diff options
| -rw-r--r-- | NEWS.md | 4 | ||||
| -rw-r--r-- | R/summary.saem.mmkin.R | 11 | ||||
| -rw-r--r-- | log/build.log | 2 | ||||
| -rw-r--r-- | log/test.log | 34 | ||||
| -rw-r--r-- | tests/testthat/illparms_hfits_synth_no_ranef_auto.txt | 4 | ||||
| -rw-r--r-- | tests/testthat/print_hfits_synth_no_ranef_auto.txt | 9 | ||||
| -rw-r--r-- | tests/testthat/summary_hfit_sfo_tc.txt | 11 | ||||
| -rw-r--r-- | tests/testthat/summary_saem_dfop_sfo_s.txt | 15 | ||||
| -rw-r--r-- | tests/testthat/test_mhmkin.R | 10 |
9 files changed, 55 insertions, 45 deletions
@@ -1,6 +1,8 @@ # mkin 1.2.2 -- 'R/mhmkin.R': Allow an 'illparms.mhmkin' object as value of the argument 'no_random_effects', making it possible to exclude random effects that were ill-defined in simpler variants of the set of degradation models. +- 'R/mhmkin.R': Allow an 'illparms.mhmkin' object as value of the argument 'no_random_effects', making it possible to exclude random effects that were ill-defined in simpler variants of the set of degradation models. Remove the possibility to exclude random effects based on separate fits, as it did not work well. + +- 'R/summary.saem.mmkin.R': List all initial parameter values in the summary, including random effects and error model parameters # mkin 1.2.1 (2022-11-19) diff --git a/R/summary.saem.mmkin.R b/R/summary.saem.mmkin.R index 2754e9f0..7337b0f3 100644 --- a/R/summary.saem.mmkin.R +++ b/R/summary.saem.mmkin.R @@ -225,13 +225,22 @@ print.summary.saem.mmkin <- function(x, digits = max(3, getOption("digits") - 3) obs = "Variance unique to each observed variable", tc = "Two-component variance function"), "\n") - cat("\nMean of starting values for individual parameters:\n") + cat("\nStarting values for degradation parameters:\n") print(x$mean_dp_start, digits = digits) cat("\nFixed degradation parameter values:\n") if(length(x$fixed$value) == 0) cat("None\n") else print(x$fixed, digits = digits) + cat("\nStarting values for random effects (square root of initial entries in omega):\n") + print(sqrt(x$so@model@omega.init), digits = digits) + + cat("\nStarting values for error model parameters:\n") + errparms <- x$so@model@error.init + names(errparms) <- x$so@model@name.sigma + errparms <- errparms[x$so@model@indx.res] + print(errparms, digits = digits) + cat("\nResults:\n\n") cat("Likelihood computed by importance sampling\n") print(data.frame(AIC = x$AIC, BIC = x$BIC, logLik = x$logLik, diff --git a/log/build.log b/log/build.log index 6be01938..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_1.2.1.tar.gz’ +* building ‘mkin_1.2.2.tar.gz’ diff --git a/log/test.log b/log/test.log index 0b9aa7eb..e17ecc1f 100644 --- a/log/test.log +++ b/log/test.log @@ -5,54 +5,54 @@ ✔ | 5 | Calculation of Akaike weights ✔ | 3 | Export dataset for reading into CAKE ✔ | 12 | Confidence intervals and p-values [1.1s] -✔ | 1 12 | Dimethenamid data from 2018 [33.3s] +✔ | 1 12 | Dimethenamid data from 2018 [32.2s] ──────────────────────────────────────────────────────────────────────────────── 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 [5.0s] +✔ | 14 | Error model fitting [4.9s] ✔ | 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) [0.8s] -✔ | 4 | Test fitting the decline of metabolites from their maximum [0.4s] -✔ | 1 | Fitting the logistic model [0.3s] -✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [25.5s] -✔ | 1 11 | Nonlinear mixed-effects models [13.2s] +✔ | 4 | Test fitting the decline of metabolites from their maximum [0.3s] +✔ | 1 | Fitting the logistic model [0.2s] +✔ | 8 | Batch fitting and diagnosing hierarchical kinetic models [14.5s] +✔ | 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 [0.5s] +✔ | 10 | Special cases of mkinfit calls [0.4s] ✔ | 3 | mkinfit features [0.7s] ✔ | 8 | mkinmod model generation and printing [0.2s] ✔ | 3 | Model predictions with mkinpredict [0.3s] -✔ | 12 | Multistart method for saem.mmkin models [51.1s] -✔ | 16 | Evaluations according to 2015 NAFTA guidance [2.3s] -✔ | 9 | Nonlinear mixed-effects models with nlme [9.2s] -✔ | 15 | Plotting [10.3s] +✔ | 12 | Multistart method for saem.mmkin models [50.1s] +✔ | 16 | Evaluations