffr::expect_doppelganger("mixed model fit for saem object with mkin transformations", plot_dfop_sfo_saem_m) # different results when working with eigenvalues plot_errmod_fit_D_obs_eigen <- function() plot_err(fit_D_obs_eigen, sep_obs = FALSE) diff --git a/tests/testthat/test_saemix_parent.R b/tests/testthat/test_saemix_parent.R index 20889c6c..31605931 100644 --- a/tests/testthat/test_saemix_parent.R +++ b/tests/testthat/test_saemix_parent.R @@ -38,11 +38,11 @@ test_that("Parent fits using saemix are correctly implemented", { s_sfo_nlme_1 <- summary(sfo_nlme_1) # Compare with input - expect_equal(round(s_sfo_saem_1$confint_ranef["SD.k_parent", "est."], 1), 0.3) - expect_equal(round(s_sfo_saem_1_mkin$confint_ranef["SD.log_k_parent", "est."], 1), 0.3) + expect_equal(round(s_sfo_saem_1$confint_ranef["SD.k_parent", "est."], 1), 0.3, tol = 0.1) + expect_equal(round(s_sfo_saem_1_mkin$confint_ranef["SD.log_k_parent", "est."], 1), 0.3, tol = 0.1) # k_parent is a bit different from input 0.03 here - expect_equal(round(s_sfo_saem_1$confint_back["k_parent", "est."], 3), 0.035) - expect_equal(round(s_sfo_saem_1_mkin$confint_back["k_parent", "est."], 3), 0.035) + expect_equal(round(s_sfo_saem_1$confint_back["k_parent", "est."], 3), 0.033) + expect_equal(round(s_sfo_saem_1_mkin$confint_back["k_parent", "est."], 3), 0.033) # But the result is pretty unanimous between methods expect_equal(round(s_sfo_saem_1_reduced$confint_back["k_parent", "est."], 3), @@ -74,7 +74,7 @@ test_that("Parent fits using saemix are correctly implemented", { mmkin_fomc_1 <- mmkin("FOMC", ds_fomc, quiet = TRUE, error_model = "tc", cores = n_cores) fomc_saem_1 <- saem(mmkin_fomc_1, quiet = TRUE, transformations = "saemix", no_random_effect = "parent_0") - fomc_pop <- as.numeric(fomc_pop) + fomc_pop <- as.numeric(attr(ds_fomc, "pop")) ci_fomc_s1 <- summary(fomc_saem_1)$confint_back expect_true(all(ci_fomc_s1[, "lower"] < fomc_pop)) expect_true(all(ci_fomc_s1[, "upper"] > fomc_pop)) @@ -87,14 +87,14 @@ test_that("Parent fits using saemix are correctly implemented", { expect_equal(endpoints(fomc_saem_1), endpoints(fomc_saem_2), tol = 0.01) # DFOP - dfop_saemix_2 <- saem(mmkin_dfop_1, quiet = TRUE, transformations = "saemix", + dfop_saem_2 <- saem(mmkin_dfop_1, quiet = TRUE, transformations = "saemix", no_random_effect = "parent_0") - s_dfop_s1 <- summary(dfop_saemix_1) # mkin transformations - s_dfop_s2 <- summary(dfop_saemix_2) # saemix transformations + s_dfop_s1 <- summary(dfop_saem_1) # mkin transformations + s_dfop_s2 <- summary(dfop_saem_2) # saemix transformations s_dfop_n <- summary(dfop_nlme_1) - dfop_pop <- as.numeric(dfop_pop) + dfop_pop <- as.numeric(attr(ds_dfop, "pop")) expect_true(all(s_dfop_s1$confint_back[, "lower"] < dfop_pop)) expect_true(all(s_dfop_s1$confint_back[, "upper"] > dfop_pop)) @@ -111,18 +111,18 @@ test_that("Parent fits using saemix are correctly implemented", { # SFORB mmkin_sforb_1 <- mmkin("SFORB", ds_dfop, quiet = TRUE, cores = n_cores) - sforb_saemix_1 <- saem(mmkin_sforb_1, quiet = TRUE, + sforb_saem_1 <- saem(mmkin_sforb_1, quiet = TRUE, no_random_effect = c("parent_free_0"), transformations = "mkin") - sforb_saemix_2 <- saem(mmkin_sforb_1, quiet = TRUE, + sforb_saem_2 <- saem(mmkin_sforb_1, quiet = TRUE, no_random_effect = c("parent_free_0"), transformations = "saemix") expect_equal( - log(endpoints(dfop_saemix_1)$distimes[1:2]), - log(endpoints(sforb_saemix_1)$distimes[1:2]), tolerance = 0.01) + log(endpoints(dfop_saem_1)$distimes[1:2]), + log(endpoints(sforb_saem_1)$distimes[1:2]), tolerance = 0.01) expect_equal( - log(endpoints(sforb_saemix_1)$distimes[1:2]), - log(endpoints(sforb_saemix_2)$distimes[1:2]), tolerance = 0.01) + log(endpoints(sforb_saem_1)$distimes[1:2]), + log(endpoints(sforb_saem_2)$distimes[1:2]), tolerance = 0.01) mmkin_hs_1 <- mmkin("HS", ds_hs, quiet = TRUE, error_model = "const", cores = n_cores) hs_saem_1 <- saem(mmkin_hs_1, quiet = TRUE, no_random_effect = "parent_0") @@ -131,7 +131,7 @@ test_that("Parent fits using saemix are correctly implemented", { expect_equal(endpoints(hs_saem_1), endpoints(hs_saem_2), tol = 0.01) ci_hs_s1 <- summary(hs_saem_1)$confint_back - hs_pop <- as.numeric(hs_pop) + hs_pop <- as.numeric(attr(ds_hs, "pop")) #expect_true(all(ci_hs_s1[, "lower"] < hs_pop)) # k1 is overestimated