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authorJohannes Ranke <jranke@uni-bremen.de>2023-03-22 23:00:18 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2023-03-22 23:00:18 +0100
commit9e7aa351b30a0dc9b1e6e14da751c7f42a7587dd (patch)
treeb16293db1c6f268d67961018a28277fc2ab064f8
parent81bb17f887f192a5ee4f77829a65689934776471 (diff)
parentb17dc3ee5f4fda17fcbc659730cb81e447510121 (diff)
Merge branch 'main' into covariate_parms_and_endpoints
-rw-r--r--NEWS.md2
-rw-r--r--R/mkinerrmin.R2
-rw-r--r--log/check.log22
-rw-r--r--log/test.log53
-rw-r--r--man/mkinfit.Rd4
-rw-r--r--man/set_nd_nq.Rd4
-rw-r--r--tests/testthat/_snaps/multistart/llhist-for-dfop-sfo-fit.svg4
-rw-r--r--tests/testthat/_snaps/multistart/mixed-model-fit-for-saem-object-with-mkin-transformations.svg2
-rw-r--r--tests/testthat/_snaps/multistart/parplot-for-dfop-sfo-fit.svg234
-rw-r--r--tests/testthat/_snaps/plot/mixed-model-fit-for-nlme-object.svg2
10 files changed, 169 insertions, 160 deletions
diff --git a/NEWS.md b/NEWS.md
index 5f173a08..65bbe185 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -2,6 +2,8 @@
- Depend on upcoming deSolve version with the possibility to avoid resolving symbols in a shared library (compiled models) over and over.
+- 'R/mkinerrmin.R': Fix typo in subset (use of = instead of ==), thanks to Sebastian Meyer for spotting this during his work on R 4.3.0
+
# mkin 1.2.2 (unreleased)
- 'inst/rmarkdown/templates/hier': R markdown template to facilitate the application of hierarchical kinetic models.
diff --git a/R/mkinerrmin.R b/R/mkinerrmin.R
index 388060d4..b924f4ab 100644
--- a/R/mkinerrmin.R
+++ b/R/mkinerrmin.R
@@ -58,7 +58,7 @@ mkinerrmin <- function(fit, alpha = 0.05)
# Remove values at time zero for variables whose value for state.ini is fixed,
# as these will not have any effect in the optimization and should therefore not
# be counted as degrees of freedom.
- fixed_initials = gsub("_0$", "", rownames(subset(fit$fixed, type = "state")))
+ fixed_initials = gsub("_0$", "", rownames(subset(fit$fixed, type == "state")))
errdata <- subset(errdata, !(time == 0 & variable %in% fixed_initials))
n.optim.overall <- length(parms.optim) - length(fit$errparms)
diff --git a/log/check.log b/log/check.log
index 967b51d0..b44bc1b4 100644
--- a/log/check.log
+++ b/log/check.log
@@ -1,14 +1,16 @@
* using log directory ‘/home/jranke/git/mkin/mkin.Rcheck’
-* using R version 4.2.2 Patched (2022-11-10 r83330)
+* using R version 4.2.2 (2022-10-31)
* 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 ‘1.2.3’
* package encoding: UTF-8
-* checking CRAN incoming feasibility ... Note_to_CRAN_maintainers
+* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Johannes Ranke <johannes.ranke@jrwb.de>’
+
+The Date field is over a month old.
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
@@ -41,7 +43,7 @@ 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 ... OK
+* checking R code for possible problems ... [14s/14s] OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
@@ -58,17 +60,21 @@ 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 ... [10s/10s] OK
+* checking examples ... [18s/18s] 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 ... OK
+* checking re-building of vignette outputs ... [12s/12s] OK
* checking PDF version of manual ... OK
-* checking HTML version of manual ... OK
+* skipping checking HTML version of manual: no command ‘tidy’ found
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
-Status: OK
+Status: 1 NOTE
+See
+ ‘/home/jranke/git/mkin/mkin.Rcheck/00check.log’
+for details.