according to 2015 NAFTA guidance [2.2s] +✔ | 9 | Nonlinear mixed-effects models with nlme [8.7s] +✔ | 15 | Plotting [10.2s] ✔ | 4 | Residuals extracted from mkinfit models -✔ | 1 36 | saemix parent models [73.7s] +✔ | 1 36 | saemix parent models [103.8s] ──────────────────────────────────────────────────────────────────────────────── 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] +✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.4s] ✔ | 11 | Processing of residue series ✔ | 10 | Fitting the SFORB model [3.8s] ✔ | 1 | Summaries of old mkinfit objects ✔ | 5 | Summary [0.2s] -✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.4s] -✔ | 9 | Hypothesis tests [8.8s] +✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.2s] +✔ | 9 | Hypothesis tests [8.1s] ✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.2s] ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 251.2 s +Duration: 266.0 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 3 | PASS 270 ] +[ FAIL 0 | WARN 0 | SKIP 3 | PASS 268 ] Error while shutting down parallel: unable to terminate some child processes diff --git a/tests/testthat/illparms_hfits_synth_no_ranef_auto.txt b/tests/testthat/illparms_hfits_synth_no_ranef_auto.txt deleted file mode 100644 index a64ed222..00000000 --- a/tests/testthat/illparms_hfits_synth_no_ranef_auto.txt +++ /dev/null @@ -1,4 +0,0 @@ - error -degradation const tc - SFO sd(parent_0) - FOMC b.1 diff --git a/tests/testthat/print_hfits_synth_no_ranef_auto.txt b/tests/testthat/print_hfits_synth_no_ranef_auto.txt deleted file mode 100644 index 9af1cbcd..00000000 --- a/tests/testthat/print_hfits_synth_no_ranef_auto.txt +++ /dev/null @@ -1,9 +0,0 @@ -<mhmkin> object -Status of individual fits: - - error -degradation const tc - SFO OK OK - FOMC OK OK - -OK: Fit terminated successfully diff --git a/tests/testthat/summary_hfit_sfo_tc.txt b/tests/testthat/summary_hfit_sfo_tc.txt index bb5bf6fb..0a61f75f 100644 --- a/tests/testthat/summary_hfit_sfo_tc.txt +++ b/tests/testthat/summary_hfit_sfo_tc.txt @@ -17,13 +17,22 @@ Using 300, 100 iterations and 9 chains Variance model: Two-component variance function -Mean of starting values for individual parameters: +Starting values for degradation parameters: parent_0 log_k_parent 101 -3 Fixed degradation parameter values: None +Starting values for random effects (square root of initial entries in omega): + parent_0 log_k_parent +parent_0 4 0.0 +log_k_parent 0 0.4 + +Starting values for error model parameters: +a.1 b.1 + 1 1 + Results: Likelihood computed by importance sampling diff --git a/tests/testthat/summary_saem_dfop_sfo_s.txt b/tests/testthat/summary_saem_dfop_sfo_s.txt index 7c337843..6468ff17 100644 --- a/tests/testthat/summary_saem_dfop_sfo_s.txt +++ b/tests/testthat/summary_saem_dfop_sfo_s.txt @@ -22,7 +22,7 @@ Using 300, 100 iterations and 4 chains Variance model: Two-component variance function -Mean of starting values for individual parameters: +Starting values for degradation parameters: parent_0 k_m1 f_parent_to_m1 k1 k2 1e+02 7e-03 5e-01 1e-01 2e-02 g @@ -31,6 +31,19 @@ Mean of starting values for individual parameters: Fixed degradation parameter values: None +Starting values for random effects (square root of initial entries in omega): + parent_0 k_m1 f_parent_to_m1 k1 k2 g +parent_0 101 0 0 0 0 0 +k_m1 0 1 0 0 0 0 +f_parent_to_m1 0 0 1 0 0 0 +k1 0 0 0 1 0 0 +k2 0 0 0 0 1 0 +g 0 0 0 0 0 1 + +Starting values for error model parameters: +a.1 b.1 + 1 1 + Results: Likelihood computed by importance sampling diff --git a/tests/testthat/test_mhmkin.R b/tests/testthat/test_mhmkin.R index 93333ac1..e2339f28 100644 --- a/tests/testthat/test_mhmkin.R +++ b/tests/testthat/test_mhmkin.R @@ -46,14 +46,4 @@ test_that("Multiple hierarchical kinetic models can be fitted and diagnosed", { print(fits_synth_const), "print_fits_synth_const.txt") - hfits_no_ranef_auto <- update(hfits, no_random_effect = "auto", auto_ranef_threshold = 2) - - expect_known_output( - print(hfits_no_ranef_auto), - "print_hfits_synth_no_ranef_auto.txt") - - expect_known_output( - print(illparms(hfits_no_ranef_auto)), - "illparms_hfits_synth_no_ranef_auto.txt") - }) |