Bump version, fix test from last commit, check and test

6 files changed, 68 insertions, 136 deletions

diff --git a/DESCRIPTION b/DESCRIPTION
index 88f4f33c..8a97fe34 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: mkin
 Type: Package
 Title: Kinetic Evaluation of Chemical Degradation Data
-Version: 1.2.6
-Date: 2023-10-13
+Version: 1.2.7
+Date: 2023-11-23
 Authors@R: c(
   person("Johannes", "Ranke", role = c("aut", "cre", "cph"),
     email = "johannes.ranke@jrwb.de",
diff --git a/log/build.log b/log/build.log
index 6f7ac8ab..b4269860 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_1.2.6.tar.gz’
+* building ‘mkin_1.2.7.tar.gz’
 
diff --git a/log/check.log b/log/check.log
index 64457e57..26fdc5a0 100644
--- a/log/check.log
+++ b/log/check.log
@@ -1,17 +1,17 @@
-* using log directory ‘/home/agsad.admin.ch/f80868656/projects/mkin/mkin.Rcheck’
-* using R version 4.3.1 (2023-06-16)
+* 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)
 * R was compiled by
-    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
-    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
-* running under: Ubuntu 22.04.3 LTS
+    gcc (Debian 12.2.0-14) 12.2.0
+    GNU Fortran (Debian 12.2.0-14) 12.2.0
+* running under: Debian GNU/Linux 12 (bookworm)
 * 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 ‘1.2.5’
+* this is package ‘mkin’ version ‘1.2.7’
 * package encoding: UTF-8
-* checking CRAN incoming feasibility ... [5s/26s] Note_to_CRAN_maintainers
+* checking CRAN incoming feasibility ... [2s/15s] Note_to_CRAN_maintainers
 Maintainer: ‘Johannes Ranke <johannes.ranke@jrwb.de>’
 * checking package namespace information ... OK
 * checking package dependencies ... OK
@@ -45,7 +45,7 @@ Maintainer: ‘Johannes Ranke <johannes.ranke@jrwb.de>’
 * checking S3 generic/method consistency ... OK
 * checking replacement functions ... OK
 * checking foreign function calls ... OK
-* checking R code for possible problems ... [14s/15s] OK
+* checking R code for possible problems ... OK
 * checking Rd files ... OK
 * checking Rd metadata ... OK
 * checking Rd line widths ... OK
@@ -62,22 +62,17 @@ 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 ... [20s/22s] 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 re-building of vignette outputs ... [17s/18s] OK
+* checking re-building of vignette outputs ... OK
 * checking PDF version of manual ... OK
-* checking HTML version of manual ... NOTE
-Skipping checking HTML validation: no command 'tidy' found
+* checking HTML version of manual ... OK
 * checking for non-standard things in the check directory ... OK
 * checking for detritus in the temp directory ... OK
 * DONE
 
-Status: 1 NOTE
-See
-  ‘/home/agsad.admin.ch/f80868656/projects/mkin/mkin.Rcheck/00check.log’
-for details.
-
+Status: OK
 