expect_true(all(ci_hs_s1[, "upper"] > hs_pop)) }) @@ -141,10 +141,10 @@ test_that("We can also use mkin solution methods for saem", { "saemix transformations is only supported if an analytical solution is implemented" ) skip("This still takes almost 2.5 minutes although we do not solve ODEs") - dfop_saemix_3 <- saem(mmkin_dfop_1, quiet = TRUE, transformations = "mkin", - solution_type = "analytical", no_random_effect = "parent_0") - distimes_dfop <- endpoints(dfop_saemix_1)$distimes - distimes_dfop_analytical <- endpoints(dfop_saemix_3)$distimes + dfop_saem_3 <- saem(mmkin_dfop_1, quiet = TRUE, transformations = "mkin", + solution_type = "analytical", no_random_effect = c("parent_0", "g_qlogis")) + distimes_dfop <- endpoints(dfop_saem_1)$distimes + distimes_dfop_analytical <- endpoints(dfop_saem_3)$distimes rel_diff <- abs(distimes_dfop_analytical - distimes_dfop) / distimes_dfop expect_true(all(rel_diff < 0.01)) }) -- cgit v1.2.3 From 5ec8e1bad1aa7d79ee9c19bdd50be07f81a14278 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 18 Nov 2022 22:11:02 +0100 Subject: Move two saem fits from setup script to skipped tests Save winbuilder/CRAN check time... --- log/test.log | 44 +- ...t-for-saem-object-with-mkin-transformations.svg | 2502 ++++++++++++++++++++ ...t-for-saem-object-with-mkin-transformations.svg | 2502 -------------------- tests/testthat/setup_script.R | 3 - tests/testthat/test_mixed.R | 8 +- tests/testthat/test_multistart.R | 15 + tests/testthat/test_plot.R | 4 - 7 files changed, 2542 insertions(+), 2536 deletions(-) create mode 100644 tests/testthat/_snaps/multistart/mixed-model-fit-for-saem-object-with-mkin-transformations.svg delete mode 100644 tests/testthat/_snaps/plot/mixed-model-fit-for-saem-object-with-mkin-transformations.svg (limited to 'tests/testthat/_snaps') diff --git a/log/test.log b/log/test.log index 8fdaec48..897bf896 100644 --- a/log/test.log +++ b/log/test.log @@ -1,53 +1,53 @@ ℹ Testing mkin ✔ | F W S OK | Context ✔ | 5 | AIC calculation -✔ | 5 | Analytical solutions for coupled models [3.4s] +✔ | 5 | Analytical solutions for coupled models [3.5s] ✔ | 5 | Calculation of Akaike weights ✔ | 3 | Export dataset for reading into CAKE ✔ | 12 | Confidence intervals and p-values [1.2s] -✔ | 1 12 | Dimethenamid data from 2018 [34.0s] +✔ | 1 12 | Dimethenamid data from 2018 [33.2s] ──────────────────────────────────────────────────────────────────────────────── Skip ('test_dmta.R:98'): Different backends get consistent results for SFO-SFO3+, dimethenamid data Reason: Fitting this ODE model with saemix takes about 15 minutes on my system ──────────────────────────────────────────────────────────────────────────────── -✔ | 14 | Error model fitting [5.4s] +✔ | 14 | Error model fitting [5.0s] ✔ | 5 | Time step normalisation ✔ | 4 | Calculation of FOCUS chi2 error levels [0.6s] -✔ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [0.9s] -✔ | 4 | Test fitting the decline of metabolites from their maximum [0.4s] -✔ | 1 | Fitting the logistic model [0.3s] -✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [25.8s] -✔ | 1 13 | Nonlinear mixed-effects models [0.4s] +✔ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [0.8s] +✔ | 4 | Test fitting the decline of metabolites from their maximum [0.3s] +✔ | 1 | Fitting the logistic model [0.2s] +✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [24.7s] +✔ | 1 11 | Nonlinear mixed-effects models [13.1s] ──────────────────────────────────────────────────────────────────────────────── -Skip ('test_mixed.R:79'): saemix results are reproducible for biphasic fits +Skip ('test_mixed.R:77'): saemix results are reproducible for biphasic fits Reason: Fitting with saemix takes around 10 minutes when using deSolve ──────────────────────────────────────────────────────────────────────────────── ✔ | 3 | Test dataset classes mkinds and mkindsg -✔ | 10 | Special cases of mkinfit calls [0.6s] +✔ | 10 | Special cases of mkinfit calls [0.4s] ✔ | 3 | mkinfit features [0.7s] ✔ | 8 | mkinmod model generation and printing [0.2s] -✔ | 3 | Model predictions with mkinpredict [0.4s] -✔ | 9 | Multistart method for saem.mmkin models [38.2s] -✔ | 16 | Evaluations according to 2015 NAFTA guidance [2.4s] -✔ | 9 | Nonlinear mixed-effects models with nlme [9.2s] -✔ | 16 | Plotting [10.5s] +✔ | 3 | Model predictions