diff options
| -rw-r--r-- | R/saem.R | 5 | ||||
| -rw-r--r-- | log/test.log | 22 | ||||
| -rw-r--r-- | tests/testthat/anova_sfo_saem.txt | 7 | ||||
| -rw-r--r-- | tests/testthat/test_saemix_parent.R | 20 | ||||
| -rw-r--r-- | vignettes/web_only/multistart.R | 36 |
5 files changed, 38 insertions, 52 deletions
@@ -738,6 +738,11 @@ update.saem.mmkin <- function(object, ..., evaluate = TRUE) { # so we need to fix this so we do not have to export saem.mmkin in # addition to the S3 method call[[1]] <- saem + + # We also need to provide the mmkin object in the call, so it + # will also be found when called by testthat or pkgdown + call[[2]] <- object$mmkin + update_arguments <- match.call(expand.dots = FALSE)$... if (length(update_arguments) > 0) { diff --git a/log/test.log b/log/test.log index d9dcffb9..6f6d0f23 100644 --- a/log/test.log +++ b/log/test.log @@ -1,11 +1,11 @@ ℹ Testing mkin ✔ | F W S OK | Context ✔ | 5 | AIC calculation -✔ | 5 | Analytical solutions for coupled models [3.3s] +✔ | 5 | Analytical solutions for coupled models [3.2s] ✔ | 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 [32.1s] +✔ | 1 12 | Dimethenamid data from 2018 [31.8s] ──────────────────────────────────────────────────────────────────────────────── Skip (test_dmta.R:98:3): Different backends get consistent results for SFO-SFO3+, dimethenamid data Reason: Fitting this ODE model with saemix takes about 15 minutes on my system @@ -16,7 +16,7 @@ Reason: Fitting this ODE model with saemix takes about 15 minutes on my system ✔ | 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] -✔ | 7 | Batch fitting and diagnosing hierarchical kinetic models [14.2s] +✔ | 7 | Batch fitting and diagnosing hierarchical kinetic models [14.6s] ✔ | 1 12 | Nonlinear mixed-effects models [0.3s] ──────────────────────────────────────────────────────────────────────────────── Skip (test_mixed.R:74:3): saemix results are reproducible for biphasic fits @@ -26,18 +26,18 @@ Reason: Fitting with saemix takes around 10 minutes when using deSolve ✔ | 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] -✔ | 5 | Multistart method for saem.mmkin models [34.8s] +✔ | 3 | Model predictions with mkinpredict [0.4s] +✔ | 7 | Multistart method for saem.mmkin models [36.0s] ✔ | 16 | Evaluations according to 2015 NAFTA guidance [2.3s] -✔ | 9 | Nonlinear mixed-effects models with nlme [8.5s] +✔ | 9 | Nonlinear mixed-effects models with nlme [8.6s] ✔ | 16 | Plotting [10.0s] ✔ | 4 | Residuals extracted from mkinfit models -✔ | 1 35 | saemix parent models [65.3s] +✔ | 1 36 | saemix parent models [71.5s] ──────────────────────────────────────────────────────────────────────────────── -Skip (test_saemix_parent.R:142:3): We can also use mkin solution methods for saem +Skip (test_saemix_parent.R:152:3): 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 [1.5s] +✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.4s] ✔ | 11 | Processing of residue series ✔ | 7 | Fitting the SFORB model [3.7s] ✔ | 1 | Summaries of old mkinfit objects @@ -47,11 +47,11 @@ Reason: This still takes almost 2.5 minutes although we do not solve ODEs ✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.2s] ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 198.3 s +Duration: 206.0 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 258 ] +[ FAIL 0 | WARN 0 | SKIP 3 | PASS 261 ] diff --git a/tests/testthat/anova_sfo_saem.txt b/tests/testthat/anova_sfo_saem.txt index e69de29b..4a21e81f 100644 --- a/tests/testthat/anova_sfo_saem.txt +++ b/tests/testthat/anova_sfo_saem.txt @@ -0,0 +1,7 @@ +Data: 