Merge branch 'main' into custom_lsoda_call

4 files changed, 142 insertions, 74 deletions

diff --git a/log/build.log b/log/build.log
index 245bd205..dbe0cd5b 100644
--- a/log/build.log
+++ b/log/build.log
@@ -5,5 +5,5 @@
 * creating vignettes ... OK
 * checking for LF line-endings in source and make files and shell scripts
 * checking for empty or unneeded directories
-* building ‘mkin_1.3.0.tar.gz’
+* building ‘mkin_1.2.2.tar.gz’
 
diff --git a/log/check.log b/log/check.log
index e7d4d327..a81475d9 100644
--- a/log/check.log
+++ b/log/check.log
@@ -1,17 +1,34 @@
 * using log directory ‘/home/jranke/git/mkin/mkin.Rcheck’
-* using R version 4.2.2 (2022-10-31)
+* using R version 4.2.2 Patched (2022-11-10 r83330)
 * using platform: x86_64-pc-linux-gnu (64-bit)
 * using session charset: UTF-8
 * using options ‘--no-tests --as-cran’
 * checking for file ‘mkin/DESCRIPTION’ ... OK
 * checking extension type ... Package
-* this is package ‘mkin’ version ‘1.3.0’
+* this is package ‘mkin’ version ‘1.2.2’
 * package encoding: UTF-8
-* checking CRAN incoming feasibility ... Note_to_CRAN_maintainers
+* checking CRAN incoming feasibility ... NOTE
 Maintainer: ‘Johannes Ranke <johannes.ranke@jrwb.de>’
+
+Size of tarball: 6636884 bytes
 * checking package namespace information ... OK
 * checking package dependencies ... OK
-* checking if this is a source package ... OK
+* checking if this is a source package ... NOTE
+Found the following apparent object files/libraries:
+  vignettes/2022_wp_1/cyan_dlls/dfop_path_1.so
+  vignettes/2022_wp_1/cyan_dlls/dfop_path_2.so
+  vignettes/2022_wp_1/cyan_dlls/fomc_path_1.so
+  vignettes/2022_wp_1/cyan_dlls/fomc_path_2.so
+  vignettes/2022_wp_1/cyan_dlls/hs_path_1.so
+  vignettes/2022_wp_1/cyan_dlls/sfo_path_1.so
+  vignettes/2022_wp_1/cyan_dlls/sforb_path_1.so
+  vignettes/2022_wp_1/cyan_dlls/sforb_path_2.so
+  vignettes/2022_wp_1/dmta_dlls/m_dfop_path.so
+  vignettes/2022_wp_1/dmta_dlls/m_fomc_path.so
+  vignettes/2022_wp_1/dmta_dlls/m_hs_path.so
+  vignettes/2022_wp_1/dmta_dlls/m_sfo_path.so
+  vignettes/2022_wp_1/dmta_dlls/m_sforb_path.so
+Object files/libraries should not be included in a source package.
 * checking if there is a namespace ... OK
 * checking for executable files ... OK
 * checking for hidden files and directories ... OK
@@ -37,18 +54,11 @@ Maintainer: ‘Johannes Ranke <johannes.ranke@jrwb.de>’
 * checking whether the namespace can be unloaded cleanly ... OK
 * checking loading without being on the library search path ... OK
 * checking use of S3 registration ... OK
-* checking dependencies in R code ... NOTE
-Package in Depends field not imported from: ‘deSolve’
-  These packages need to be imported from (in the NAMESPACE file)
-  for when this namespace is loaded but not attached.
+* checking dependencies in R code ... OK
 * checking S3 generic/method consistency ... OK
 * checking replacement functions ... OK
-* checking foreign function calls ... NOTE
-Foreign function call to a different package:
-  .C("unlock_solver", ..., PACKAGE = "deSolve")
-See chapter ‘System and foreign language interfaces’ in the ‘Writing R
-Extensions’ manual.
-* checking R code for possible problems ... [17s/17s] OK
+* checking foreign function calls ... OK
+* checking R code for possible problems ... OK
 * checking Rd files ... OK
 * checking Rd metadata ... OK
 * checking Rd line widths ... OK
@@ -64,7 +74,7 @@ Extensions’ manual.
 * checking data for ASCII and uncompressed saves ... OK
 * checking installed files from ‘inst/doc’ ... OK
 * checking files in ‘vignettes’ ... OK
-* checking examples ... [20s/20s] OK
+* checking examples ... [10s/10s] OK
 * checking for unstated dependencies in ‘tests’ ... OK
 * checking tests ... SKIPPED
 * checking for unstated dependencies in vignettes ... OK
diff --git a/log/test.log b/log/test.log
index 10c0aa76..dc1b6c74 100644
--- a/log/test.log
+++ b/log/test.log
@@ -1,57 +1,57 @@
 ℹ Testing mkin
 ✔ | F W S  OK | Context
 ✔ |         5 | AIC calculation
-✔ |         5 | Analytical solutions for coupled models [2.9s]
+✔ |         5 | Analytical solutions for coupled models [1.6s]
 ✔ |         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 [29.5s]
+✔ |        12 | Confidence intervals and p-values [0.4s]
+✔ |     1  12 | Dimethenamid data from 2018 [12.4s]
 ────────────────────────────────────────────────────────────────────────────────
-Skip ('test_dmta.R:99'): Different backends get consistent results for SFO-SFO3+, dimethenamid data
+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 [2.3s]
 ✔ |         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) [0.7s]
-✔ |         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  12 | Nonlinear mixed-effects models [0.3s]
+✔ |         4 | Calculation of FOCUS chi2 error levels [0.3s]
+✔ |        14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [0.4s]
+✔ |         4 | Test fitting the decline of metabolites from their maximum [0.2s]
+✔ |         1 | Fitting the logistic model [0.1s]
+✔ |        10 | Batch fitting and diagnosing hierarchical kinetic models [19.1s]
+✔ |     1  11 | Nonlinear mixed-effects models [5.9s]
 ────────────────────────────────────────────────────────────────────────────────
-Skip ('test_mixed.R:74'): saemix results are reproducible for biphasic fits
+Skip ('test_mixed.R:78'): 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 [0.5s]
-✔ |         3 | mkinfit features [0.7s]
-✔ |         8 | mkinmod model generation and printing [0.2s]
-✔ |         3 | Model predictions with mkinpredict [0.4s]
-✔ |         7 | Multistart method for saem.mmkin models [36.8s]
-✔ |        16 | Evaluations according to 2015 NAFTA guidance [2.5s]
-✔ |         9 | Nonlinear mixed-effects models with nlme [8.8s]
-✔ |        16 | Plotting [10.0s]
+✔ |        10 | Special cases of mkinfit calls [0.4s]
+✔ |         3 | mkinfit features [0.5s]
+✔ |         8 | mkinmod model generation and printing
+✔ |         3 | Model predictions with mkinpredict [0.1s]
+✔ |        12 | Multistart method for saem.mmkin models [21.6s]
+✔ |        16 | Evaluations according to 2015 NAFTA guidance [1.5s]
+✔ |         9 | Nonlinear mixed-effects models with nlme [3.7s]
+✔ |        15 | Plotting [4.6s]
 ✔ |         4 | Residuals extracted from mkinfit models
-✔ |     1  36 | saemix parent models [66.1s]
+✔ |     1  36 | saemix parent models [30.9s]
 ────────────────────────────────────────────────────────────────────────────────
 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 [1.1s]
+✔ |         2 | Complex test case from Schaefer et al. (2007) Piacenza paper [0.6s]
 ✔ |        11 | Processing of residue series
-✔ |        10 | Fitting the SFORB model [3.4s]
+✔ |        10 | Fitting the SFORB model [1.7s]
 ✔ |         1 | Summaries of old mkinfit objects
-✔ |         5 | Summary [0.2s]
-✔ |         4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [1.6s]
-✔ |         9 | Hypothesis tests [6.1s]
-✔ |         4 | Calculation of maximum time weighted average concentrations (TWAs) [2.2s]
+✔ |         5 | Summary
+✔ |         4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [0.9s]
+✔ |         9 | Hypothesis tests [3.3s]
+✔ |         4 | Calculation of maximum time weighted average concentrations (TWAs) [0.7s]
 
