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-rw-r--r--DESCRIPTION6
-rw-r--r--NAMESPACE1
-rw-r--r--NEWS.md4
-rw-r--r--R/create_deg_func.R38
-rw-r--r--log/build.log2
-rw-r--r--log/check.log14
-rw-r--r--log/test.log29
-rw-r--r--tests/testthat/print_dfop_saem_1.txt2
-rw-r--r--tests/testthat/summary_hfit_sfo_tc.txt4
-rw-r--r--tests/testthat/summary_saem_dfop_sfo_s.txt2
-rw-r--r--tests/testthat/test_water-sediment.R17
-rw-r--r--vignettes/mkin.html2
12 files changed, 80 insertions, 41 deletions
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 <johannes.ranke@jrwb.de>’
* checking package namespace information ... OK
* checking package dependencies ... OK
@@ -32,7 +32,7 @@ Maintainer: ‘Johannes Ranke <johannes.ranke@jrwb.de>’
* 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 <johannes.ranke@jrwb.de>’
* 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; }
<h1 class="title toc-ignore">Short introduction to mkin</h1>
<h4 class="author">Johannes Ranke</h4>
-<h4 class="date">Last change 18 May 2023 (rebuilt 2023-05-19)</h4>
+<h4 class="date">Last change 18 May 2023 (rebuilt 2024-04-27)</h4>
<div id="TOC">

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