262 observations of 1 variable(s) grouped in 15 datasets + + npar AIC BIC Lik Chisq Df Pr(>Chisq) +sfo_saem_1_reduced 5 1310 1313 -650 +sfo_saem_1_reduced_mkin 5 1310 1313 -650 0 0 +sfo_saem_1 6 1312 1316 -650 0 1 1 +sfo_saem_1_mkin 6 1310 1315 -649 1 0 diff --git a/tests/testthat/test_saemix_parent.R b/tests/testthat/test_saemix_parent.R index 193dcdcd..39efa18f 100644 --- a/tests/testthat/test_saemix_parent.R +++ b/tests/testthat/test_saemix_parent.R @@ -53,11 +53,21 @@ test_that("Parent fits using saemix are correctly implemented", { expect_equal(round(s_sfo_nlme_1$confint_back["k_parent", "est."], 3), round(s_sfo_saem_1$confint_back["k_parent", "est."], 3)) - # Compare fits - expect_known_output(anova(sfo_saem_1, sfo_saem_1_reduced, - sfo_saem_1_mkin, sfo_saem_1_reduced_mkin, test = TRUE), - file = "anova_sfo_saem.txt" - ) + # Compare fits with heavy rounding to avoid platform dependent results + anova_sfo <- anova( + sfo_saem_1, sfo_saem_1_reduced, + sfo_saem_1_mkin, sfo_saem_1_reduced_mkin, + test = TRUE) + anova_sfo_rounded <- round(anova_sfo, 0) + expect_known_output(print(anova_sfo_rounded), file = "anova_sfo_saem.txt") + + # Check the influence of an invented covariate + set.seed(123456) # In my first attempt I hit a false positive by chance... + pH <- data.frame(pH = runif(15, 5, 8), row.names = as.character(1:15)) + sfo_saem_pH <- update(sfo_saem_1_reduced_mkin, covariates = pH, + covariate_models = list(log_k_parent ~ pH)) + # We expect that this is not significantly better, as the covariate values were completely random + expect_true(anova(sfo_saem_1_reduced_mkin, sfo_saem_pH, test = TRUE)[2, "Pr(>Chisq)"] > 0.05) # FOMC mmkin_fomc_1 <- mmkin("FOMC", ds_fomc, quiet = TRUE, error_model = "tc", cores = n_cores) diff --git a/vignettes/web_only/multistart.R b/vignettes/web_only/multistart.R deleted file mode 100644 index 36612443..00000000 --- a/vignettes/web_only/multistart.R +++ /dev/null @@ -1,36 +0,0 @@ -## ----------------------------------------------------------------------------- -library(mkin) -dmta_ds <- lapply(1:7, function(i) { - ds_i <- dimethenamid_2018$ds[[i]]$data - ds_i[ds_i$name == "DMTAP", "name"] <- "DMTA" - ds_i$time <- ds_i$time * dimethenamid_2018$f_time_norm[i] - ds_i -}) -names(dmta_ds) <- sapply(dimethenamid_2018$ds, function(ds) ds$title) -dmta_ds[["Elliot"]] <- rbind(dmta_ds[["Elliot 1"]], dmta_ds[["Elliot 2"]]) -dmta_ds[["Elliot 1"]] <- dmta_ds[["Elliot 2"]] <- NULL - -## ----------------------------------------------------------------------------- -f_mmkin <- mmkin("DFOP", dmta_ds, error_model = "tc", cores = 7, quiet = TRUE) -f_saem_full <- saem(f_mmkin) -illparms(f_saem_full) - -## ----------------------------------------------------------------------------- -f_saem_full_multi <- multistart(f_saem_full, n = 16, cores = 16) -parhist(f_saem_full_multi) - -## ----------------------------------------------------------------------------- -f_saem_reduced <- update(f_saem_full, no_random_effect = "log_k2") -illparms(f_saem_reduced) -f_saem_reduced_multi <- multistart(f_saem_reduced, n = 16, cores = 16) -parhist(f_saem_reduced_multi, lpos = "topright") - -## ----------------------------------------------------------------------------- -llhist(f_saem_reduced_multi) - -## ----------------------------------------------------------------------------- -parhist(f_saem_reduced_multi, lpos = "topright", llmin = -326, ylim = c(0.5, 2)) - -## ----------------------------------------------------------------------------- -anova(f_saem_full, best(f_saem_reduced_multi), test = TRUE) - |