Increase test coverage

3 files changed, 37 insertions, 12 deletions

diff --git a/test.log b/test.log
index 5dae193a..128ea38b 100644
--- a/test.log
+++ b/test.log
@@ -6,30 +6,30 @@ Testing mkin
 ✔ |   4       | Calculation of FOCUS chi2 error levels [2.2 s]
 ✔ |   4       | Fitting the SFORB model [1.7 s]
 ✔ |   5       | Calculation of Akaike weights
-✔ |  10       | Confidence intervals and p-values [9.5 s]
-✔ |  14       | Error model fitting [38.0 s]
+✔ |  10       | Confidence intervals and p-values [9.4 s]
+✔ |  14       | Error model fitting [38.1 s]
 ✔ |   6       | Test fitting the decline of metabolites from their maximum [0.8 s]
 ✔ |   1       | Fitting the logistic model [0.9 s]
 ✔ |   1       | Test dataset class mkinds used in gmkin
 ✔ |  12       | Special cases of mkinfit calls [2.3 s]
 ✔ |   9       | mkinmod model generation and printing [0.2 s]
-✔ |   3       | Model predictions with mkinpredict [0.3 s]
+✔ |   3       | Model predictions with mkinpredict [0.4 s]
 ✔ |  16       | Evaluations according to 2015 NAFTA guidance [4.1 s]
-✔ |   5       | Nonlinear mixed-effects models [11.1 s]
-✔ |   4       | Calculation of maximum time weighted average concentrations (TWAs) [2.3 s]
+✔ |   8       | Nonlinear mixed-effects models [11.9 s]
+✔ |   4       | Calculation of maximum time weighted average concentrations (TWAs) [2.2 s]
 ✔ |   3       | Summary
-✔ |  14       | Plotting [4.8 s]
+✔ |  14       | Plotting [4.9 s]
 ✔ |   4       | AIC calculation
 ✔ |   4       | Residuals extracted from mkinfit models
 ✔ |   2       | Complex test case from Schaefer et al. (2007) Piacenza paper [5.3 s]
 ✔ |   1       | Summaries of old mkinfit objects
-✔ |   4       | Results for synthetic data established in expertise for UBA (Ranke 2014) [6.9 s]
-✔ |   9       | Hypothesis tests [36.8 s]
+✔ |   4       | Results for synthetic data established in expertise for UBA (Ranke 2014) [7.1 s]
+✔ |   9       | