From e18c8da322ddb11105b7fdf93e9dd538673fb946 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Sat, 27 Apr 2024 19:22:10 +0200 Subject: Fix bug in R/create_deg_func.R Closes #13 --- DESCRIPTION | 6 ++--- NAMESPACE | 1 + NEWS.md | 4 ++++ R/create_deg_func.R | 38 +++++++++++++++++++++--------- log/build.log | 2 +- log/check.log | 14 +++++------ log/test.log | 29 ++++++++++++----------- tests/testthat/print_dfop_saem_1.txt | 2 +- tests/testthat/summary_hfit_sfo_tc.txt | 4 ++-- tests/testthat/summary_saem_dfop_sfo_s.txt | 2 +- tests/testthat/test_water-sediment.R | 17 +++++++++++++ vignettes/mkin.html | 2 +- 12 files changed, 80 insertions(+), 41 deletions(-) create mode 100644 tests/testthat/test_water-sediment.R diff --git a/DESCRIPTION b/DESCRIPTION index 0d924faf..6aa012b5 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Package: mkin Type: Package Title: Kinetic Evaluation of Chemical Degradation Data -Version: 1.2.8 -Date: 2023-11-26 +Version: 1.2.9 +Date: 2024-04-27 Authors@R: c( person("Johannes", "Ranke", role = c("aut", "cre", "cph"), email = "johannes.ranke@jrwb.de", @@ -36,4 +36,4 @@ VignetteBuilder: knitr BugReports: https://github.com/jranke/mkin/issues/ URL: https://pkgdown.jrwb.de/mkin/ Roxygen: list(markdown = TRUE) -RoxygenNote: 7.2.3 +RoxygenNote: 7.3.1 diff --git a/NAMESPACE b/NAMESPACE index bcea2b1b..5b9a1c85 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -158,6 +158,7 @@ importFrom(lmtest,lrtest) importFrom(methods,is) importFrom(methods,signature) importFrom(nlme,intervals) +importFrom(nlme,nlme) importFrom(parallel,detectCores) importFrom(parallel,mclapply) importFrom(parallel,parLapply) diff --git a/NEWS.md b/NEWS.md index f7c38915..d6139aae 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,7 @@ +# mkin 1.2.9 + +- 'R/create_deg_func.R: Make sure that no reversible reactions are specified in the case of two observed variables, as this is not supported + # mkin 1.2.8 - 'R/{mhmkin,status}.R': Deal with 'saem' fits that fail when updating an 'mhmkin' object diff --git a/R/create_deg_func.R b/R/create_deg_func.R index 5794c65c..d3e11f78 100644 --- a/R/create_deg_func.R +++ b/R/create_deg_func.R @@ -61,16 +61,21 @@ create_deg_func <- function(spec, use_of_ff = c("min", "max")) { ), ")") - if (length(obs_vars) >= 2) { - supported <- FALSE # except for the following cases + if (length(obs_vars) >= 2) supported <- FALSE + # Except for the following cases: + + if (length(obs_vars) == 2) { n1 <- obs_vars[1] n2 <- obs_vars[2] n10 <- paste0("odeini['", parent, "']") n20 <- paste0("odeini['", n2, "']") # sfo_sfo - if (all(spec[[1]]$sink == FALSE, length(obs_vars) == 2, - spec[[1]]$type == "SFO", spec[[2]]$type == "SFO")) { + if (all( + spec[[1]]$sink == FALSE, + spec[[1]]$type == "SFO", + spec[[2]]$type == "SFO", + is.null(spec[[2]]$to))) { supported <- TRUE k1 <- k_parent k2 <- paste0("k_", n2, if(min_ff) "_sink" else "") @@ -80,8 +85,12 @@ create_deg_func <- function(spec, use_of_ff = c("min", "max")) { } # sfo_f12_sfo - if (all(use_of_ff == "max", spec[[1]]$sink == TRUE, length(obs_vars) == 2, - spec[[1]]$type == "SFO", spec[[2]]$type == "SFO")) { + if (all( + use_of_ff == "max", + spec[[1]]$sink == TRUE, + spec[[1]]$type == "SFO", + spec[[2]]$type == "SFO", + is.null(spec[[2]]$to))) { supported <- TRUE k1 <- k_parent k2 <- paste0("k_", n2) @@ -92,8 +101,12 @@ create_deg_func <- function(spec, use_of_ff = c("min", "max")) { } # sfo_k120_sfo - if (all(use_of_ff == "min", spec[[1]]$sink == TRUE, length(obs_vars) == 2, - spec[[1]]$type == "SFO", spec[[2]]$type == "SFO")) { + if (all( + use_of_ff == "min", + spec[[1]]$sink == TRUE, + spec[[1]]$type == "SFO", + spec[[2]]$type == "SFO", + is.null(spec[[2]]$to))) { supported <- TRUE k12 <- paste0("k_", n1, "_", n2) k10 <- paste0("k_", n1, "_sink") @@ -104,8 +117,12 @@ create_deg_func <- function(spec, use_of_ff = c("min", "max")) { } # dfop_f12_sfo - if (all(use_of_ff == "max", spec[[1]]$sink == TRUE, length(obs_vars) == 2, - spec[[1]]$type == "DFOP", spec[[2]]$type == "SFO")) { + if (all( + use_of_ff == "max", + spec[[1]]$sink == TRUE, + spec[[1]]$type == "DFOP", + spec[[2]]$type == "SFO", + is.null(spec[[2]]$to))) { supported <- TRUE f12 <- paste0("f_", n1, "_to_", n2) k2 <- paste0("k_", n2) @@ -119,7 +136,6 @@ create_deg_func <- function(spec, use_of_ff = c("min", "max")) { } - if (supported) { deg_func <- function(observed, odeini, odeparms) {} diff --git a/log/build.log b/log/build.log index c2001830..de7e4488 100644 --- a/log/build.log +++ b/log/build.log @@ -7,5 +7,5 @@ * checking for empty or unneeded directories Removed empty directory ‘mkin/inst/rmarkdown/templates/hierarchical_kinetics_parent’ Removed empty directory ‘mkin/vignettes/web_only’ -* building ‘mkin_1.2.8.tar.gz’ +* building ‘mkin_1.2.9.tar.gz’ diff --git a/log/check.log b/log/check.log index 5e777a87..58615282 100644 --- a/log/check.log +++ b/log/check.log @@ -1,6 +1,6 @@ * using log directory ‘/home/jranke/git/mkin/mkin.Rcheck’ -* using R version 4.3.2 (2023-10-31) -* using platform: x86_64-pc-linux-gnu (64-bit) +* using R version 4.4.0 (2024-04-24) +* using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Debian 12.2.0-14) 12.2.0 GNU Fortran (Debian 12.2.0-14) 12.2.0 @@ -9,9 +9,9 @@ * using options ‘--no-tests --as-cran’ * checking for file ‘mkin/DESCRIPTION’ ... OK * checking extension type ... Package -* this is package ‘mkin’ version ‘1.2.8’ +* this is package ‘mkin’ version ‘1.2.9’ * package encoding: UTF-8 -* checking CRAN incoming feasibility ... [2s/14s] Note_to_CRAN_maintainers +* checking CRAN incoming feasibility ... Note_to_CRAN_maintainers Maintainer: ‘Johannes Ranke ’ * checking package namespace information ... OK * checking package dependencies ... OK @@ -32,7 +32,7 @@ Maintainer: ‘Johannes Ranke ’ * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK -* checking R files for non-ASCII characters ... OK +* checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK @@ -62,11 +62,11 @@ Maintainer: ‘Johannes Ranke ’ * checking sizes of PDF files under ‘inst/doc’ ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK -* checking examples ... OK +* checking examples ... [10s/10s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... SKIPPED * checking for unstated dependencies in vignettes ... OK -* checking package vignettes in ‘inst/doc’ ... OK +* checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * checking HTML version of manual ... OK diff --git a/log/test.log b/log/test.log index 9dc63675..e92a7409 100644 --- a/log/test.log +++ b/log/test.log @@ -4,39 +4,40 @@ ✔ | 5 | Analytical solutions for coupled models [1.5s] ✔ | 5 | Calculation of Akaike weights ✔ | 3 | Export dataset for reading into CAKE -✔ | 6 | Use of precompiled symbols in mkinpredict [3.2s] +✔ | 6 | Use of precompiled symbols in mkinpredict [3.1s] ✔ | 12 | Confidence intervals and p-values -✔ | 1 12 | Dimethenamid data from 2018 [13.8s] -✔ | 14 | Error model fitting [2.5s] +✔ | 1 12 | Dimethenamid data from 2018 [13.0s] +✔ | 14 | Error model fitting [2.6s] ✔ | 5 | Time step normalisation ✔ | 4 | Calculation of FOCUS chi2 error levels ✔ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ✔ | 4 | Test fitting the decline of metabolites from their maximum ✔ | 1 | Fitting the logistic model -✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [19.8s] -✔ | 2 16 | Nonlinear mixed-effects models [149.6s] +✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [19.7s] +✔ | 2 16 | Nonlinear mixed-effects models [144.7s] ✔ | 3 | Test dataset classes mkinds and mkindsg ✔ | 10 | Special cases of mkinfit calls ✔ | 3 | mkinfit features ✔ | 8 | mkinmod model generation and printing ✔ | 3 | Model predictions with mkinpredict -✔ | 12 | Multistart method for saem.mmkin models [23.6s] -✔ | 16 | Evaluations according to 2015 NAFTA guidance [1.6s] -✔ | 9 | Nonlinear mixed-effects models with nlme [4.0s] -✔ | 15 | Plotting [4.7s] +✔ | 12 | Multistart method for saem.mmkin models [23.3s] +✔ | 16 | Evaluations