diff --git a/log/test.log b/log/test.log
index 6d5bc470..a6ac83ed 100644
--- a/log/test.log
+++ b/log/test.log
@@ -1,117 +1,50 @@
 ℹ Testing mkin
-✔ | F W S  OK | Context
-✔ |         5 | AIC calculation
-✔ |         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 [3.1s]
-✔ |        12 | Confidence intervals and p-values [0.4s]
-✔ |     1  12 | Dimethenamid data from 2018 [13.2s]
-────────────────────────────────────────────────────────────────────────────────
-Skip ('test_dmta.R:88:3'): Different backends get consistent results for SFO-SFO3+, dimethenamid data
-Reason: Fitting this ODE model with saemix takes about 5 minutes on my new system
-────────────────────────────────────────────────────────────────────────────────
-✔ |        14 | Error model fitting [2.5s]
-✔ |         5 | Time step normalisation
-✔ |         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 [19.0s]
-✖ | 1   2  15 | Nonlinear mixed-effects models [149.2s]
-────────────────────────────────────────────────────────────────────────────────
-Failure ('test_mixed.R:21:3'): 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:80:3'): saemix results are reproducible for biphasic fits
-Reason: Fitting with saemix takes around 10 minutes when using deSolve
-
-Skip ('test_mixed.R:133:3'): SFO-SFO saemix specific analytical solution work
-Reason: This is seldom used, so save some time
-────────────────────────────────────────────────────────────────────────────────
-✔ |         3 | Test dataset classes mkinds and mkindsg
-✔ |        10 | Special cases of mkinfit calls [0.3s]
-✔ |         3 | mkinfit features [0.5s]
-✔ |         8 | mkinmod model generation and printing
-✔ |         3 | Model predictions with mkinpredict [0.1s]
-✖ | 3       9 | Multistart method for saem.mmkin models [23.2s]
-────────────────────────────────────────────────────────────────────────────────
-Failure ('test_multistart.R:44:3'): 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:55:3'): 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:56:3'): 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 [1.6s]
-✔ |         9 | Nonlinear mixed-effects models with nlme [3.8s]
-✖ | 1      14 | Plotting [4.7s]
-────────────────────────────────────────────────────────────────────────────────
-Failure ('test_plot.R:55:3'): 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
-✔ |     1  36 | saemix parent models [31.4s]
-────────────────────────────────────────────────────────────────────────────────
-Skip ('test_saemix_parent.R:143:3'): 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 [0.5s]
-✔ |        11 | Processing of residue series
-✔ |        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) [0.8s]
-✔ |         9 | Hypothesis tests [2.9s]
-✔ |         4 | Calculation of maximum time weighted average concentrations (TWAs) [0.7s]
+✔ | F W  S  OK | Context
+✔ |          5 | AIC calculation
+✔ |          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 [3.3s]
+✔ |         12 | Confidence intervals and p-values
+✔ |      1  12 | Dimethenamid data from 2018 [13.1s]
+✔ |         14 | Error model fitting [2.5s]
+✔ |          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 [20.4s]
+✔ |      2  16 | Nonlinear mixed-effects models [149.9s]
+✔ |          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 [23.0s]
+✔ |         16 | Evaluations according to 2015 NAFTA guidance [1.5s]
+✔ |          9 | Nonlinear mixed-effects models with nlme [3.6s]
+✔ |         15 | Plotting [4.8s]
+✔ |          4 | Residuals extracted from mkinfit models
+✔ |      1  38 | saemix parent models [35.2s]
+✔ |          2 | Complex test case from Schaefer et al. (2007) Piacenza paper
+✔ |         11 | Processing of residue series
+✔ |         10 | Fitting the SFORB model [1.6s]
+✔ |          1 | Summaries of old mkinfit objects
+✔ |          5 | Summary
+✔ |          4 | Results for synthetic data established in expertise for UBA (Ranke 2014)
+✔ |          9 | Hypothesis tests [2.8s]
+✔ |          4 | Calculation of maximum time weighted average concentrations (TWAs)
 
 ══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 262.6 s
-
-── Skipped tests  ──────────────────────────────────────────────────────────────
-• Fitting this ODE model with saemix takes about 5 minutes on my new system (1)
-• Fitting with saemix takes around 10 minutes when using deSolve (1)
-• This is seldom used, so save some time (1)
-• This still takes almost 2.5 minutes although we do not solve ODEs (1)
-
-[ FAIL 5 | WARN 0 | SKIP 4 | PASS 276 ]
+Duration: 268.2 s
+
+── Skipped tests (4) ───────────────────────────────────────────────────────────
+• Fitting this ODE model with saemix takes about 5 minutes on my new system
+  (1): 'test_dmta.R:88:3'
+• Fitting with saemix takes around 10 minutes when using deSolve (1):
+  'test_mixed.R:80:3'
+• This is seldom used, so save some time (1): 'test_mixed.R:133:3'
+• 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 ]
diff --git a/man/hierarchical_kinetics.Rd b/man/hierarchical_kinetics.Rd
index bcbe1e06..8330fe68 100644
--- a/man/hierarchical_kinetics.Rd
+++ b/man/hierarchical_kinetics.Rd
@@ -9,7 +9,11 @@ hierarchical_kinetics(..., keep_tex = FALSE)
 \arguments{
 \item{...}{Arguments to \code{rmarkdown::pdf_document}}
 
-\item{keep_tex}{Keep the intermediate tex file used in the conversion to PDF}
+\item{keep_tex}{Keep the intermediate tex file used in the conversion to PDF.
+Note that this argument does not control whether to keep the auxiliary
+files (e.g., \file{.aux}) generated by LaTeX when compiling \file{.tex} to
+\file{.pdf}. To keep these files, you may set \code{options(tinytex.clean =
+FALSE)}.}
 }
 \value{
 R Markdown output format to pass to
diff --git a/tests/testthat/test_saemix_parent.R b/tests/testthat/test_saemix_parent.R
index c80b4fa1..88b406b6 100644
--- a/tests/testthat/test_saemix_parent.R
+++ b/tests/testthat/test_saemix_parent.R
@@ -174,4 +174,4 @@ test_that("illparms finds a single random effect that is ill-defined", {
   expect_equal(
     as.character(illparms(m_saem_2)),
     "sd(log_k_parent)")
-}
+})