with mkinpredict [0.3s] +✔ | 12 | Multistart method for saem.mmkin models [49.5s] +✔ | 16 | Evaluations according to 2015 NAFTA guidance [2.3s] +✔ | 9 | Nonlinear mixed-effects models with nlme [8.8s] +✔ | 15 | Plotting [10.3s] ✔ | 4 | Residuals extracted from mkinfit models -✔ | 1 36 | saemix parent models [75.0s] +✔ | 1 36 | saemix parent models [72.5s] ──────────────────────────────────────────────────────────────────────────────── Skip ('test_saemix_parent.R:143'): We can also use mkin solution methods for saem Reason: This still takes almost 2.5 minutes although we do not solve ODEs ──────────────────────────────────────────────────────────────────────────────── -✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.6s] +✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.4s] ✔ | 11 | Processing of residue series -✔ | 10 | Fitting the SFORB model [4.0s] +✔ | 10 | Fitting the SFORB model [3.8s] ✔ | 1 | Summaries of old mkinfit objects ✔ | 5 | Summary [0.2s] -✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.5s] -✔ | 9 | Hypothesis tests [9.0s] -✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.3s] +✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.2s] +✔ | 9 | Hypothesis tests [8.2s] +✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.2s] ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 229.5 s +Duration: 246.1 s ── Skipped tests ────────────────────────────────────────────────────────────── • Fitting this ODE model with saemix takes about 15 minutes on my system (1) diff --git 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-20 -30 -40 - - - - - - - - --3 --2 --1 -0 -1 -2 -3 - - - - - - - - -Predicted -Standardized residual - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/tests/testthat/setup_script.R b/tests/testthat/setup_script.R index 2448886d..4e2f76ab 100644 --- a/tests/testthat/setup_script.R +++ b/tests/testthat/setup_script.R @@ -109,7 +109,4 @@ sfo_saem_1_reduced <- update(sfo_saem_1, no_random_effect = "parent_0") dfop_saem_1 <- saem(mmkin_dfop_1, quiet = TRUE, transformations = "mkin", no_random_effect = c("parent_0", "g_qlogis")) -saem_dfop_sfo_m <- saem(mmkin_dfop_sfo, transformations = "mkin", quiet = TRUE) -saem_dfop_sfo_s <- saem(mmkin_dfop_sfo, transformations = "saemix", quiet = TRUE) - parallel::stopCluster(cl) diff --git a/tests/testthat/test_mixed.R b/tests/testthat/test_mixed.R index ab8dfc27..8c257738 100644 --- a/tests/testthat/test_mixed.R +++ b/tests/testthat/test_mixed.R @@ -46,6 +46,9 @@ test_that("nlme results are reproducible to some degree", { test_that("saemix results are reproducible for biphasic fits", { + skip_on_cran() + saem_dfop_sfo_s <- saem(mmkin_dfop_sfo, transformations = "saemix", quiet = TRUE) + test_summary <- summary(saem_dfop_sfo_s) test_summary$saemixversion <- "Dummy 0.0 for testing" test_summary$mkinversion <- "Dummy 0.0 for testing" @@ -65,11 +68,6 @@ test_that("saemix results are reproducible for biphasic fits", { expect_true(all(ci_dfop_sfo_s_s[, "lower"] < dfop_sfo_pop)) expect_true(all(ci_dfop_sfo_s_s[, "upper"] > dfop_sfo_pop)) - # k2 is not fitted well - ci_dfop_sfo_s_m <- summary(saem_dfop_sfo_m)$confint_back - expect_true(all(ci_dfop_sfo_s_m[no_k2, "lower"] < dfop_sfo_pop[no_k2])) - expect_true(all(ci_dfop_sfo_s_m[no_k1, "upper"] > dfop_sfo_pop[no_k1])) - # I tried to only do few iterations in routine tests as this is so slow # but then deSolve fails at some point (presumably at the switch between # the two types of iterations) diff --git a/tests/testthat/test_multistart.R b/tests/testthat/test_multistart.R index 3a511e06..91ef71f0 100644 --- a/tests/testthat/test_multistart.R +++ b/tests/testthat/test_multistart.R @@ -4,6 +4,7 @@ test_that("multistart works for saem.mmkin models", { skip_on_cran() # Save CRAN time set.seed(123456) saem_sfo_s_multi <- multistart(sfo_saem_1_reduced, n = 8, cores = n_cores) + anova_sfo <- anova(sfo_saem_1, sfo_saem_1_reduced, best(saem_sfo_s_multi), @@ -13,6 +14,17 @@ test_that("multistart works for saem.mmkin models", { expect_equal(round(anova_sfo, 1)["best(saem_sfo_s_multi)", "AIC"], 1302.2) expect_true(anova_sfo[3, "Pr(>Chisq)"] > 0.2) # Local: 1, win-builder: 0.4 + saem_dfop_sfo_m <- saem(mmkin_dfop_sfo, transformations = "mkin", quiet = TRUE) + dfop_sfo_pop <- attr(ds_dfop_sfo, "pop") + + # k2 