 ══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 206.2 s
+Duration: 113.6 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 267 ]
+[ FAIL 0 | WARN 0 | SKIP 3 | PASS 270 ]
diff --git a/log/test_dev.log b/log/test_dev.log
index 24905a1a..370dc5af 100644
--- a/log/test_dev.log
+++ b/log/test_dev.log
@@ -1,54 +1,112 @@
-ℹ Loading mkin
-Loading required package: parallel
 ℹ Testing mkin
 ✔ | F W S  OK | Context
 ✔ |         5 | AIC calculation
-✔ |         5 | Analytical solutions for coupled models [14.6s]
+✔ |         5 | Analytical solutions for coupled models [3.0s]
 ✔ |         5 | Calculation of Akaike weights
-✔ |         2 | Export dataset for reading into CAKE
+✔ |         3 | Export dataset for reading into CAKE
 ✔ |        12 | Confidence intervals and p-values [1.0s]
-⠋ |         1 | Dimethenamid data from 2018                                     
-✔ |     1  27 | Dimethenamid data from 2018 [116.1s]
+✔ |     1  12 | Dimethenamid data from 2018 [31.6s]
 ────────────────────────────────────────────────────────────────────────────────
-Skip (test_dmta.R:164:3): Different backends get consistent results for SFO-SFO3+, dimethenamid data
+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 [6.6s]
+✔ |        14 | Error model fitting [5.2s]
 ✔ |         5 | Time step normalisation
-✔ |         4 | Calculation of FOCUS chi2 error levels [0.8s]
-✔ |        14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [3.5s]
-✔ |         4 | Test fitting the decline of metabolites from their maximum [0.6s]
-✔ |         1 | Fitting the logistic model [0.3s]
-⠋ |        11 | Nonlinear mixed-effects models                                  
-✔ |     1  14 | Nonlinear mixed-effects models [1.3s]
-────────────────────────────────────────────────────────────────────────────────
-Skip (test_mixed.R:68:3): saemix results are reproducible for biphasic fits
+✔ |         4 | Calculation of FOCUS chi2 error levels [0.5s]
+✔ |        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 [40.7s]
+✖ | 1   1  10 | Nonlinear mixed-effects models [13.2s]
+────────────────────────────────────────────────────────────────────────────────
+Failure ('test_mixed.R:21'): Print methods work
+Results have changed from known value recorded in 'print_dfop_saem_1.txt'.
+
+old[13:23] vs new[13:23]
+  ""
+  "Fitted parameters:"
+  "          estimate lower  upper"
+- "parent_0     99.92 98.77 101.06"
++ "parent_0     99.96 98.82 101.11"
+- "log_k1       -2.72 -2.95  -2.50"
++ "log_k1       -2.71 -2.94  -2.49"
+- "log_k2       -4.14 -4.27  -4.01"
++ "log_k2       -4.14 -4.26  -4.01"
+- "g_qlogis     -0.35 -0.53  -0.16"
++ "g_qlogis     -0.36 -0.54  -0.17"
+- "a.1           0.92  0.68   1.16"
++ "a.1           0.93  0.69   1.17"
+  "b.1           0.05  0.04   0.06"
+  "SD.log_k1     0.37  0.23   0.51"
+and 1 more ...
+
+Skip ('test_mixed.R:78'): 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]
-✔ |         3 | mkinfit features [1.1s]
+✔ |         3 | mkinfit features [0.7s]
 ✔ |         8 | mkinmod model generation and printing [0.2s]
 ✔ |         3 | Model predictions with mkinpredict [0.3s]
-✔ |        16 | Evaluations according to 2015 NAFTA guidance [2.1s]
-✔ |         9 | Nonlinear mixed-effects models with nlme [8.7s]
-✔ |        16 | Plotting [1.4s]
+✖ | 3       9 | Multistart method for saem.mmkin models [45.8s]
+────────────────────────────────────────────────────────────────────────────────
+Failure ('test_multistart.R:44'): multistart works for saem.mmkin models
+Snapshot of `testcase` to 'multistart/mixed-model-fit-for-saem-object-with-mkin-transformations.svg' has changed
+Run `testthat::snapshot_review('multistart/')` to review changes
+Backtrace:
+ 1. vdiffr::expect_doppelganger(...)
+      at test_multistart.R:44:2
+ 3. testthat::expect_snapshot_file(...)
+
+Failure ('test_multistart.R:55'): multistart works for saem.mmkin models
+Snapshot of `testcase` to 'multistart/llhist-for-dfop-sfo-fit.svg' has changed
+Run `testthat::snapshot_review('multistart/')` to review changes
+Backtrace:
+ 1. vdiffr::expect_doppelganger("llhist for dfop sfo fit", llhist_dfop_sfo)
+      at test_multistart.R:55:2
+ 3. testthat::expect_snapshot_file(...)
+
+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 [2.3s]
+✔ |         9 | Nonlinear mixed-effects models with nlme [9.0s]
+✖ | 1      14 | Plotting [10.2s]
+────────────────────────────────────────────────────────────────────────────────
+Failure ('test_plot.R:55'): Plotting mkinfit, mmkin and mixed model objects is reproducible
+Snapshot of `testcase` to 'plot/mixed-model-fit-for-nlme-object.svg' has changed
+Run `testthat::snapshot_review('plot/')` to review changes
+Backtrace:
+ 1. vdiffr::expect_doppelganger(...)
+      at test_plot.R:55:2
+ 3. testthat::expect_snapshot_file(...)
+────────────────────────────────────────────────────────────────────────────────
 ✔ |         4 | Residuals extracted from mkinfit models
-✔ |        23 | saemix parent models [28.4s]
-✔ |         2 | Complex test case from Schaefer et al. (2007) Piacenza paper [12.0s]
-✔ |         7 | Fitting the SFORB model [16.9s]
+✔ |     1  36 | saemix parent models [71.7s]
+────────────────────────────────────────────────────────────────────────────────
+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]
+✔ |        11 | Processing of residue series
+✔ |        10 | Fitting the SFORB model [3.5s]
 ✔ |         1 | Summaries of old mkinfit objects
-✔ |         4 | Summary [0.1s]
-✔ |         4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [18.1s]
-✔ |         9 | Hypothesis tests [78.9s]
-✔ |         2 | tffm0
+✔ |         5 | Summary [0.2s]
+✔ |         4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.2s]
+✔ |         9 | Hypothesis tests [7.7s]
 ✔ |         4 | Calculation of maximum time weighted average concentrations (TWAs) [2.0s]
 
 ══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 315.9 s
+Duration: 255.0 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 2 | PASS 240 ]
+[ FAIL 5 | WARN 0 | SKIP 3 | PASS 265 ]