+
diff --git a/log/test.log b/log/test.log
index 42ed75e4..d4fb85a2 100644
--- a/log/test.log
+++ b/log/test.log
@@ -1,53 +1,54 @@
+ℹ Loading mkin
ℹ Testing mkin
✔ | F W S OK | Context
✔ | 5 | AIC calculation
-✔ | 5 | Analytical solutions for coupled models [1.4s]
+✔ | 5 | Analytical solutions for coupled models [2.8s]
✔ | 5 | Calculation of Akaike weights
✔ | 3 | Export dataset for reading into CAKE
-✔ | 12 | Confidence intervals and p-values [0.4s]
-✔ | 1 12 | Dimethenamid data from 2018 [11.6s]
+✔ | 12 | Confidence intervals and p-values [1.0s]
+✔ | 1 12 | Dimethenamid data from 2018 [31.3s]
────────────────────────────────────────────────────────────────────────────────
Skip ('test_dmta.R:99'): 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 [2.3s]
+✔ | 14 | Error model fitting [6.9s]
✔ | 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 [18.5s]
-✔ | 1 11 | Nonlinear mixed-effects models [5.9s]
+✔ | 4 | Calculation of FOCUS chi2 error levels [0.5s]
+✔ | 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 [42.7s]
+✔ | 1 11 | Nonlinear mixed-effects models [13.1s]
────────────────────────────────────────────────────────────────────────────────
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 [0.4s]
-✔ | 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 [21.1s]
-✔ | 16 | Evaluations according to 2015 NAFTA guidance [1.5s]
-✔ | 9 | Nonlinear mixed-effects models with nlme [3.4s]
-✔ | 15 | Plotting [4.4s]
+✔ | 10 | Special cases of mkinfit calls [0.6s]
+✔ | 3 | mkinfit features [0.6s]
+✔ | 8 | mkinmod model generation and printing [0.2s]
+✔ | 3 | Model predictions with mkinpredict [0.3s]
+✔ | 12 | Multistart method for saem.mmkin models [74.1s]
+✔ | 16 | Evaluations according to 2015 NAFTA guidance [1.9s]
+✔ | 9 | Nonlinear mixed-effects models with nlme [8.5s]
+✔ | 15 | Plotting [11.4s]
✔ | 4 | Residuals extracted from mkinfit models
-✔ | 1 36 | saemix parent models [29.4s]
+✔ | 1 36 | saemix parent models [73.9s]
────────────────────────────────────────────────────────────────────────────────
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 [0.5s]
+✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.1s]
✔ | 11 | Processing of residue series
-✔ | 10 | Fitting the SFORB model [1.6s]
+✔ | 10 | Fitting the SFORB model [3.1s]
✔ | 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]
+✔ | 5 | Summary [0.1s]
+✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [1.7s]
+✔ | 9 | Hypothesis tests [6.0s]
+✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [1.9s]
══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 108.9 s
+Duration: 285.4 s
── Skipped tests ──────────────────────────────────────────────────────────────
• Fitting this ODE model with saemix takes about 15 minutes on my system (1)
diff --git a/man/mkinfit.Rd b/man/mkinfit.Rd
index f96b4d22..b5b24449 100644
--- a/man/mkinfit.Rd
+++ b/man/mkinfit.Rd
@@ -23,8 +23,8 @@ mkinfit(
atol = 1e-08,
rtol = 1e-10,
error_model = c("const", "obs", "tc"),
- error_model_algorithm = c("auto", "d_3", "direct", "twostep", "threestep", "fourstep",
- "IRLS", "OLS"),
+ error_model_algorithm = c("auto", "d_3", "direct", "twostep", "threestep",
+ "fourstep", "IRLS", "OLS"),
reweight.tol = 1e-08,
reweight.max.iter = 10,
trace_parms = FALSE,
diff --git a/man/set_nd_nq.Rd b/man/set_nd_nq.Rd
index 87a3fae1..796c27a2 100644
--- a/man/set_nd_nq.Rd
+++ b/man/set_nd_nq.Rd
@@ -54,9 +54,9 @@ it automates the proposal of Boesten et al (2015).
}
\section{Functions}{
\itemize{
-\item \code{set_nd_nq_focus()}: Set non-detects in residue time series according to FOCUS rules
-
+\item \code{set_nd_nq_focus}: Set non-detects in residue time series according to FOCUS rules
}}
+
\examples{
# FOCUS (2014) p. 75/76 and 131/132
parent_1 <- c(.12, .09, .05, .03, "nd", "nd", "nd", "nd", "nd", "nd")
diff --git a/tests/testthat/_snaps/multistart/llhist-for-dfop-sfo-fit.svg b/tests/testthat/_snaps/multistart/llhist-for-dfop-sfo-fit.svg
index 6015aed8..6be8b9dd 100644
--- a/tests/testthat/_snaps/multistart/llhist-for-dfop-sfo-fit.svg
+++ b/tests/testthat/_snaps/multistart/llhist-for-dfop-sfo-fit.svg
@@ -52,8 +52,8 @@
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+<rect x='316.00' y='383.47' width='116.80' height='102.67' style='stroke-width: 0.75; fill: #D3D3D3;' />
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diff --git a/tests/testthat/_snaps/multistart/mixed-model-fit-for-saem-object-with-mkin-transformations.svg b/tests/testthat/_snaps/multistart/mixed-model-fit-for-saem-object-with-mkin-transformations.svg
index 69fa6a4d..ed8dcd4d 100644
--- a/tests/testthat/_snaps/multistart/mixed-model-fit-for-saem-object-with-mkin-transformations.svg
+++ b/tests/testthat/_snaps/multistart/mixed-model-fit-for-saem-object-with-mkin-transformations.svg
@@ -2099,7 +2099,7 @@
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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 b01dac74..990b17c0 100644
--- a/tests/testthat/_snaps/multistart/parplot-for-dfop-sfo-fit.svg
+++ b/tests/testthat/_snaps/multistart/parplot-for-dfop-sfo-fit.svg
@@ -25,104 +25,104 @@
</clipPath>
</defs>
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