is not fitted well (compare saem_dfop_sfo_s in test_mixed.R) + ci_dfop_sfo_s_m <- summary(saem_dfop_sfo_m)$confint_back + no_k1 <- c(1, 2, 3, 5, 6) + no_k2 <- c(1, 2, 3, 4, 6) + expect_true(all(ci_dfop_sfo_s_m[no_k2, "lower"] < dfop_sfo_pop[no_k2])) + expect_true(all(ci_dfop_sfo_s_m[no_k1, "upper"] > dfop_sfo_pop[no_k1])) + + set.seed(123456) saem_dfop_sfo_m_multi <- multistart(saem_dfop_sfo_m, n = 8, cores = n_cores) @@ -28,6 +40,9 @@ test_that("multistart works for saem.mmkin models", { tolerance = 1e-4) skip_on_travis() # Plots are platform dependent + plot_dfop_sfo_saem_m <- function() plot(saem_dfop_sfo_m) + vdiffr::expect_doppelganger("mixed model fit for saem object with mkin transformations", plot_dfop_sfo_saem_m) + llhist_sfo <- function() llhist(saem_sfo_s_multi) parplot_sfo <- function() parplot(saem_sfo_s_multi, ylim = c(0.5, 2)) vdiffr::expect_doppelganger("llhist for sfo fit", llhist_sfo) diff --git a/tests/testthat/test_plot.R b/tests/testthat/test_plot.R index 01b0c1ee..f5da5982 100644 --- a/tests/testthat/test_plot.R +++ b/tests/testthat/test_plot.R @@ -41,7 +41,6 @@ test_that("Plotting mkinfit, mmkin and mixed model objects is reproducible", { f_uba_mmkin <- mmkin(list("DFOP-SFO" = dfop_sfo_uba), ds_uba, quiet = TRUE, cores = n_cores) f_uba_dfop_sfo_mixed <- mixed(f_uba_mmkin["DFOP-SFO", ]) - f_uba_dfop_sfo_saem <- saem(f_uba_mmkin["DFOP-SFO", ], quiet = TRUE, transformations = "saemix") plot_dfop_sfo_mmkin <- function() plot(f_uba_dfop_sfo_mixed, pop_curve = TRUE) @@ -59,9 +58,6 @@ test_that("Plotting mkinfit, mmkin and mixed model objects is reproducible", { # Biphasic fits with lots of data and fits have lots of potential for differences plot_dfop_sfo_nlme <- function() plot(nlme_dfop_sfo) #plot_dfop_sfo_saem_s <- function() plot(saem_dfop_sfo_s) - plot_dfop_sfo_saem_m <- function() plot(saem_dfop_sfo_m) - - vdiffr::expect_doppelganger("mixed model fit for saem object with mkin transformations", plot_dfop_sfo_saem_m) # different results when working with eigenvalues plot_errmod_fit_D_obs_eigen <- function() plot_err(fit_D_obs_eigen, sep_obs = FALSE) -- cgit v1.2.3 From 478c6d5eec4c84b22b43adcbdf36888b302ead00 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 6 Dec 2022 10:33:24 +0100 Subject: Some parplot improvements llquant argument, improved legend text, tests --- NEWS.md | 2 + R/parplot.R | 16 +- log/test.log | 41 +++-- man/parplot.Rd | 7 +- .../_snaps/multistart/parplot-for-dfop-sfo-fit.svg | 169 ++++++++++----------- .../_snaps/multistart/parplot-for-sfo-fit.svg | 4 +- tests/testthat/test_multistart.R | 2 +- vignettes/FOCUS_D.html | 37 ++--- vignettes/FOCUS_L.html | 83 +++++----- 9 files changed, 183 insertions(+), 178 deletions(-) (limited to 'tests/testthat/_snaps') diff --git a/NEWS.md b/NEWS.md index 15c45cc9..c7929fbe 100644 --- a/NEWS.md +++ b/NEWS.md @@ -4,6 +4,8 @@ - 'R/summary.saem.mmkin.R': List all initial parameter values in the summary, including random effects and error model parameters. Avoid redundant warnings that occurred in the calculation of correlations of the fixed effects in the case that the Fisher information matrix could not be inverted. +- 'R/parplot.R': Possibility to select the top 'llquant' fraction of the fits for the parameter plots, and improved legend text. + # mkin 1.2.1 (2022-11-19) - '{data,R}/ds_mixed.rda': Include the test data in the package instead of generating it in 'tests/testthat/setup_script.R'. Refactor the generating code to make it consistent and update tests. diff --git a/R/parplot.R b/R/parplot.R index 98579779..63306ac2 100644 --- a/R/parplot.R +++ b/R/parplot.R @@ -10,7 +10,10 @@ #' #' @param object The [multistart] object #' @param llmin The minimum likelihood of objects to be shown -#' @param scale By default, scale parameters using the best available fit. +#' @param llquant Fractional value for selecting only the fits with higher +#' likelihoods. Overrides 'llmin'. +#' @param scale By default, scale parameters using the best +#' available fit. #' If 'median', parameters are scaled using the median parameters from all fits. #' @param main Title of the plot #' @param lpos Positioning of the legend. @@ -28,7 +31,8 @@ parplot <- function(object, ...) { #' @rdname parplot #' @export -parplot.multistart.saem.mmkin <- function(object, llmin = -Inf, scale = c("best", "median"), +parplot.multistart.saem.mmkin <- function(object, llmin = -Inf, llquant = NA, + scale = c("best", "median"), lpos = "bottomleft", main = "", ...) { oldpar <- par(no.readonly = TRUE) @@ -48,6 +52,10 @@ parplot.multistart.saem.mmkin <- function(object, llmin = -Inf, scale = c("best" stop("parplot is only implemented for multistart.saem.mmkin objects") } ll <- sapply(object, llfunc) + if (!is.na(llquant[1])) { + if (llmin != -Inf) warning("Overriding 'llmin' because 'llquant' was specified") + llmin <- quantile(ll, 1 - llquant) + } selected <- which(ll > llmin) selected_parms <- all_parms[selected, ] @@ -110,7 +118,7 @@ parplot.multistart.saem.mmkin <- function(object, llmin = -Inf, scale = c("best" legend(lpos, inset = c(0.05, 0.05), bty = "n", pch = 1, col = 3:1, lty = c(NA, NA, 1), legend = c( - "Starting parameters", - "Original run", + "Original start", + "Original results", "Multistart runs")) } diff --git a/log/test.log b/log/test.log index 5764f209..7614b136 100644 --- a/log/test.log +++ b/log/test.log @@ -1,22 +1,22 @@ ℹ Testing mkin ✔ | F W S OK | Context ✔ | 5 | AIC calculation -✔ | 5 | Analytical solutions for coupled models [3.3s] +✔ | 5 | Analytical solutions for coupled models [3.2s] ✔ | 5 | Calculation of Akaike weights ✔ | 3 | Export dataset for reading into CAKE ✔ | 12 | Confidence intervals and p-values [1.1s] -✔ | 1 12 | Dimethenamid data from 2018 [31.9s] +✔ | 1 12 | Dimethenamid data from 2018 [32.0s] ──────────────────────────────────────────────────────────────────────────────── Skip ('test_dmta.R:98'): Different backends get consistent results for SFO-SFO3+, dimethenamid data Reason: Fitting this ODE model with saemix takes about 15 minutes on my system ──────────────────────────────────────────────────────────────────────────────── -✔ | 14 | Error model fitting [4.9s] +✔ | 14 | Error model fitting [4.8s] ✔ | 5 | Time step normalisation ✔ | 4 | Calculation of FOCUS chi2 error levels [0.6s] ✔ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [0.8s] ✔ | 4 | Test fitting the decline of metabolites from their maximum [0.3s] ✔ | 1 | Fitting the logistic model [0.2s] -✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [41.4s] +✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [42.2s] ✔ | 1 11 | Nonlinear mixed-effects models [13.3s] ──────────────────────────────────────────────────────────────────────────────── Skip ('test_mixed.R:78'): saemix results are reproducible for biphasic fits @@ -26,32 +26,41 @@ Reason: Fitting with saemix takes around 10 minutes when using deSolve ✔ | 10 | Special cases of mkinfit calls [0.6s] ✔ | 3 | mkinfit features [0.7s] ✔ | 8 | mkinmod model generation and printing [0.2s] -✔ | 3 | Model predictions with mkinpredict [0.3s] -✔ | 12 | Multistart method for saem.mmkin models [47.5s] -✔ | 16 | Evaluations according to 2015 NAFTA guidance [2.3s] -✔ | 9 | Nonlinear mixed-effects models with nlme [9.5s] -✔ | 15 | Plotting [10.2s] +✔ | 3 | Model predictions with mkinpredict [0.4s] +✖ | 1 11 | Multistart method for saem.mmkin models [46.7s] +──────────────────────────────────────────────────────────────────────────────── +Failure ('test_multistart.R:56'): multistart works for saem.mmkin models +Snapshot of `testcase` to 'multistart/parplot-for-dfop-sfo-fit.svg' has changed +Run `testthat::snapshot_review('multistart/')` to review changes +Backtrace: + 1. vdiffr::expect_doppelganger("parplot for dfop sfo fit", parplot_dfop_sfo) + at test_multistart.R:56:2 + 3. testthat::expect_snapshot_file(...) +──────────────────────────────────────────────────────────────────────────────── +✔ | 16 | Evaluations according to 2015 NAFTA guidance [2.2s] +✔ | 9 | Nonlinear mixed-effects models with nlme [9.4s] +✔ | 15 | Plotting [10.1s] ✔ | 4 | Residuals extracted from mkinfit models -✔ | 1 36 | saemix parent models [73.0s] +✔ | 1 36 | saemix parent models [73.6s] ──────────────────────────────────────────────────────────────────────────────── Skip ('test_saemix_parent.R:143'): We can also use mkin solution methods for saem Reason: This still takes almost 2.5 minutes although we do not solve ODEs ──────────────────────────────────────────────────────────────────────────────── -✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.5s] +✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.4s] ✔ | 11 | Processing of residue series -✔ | 10 | Fitting the SFORB model [3.9s] +✔ | 10 | Fitting the SFORB model [3.7s] ✔ | 1 | Summaries of old mkinfit objects ✔ | 5 | Summary [0.2s] -✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.2s] -✔ | 9 | Hypothesis tests [8.4s] +✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.3s] +✔ | 9 | Hypothesis tests [8.1s] ✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.2s] ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 261.1 s +Duration: 260.9 s ── Skipped tests ────────────────────────────────────────────────────────────── • Fitting this ODE model with saemix takes about 15 minutes on my system (1) • Fitting with saemix takes around 10 minutes when using deSolve (1) • This still takes almost 2.5 minutes although we do not solve ODEs (1) -[ FAIL 0 | WARN 0 | SKIP 3 | PASS 270 ] +[ FAIL 1 | WARN 0 | SKIP 3 | PASS 269 ] diff --git a/man/parplot.Rd b/man/parplot.Rd index ac9e02cf..67bf0cc1 100644 --- a/man/parplot.Rd +++ b/man/parplot.Rd @@ -10,6 +10,7 @@ parplot(object, ...) \method{parplot}{multistart.saem.mmkin}( object, llmin = -Inf, + llquant = NA, scale = c("best", "median"), lpos = "bottomleft", main = "", @@ -23,7 +24,11 @@ parplot(object, ...) \item{llmin}{The minimum likelihood of objects to be shown} -\item{scale}{By default, scale parameters using the best available fit. +\item{llquant}{Fractional value for selecting only the fits with higher +likelihoods. Overrides 'llmin'.} + +\item{scale}{By default, scale parameters using the best +available fit. If 'median', parameters are scaled using the median parameters from all fits.} \item{lpos}{Positioning of the legend.} diff --git a/tests/testthat/_snaps/multistart/parplot-for-dfop-sfo-fit.svg b/tests/testthat/_snaps/multistart/parplot-for-dfop-sfo-fit.svg index 7017908e..b01dac74 100644 --- a/tests/testthat/_snaps/multistart/parplot-for-dfop-sfo-fit.svg +++ b/tests/testthat/_snaps/multistart/parplot-for-dfop-sfo-fit.svg @@ -25,109 +25,104 @@ - - - - + + + + - - - - - - - - + + + + + + - - - - - + + + + + - + - - - - - - - - - - - - - - + + + + + + + + + + + + - - - - - + + + + + - - - - - - + + + + + + - - - - - + + + + + - - - - - - - - + + + + + + + - - - - - + + + + + - - - - - - + + + + + + - - - - - - + + + + + + - - - - - - + + + + + + - - - - - + + + + + - + @@ -194,8 +189,8 @@ -Starting parameters -Original run +Original start +Original results Multistart runs diff --git a/tests/testthat/_snaps/multistart/parplot-for-sfo-fit.svg b/tests/testthat/_snaps/multistart/parplot-for-sfo-fit.svg index a47a585a..c8d4970b 100644 --- a/tests/testthat/_snaps/multistart/parplot-for-sfo-fit.svg +++ b/tests/testthat/_snaps/multistart/parplot-for-sfo-fit.svg @@ -103,8 +103,8 @@ -Starting parameters -Original run +Original start +Original results Multistart runs diff --git a/tests/testthat/test_multistart.R b/tests/testthat/test_multistart.R index 91ef71f0..dda0ea23 100644 --- a/tests/testthat/test_multistart.R +++ b/tests/testthat/test_multistart.R @@ -50,7 +50,7 @@ test_that("multistart works for saem.mmkin models", { llhist_dfop_sfo <- function() llhist(saem_dfop_sfo_m_multi) parplot_dfop_sfo <- function() parplot(saem_dfop_sfo_m_multi, - ylim = c(0.5, 2)) + ylim = c(0.5, 2), llquant = 0.5) vdiffr::expect_doppelganger("llhist for dfop sfo fit", llhist_dfop_sfo) vdiffr::expect_doppelganger("parplot for dfop sfo fit", parplot_dfop_sfo) diff --git a/vignettes/FOCUS_D.html b/vignettes/FOCUS_D.html index 9f768b06..b8a63a7b 100644 --- a/vignettes/FOCUS_D.html +++ b/vignettes/FOCUS_D.html @@ -299,8 +299,8 @@ pre code { border-radius: 4px; } -.tabset-dropdown > .nav-tabs > li.active:before { - content: ""; +.tabset-dropdown > .nav-tabs > li.active:before, .tabset-dropdown > .nav-tabs.nav-tabs-open:before { + content: "\e259"; font-family: 'Glyphicons Halflings'; display: inline-block; padding: 10px; @@ -308,16 +308,9 @@ pre code { } .tabset-dropdown > .nav-tabs.nav-tabs-open > li.active:before { - content: ""; - border: none; -} - -.tabset-dropdown > .nav-tabs.nav-tabs-open:before { - content: ""; + content: "\e258"; font-family: 'Glyphicons Halflings'; - display: inline-block; - padding: 10px; - border-right: 1px solid #ddd; + border: none; } .tabset-dropdown > .nav-tabs > li.active { @@ -364,7 +357,7 @@ pre code {

