Really test anova output, test covariates

5 files changed, 38 insertions, 52 deletions

diff --git a/R/saem.R b/R/saem.R
index 79b4b9ee..cf67b8e1 100644
--- a/R/saem.R
+++ b/R/saem.R
@@ -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)
-