according to 2015 NAFTA guidance [1.5s] +✔ | 9 | Nonlinear mixed-effects models with nlme [3.7s] +✔ | 15 | Plotting [4.5s] ✔ | 4 | Residuals extracted from mkinfit models -✔ | 1 38 | saemix parent models [36.4s] +✔ | 1 38 | saemix parent models [34.8s] ✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper ✔ | 11 | Processing of residue series -✔ | 10 | Fitting the SFORB model [1.8s] +✔ | 10 | Fitting the SFORB model [1.7s] ✔ | 1 | Summaries of old mkinfit objects ✔ | 5 | Summary ✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) -✔ | 9 | Hypothesis tests [3.1s] +✔ | 9 | Hypothesis tests [2.9s] ✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) +✔ | 2 | water-sediment ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 270.7 s +Duration: 262.3 s ── Skipped tests (4) ─────────────────────────────────────────────────────────── • Fitting this ODE model with saemix takes about 5 minutes on my new system @@ -47,4 +48,4 @@ Duration: 270.7 s • This still takes almost 2.5 minutes although we do not solve ODEs (1): 'test_saemix_parent.R:143:3' -[ FAIL 0 | WARN 0 | SKIP 4 | PASS 283 ] +[ FAIL 0 | WARN 0 | SKIP 4 | PASS 285 ] diff --git a/tests/testthat/print_dfop_saem_1.txt b/tests/testthat/print_dfop_saem_1.txt index f7354320..3a1f1667 100644 --- a/tests/testthat/print_dfop_saem_1.txt +++ b/tests/testthat/print_dfop_saem_1.txt @@ -18,6 +18,6 @@ log_k1 -2.71 -2.94 -2.49 log_k2 -4.14 -4.26 -4.01 g_qlogis -0.36 -0.54 -0.17 a.1 0.93 0.69 1.17 -b.1 0.05 0.04 0.06 +b.1 0.05 0.04 0.05 SD.log_k1 0.37 0.23 0.51 SD.log_k2 0.23 0.14 0.31 diff --git a/tests/testthat/summary_hfit_sfo_tc.txt b/tests/testthat/summary_hfit_sfo_tc.txt index 0618c715..ba7d1362 100644 --- a/tests/testthat/summary_hfit_sfo_tc.txt +++ b/tests/testthat/summary_hfit_sfo_tc.txt @@ -43,7 +43,7 @@ Optimised parameters: est. lower upper parent_0 92.52 89.11 95.9 log_k_parent -1.66 -2.07 -1.3 -a.1 2.03 1.60 2.5 +a.1 2.03 1.61 2.5 b.1 0.09 0.07 0.1 SD.log_k_parent 0.51 0.22 0.8 @@ -57,7 +57,7 @@ SD.log_k_parent 0.5 0.2 0.8 Variance model: est. lower upper -a.1 2.03 1.60 2.5 +a.1 2.03 1.61 2.5 b.1 0.09 0.07 0.1 Backtransformed parameters: diff --git a/tests/testthat/summary_saem_dfop_sfo_s.txt b/tests/testthat/summary_saem_dfop_sfo_s.txt index 6468ff17..a19824ce 100644 --- a/tests/testthat/summary_saem_dfop_sfo_s.txt +++ b/tests/testthat/summary_saem_dfop_sfo_s.txt @@ -86,7 +86,7 @@ SD.g 0.21 0.06 0.4 Variance model: est. lower upper -a.1 0.93 0.79 1.06 +a.1 0.93 0.80 1.06 b.1 0.05 0.05 0.06 Resulting formation fractions: diff --git a/tests/testthat/test_water-sediment.R b/tests/testthat/test_water-sediment.R new file mode 100644 index 00000000..6d5693c9 --- /dev/null +++ b/tests/testthat/test_water-sediment.R @@ -0,0 +1,17 @@ +# Issue #13 on github +water_sed_no_sed_sink <- mkinmod( + use_of_ff = "min", + water = mkinsub("SFO", "sediment"), + sediment = mkinsub("SFO", "water", sink = FALSE)) + +ws_data <- FOCUS_D +levels(ws_data$name) <- c("water", "sediment") + +test_that("An reversible reaction with the sink turned off in the second compartment works", { + # Solution method "analytical" was previously available, but erroneous + expect_error( + ws_fit_no_sed_sink <- mkinfit(water_sed_no_sed_sink, ws_data, quiet = TRUE, solution_type = "analytical"), + "Analytical solution not implemented") + ws_fit_no_sed_sink_default <- mkinfit(water_sed_no_sed_sink, ws_data, quiet = TRUE) + expect_equal(ws_fit_no_sed_sink_default$solution_type, "deSolve") +}) diff --git a/vignettes/mkin.html b/vignettes/mkin.html index 12b8671e..ea057d19 100644 --- a/vignettes/mkin.html +++ b/vignettes/mkin.html @@ -372,7 +372,7 @@ code > span.er { color: #a61717; background-color: #e3d2d2; }

Short introduction to mkin

Johannes Ranke

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Last change 18 May 2023 (rebuilt 2023-05-19)

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Last change 18 May 2023 (rebuilt 2024-04-27)

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