Example evaluation of FOCUS Example Dataset D

Johannes Ranke

-

Last change 31 January 2019 (rebuilt 2022-07-08)

+

Last change 31 January 2019 (rebuilt 2022-12-06)

@@ -438,10 +431,10 @@ print(FOCUS_2006_D)

A comprehensive report of the results is obtained using the summary method for mkinfit objects.

summary(fit)
-
## mkin version used for fitting:    1.1.0 
-## R version used for fitting:       4.2.1 
-## Date of fit:     Fri Jul  8 15:44:37 2022 
-## Date of summary: Fri Jul  8 15:44:38 2022 
+
## mkin version used for fitting:    1.2.2 
+## R version used for fitting:       4.2.2 
+## Date of fit:     Tue Dec  6 09:39:42 2022 
+## Date of summary: Tue Dec  6 09:39:42 2022 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent * parent
@@ -449,7 +442,7 @@ print(FOCUS_2006_D)

 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 401 model solutions performed in 0.13 s
+## Fitted using 401 model solutions performed in 0.158 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -492,11 +485,11 @@ print(FOCUS_2006_D)
## ## Parameter correlation: ## parent_0 log_k_parent log_k_m1 f_parent_qlogis sigma -## parent_0 1.000e+00 5.174e-01 -1.688e-01 -5.471e-01 -1.174e-06 -## log_k_parent 5.174e-01 1.000e+00 -3.263e-01 -5.426e-01 -8.492e-07 -## log_k_m1 -1.688e-01 -3.263e-01 1.000e+00 7.478e-01 8.220e-07 -## f_parent_qlogis -5.471e-01 -5.426e-01 7.478e-01 1.000e+00 1.307e-06 -## sigma -1.174e-06 -8.492e-07 8.220e-07 1.307e-06 1.000e+00 +## parent_0 1.000e+00 5.174e-01 -1.688e-01 -5.471e-01 -1.172e-06 +## log_k_parent 5.174e-01 1.000e+00 -3.263e-01 -5.426e-01 -8.483e-07 +## log_k_m1 -1.688e-01 -3.263e-01 1.000e+00 7.478e-01 8.205e-07 +## f_parent_qlogis -5.471e-01 -5.426e-01 7.478e-01 1.000e+00 1.305e-06 +## sigma -1.172e-06 -8.483e-07 8.205e-07 1.305e-06 1.000e+00 ## ## Backtransformed parameters: ## Confidence intervals for internally transformed parameters are asymmetric. diff --git a/vignettes/FOCUS_L.html b/vignettes/FOCUS_L.html index da6c11fe..b8c9ba0c 100644 --- a/vignettes/FOCUS_L.html +++ b/vignettes/FOCUS_L.html @@ -1373,8 +1373,8 @@ pre code { border-radius: 4px; } -.tabset-dropdown > .nav-tabs > li.active:before { - content: ""; +.tabset-dropdown > .nav-tabs > li.active:before, .tabset-dropdown > .nav-tabs.nav-tabs-open:before { + content: "\e259"; font-family: 'Glyphicons Halflings'; display: inline-block; padding: 10px; @@ -1382,16 +1382,9 @@ pre code { } .tabset-dropdown > .nav-tabs.nav-tabs-open > li.active:before { - content: ""; - border: none; -} - -.tabset-dropdown > .nav-tabs.nav-tabs-open:before { - content: ""; + content: "\e258"; font-family: 'Glyphicons Halflings'; - display: inline-block; - padding: 10px; - border-right: 1px solid #ddd; + border: none; } .tabset-dropdown > .nav-tabs > li.active { @@ -1517,7 +1510,7 @@ div.tocify {

Example evaluation of FOCUS Laboratory Data L1 to L3

Johannes Ranke

-

Last change 18 May 2022 (rebuilt 2022-09-14)

+

Last change 18 May 2022 (rebuilt 2022-12-06)

@@ -1536,17 +1529,17 @@ FOCUS_2006_L1_mkin <- mkin_wide_to_long(FOCUS_2006_L1)

Since mkin version 0.9-32 (July 2014), we can use shorthand notation like "SFO" for parent only degradation models. The following two lines fit the model and produce the summary report of the model fit. This covers the numerical analysis given in the FOCUS report.

m.L1.SFO <- mkinfit("SFO", FOCUS_2006_L1_mkin, quiet = TRUE)
 summary(m.L1.SFO)
-
## mkin version used for fitting:    1.1.2 
-## R version used for fitting:       4.2.1 
-## Date of fit:     Wed Sep 14 22:28:35 2022 
-## Date of summary: Wed Sep 14 22:28:35 2022 
+
## mkin version used for fitting:    1.2.2 
+## R version used for fitting:       4.2.2 
+## Date of fit:     Tue Dec  6 09:39:45 2022 
+## Date of summary: Tue Dec  6 09:39:45 2022 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 133 model solutions performed in 0.032 s
+## Fitted using 133 model solutions performed in 0.033 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -1637,10 +1630,10 @@ summary(m.L1.SFO)

 
## Warning in sqrt(1/diag(V)): NaNs produced

 
## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is
 ## doubtful

-
## mkin version used for fitting:    1.1.2 
-## R version used for fitting:       4.2.1 
-## Date of fit:     Wed Sep 14 22:28:35 2022 
-## Date of summary: Wed Sep 14 22:28:35 2022 
+
## mkin version used for fitting:    1.2.2 
+## R version used for fitting:       4.2.2 
+## Date of fit:     Tue Dec  6 09:39:45 2022 
+## Date of summary: Tue Dec  6 09:39:45 2022 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
@@ -1742,17 +1735,17 @@ plot(m.L2.FOMC, show_residuals = TRUE,
      main = "FOCUS L2 - FOMC")

 

 
summary(m.L2.FOMC, data = FALSE)

-
## mkin version used for fitting:    1.1.2 
-## R version used for fitting:       4.2.1 
-## Date of fit:     Wed Sep 14 22:28:35 2022 
-## Date of summary: Wed Sep 14 22:28:35 2022 
+
## mkin version used for fitting:    1.2.2 
+## R version used for fitting:       4.2.2 
+## Date of fit:     Tue Dec  6 09:39:45 2022 
+## Date of summary: Tue Dec  6 09:39:45 2022 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 239 model solutions performed in 0.049 s
+## Fitted using 239 model solutions performed in 0.048 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -1820,10 +1813,10 @@ plot(m.L2.DFOP, show_residuals = TRUE, show_errmin = TRUE,
      main = "FOCUS L2 - DFOP")

 

 
summary(m.L2.DFOP, data = FALSE)

-
## mkin version used for fitting:    1.1.2 
-## R version used for fitting:       4.2.1 
-## Date of fit:     Wed Sep 14 22:28:36 2022 
-## Date of summary: Wed Sep 14 22:28:36 2022 
+
## mkin version used for fitting:    1.2.2 
+## R version used for fitting:       4.2.2 
+## Date of fit:     Tue Dec  6 09:39:46 2022 
+## Date of summary: Tue Dec  6 09:39:46 2022 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -1832,7 +1825,7 @@ plot(m.L2.DFOP, show_residuals = TRUE, show_errmin = TRUE,
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 581 model solutions performed in 0.135 s
+## Fitted using 581 model solutions performed in 0.131 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -1920,10 +1913,10 @@ plot(mm.L3)

 
The objects returned by mmkin are arranged like a matrix, with models as a row index and datasets as a column index.

 
We can extract the summary and plot for e.g. the DFOP fit, using square brackets for indexing which will result in the use of the summary and plot functions working on mkinfit objects.

 
summary(mm.L3[["DFOP", 1]])

-
## mkin version used for fitting:    1.1.2 
-## R version used for fitting:       4.2.1 
-## Date of fit:     Wed Sep 14 22:28:36 2022 
-## Date of summary: Wed Sep 14 22:28:36 2022 
+
## mkin version used for fitting:    1.2.2 
+## R version used for fitting:       4.2.2 
+## Date of fit:     Tue Dec  6 09:39:46 2022 
+## Date of summary: Tue Dec  6 09:39:46 2022 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -1932,7 +1925,7 @@ plot(mm.L3)

 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 376 model solutions performed in 0.081 s
+## Fitted using 376 model solutions performed in 0.078 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -2028,17 +2021,17 @@ plot(mm.L4)

 

 
The χ2 error level of 3.3% as well as the plot suggest that the SFO model fits very well. The error level at which the χ2 test passes is slightly lower for the FOMC model. However, the difference appears negligible.

 
summary(mm.L4[["SFO", 1]], data = FALSE)

-
## mkin version used for fitting:    1.1.2 
-## R version used for fitting:       4.2.1 
-## Date of fit:     Wed Sep 14 22:28:36 2022 
-## Date of summary: Wed Sep 14 22:28:37 2022 
+
## mkin version used for fitting:    1.2.2 
+## R version used for fitting:       4.2.2 
+## Date of fit:     Tue Dec  6 09:39:47 2022 
+## Date of summary: Tue Dec  6 09:39:47 2022 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 142 model solutions performed in 0.034 s
+## Fitted using 142 model solutions performed in 0.03 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -2092,10 +2085,10 @@ plot(mm.L4)

 ##        DT50 DT90
 ## parent  106  352

 
summary(mm.L4[["FOMC", 1]], data = FALSE)

-
## mkin version used for fitting:    1.1.2 
-## R version used for fitting:       4.2.1 
-## Date of fit:     Wed Sep 14 22:28:37 2022 
-## Date of summary: Wed Sep 14 22:28:37 2022 
+
## mkin version used for fitting:    1.2.2 
+## R version used for fitting:       4.2.2 
+## Date of fit:     Tue Dec  6 09:39:47 2022 
+## Date of summary: Tue Dec  6 09:39:47 2022 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
-- 
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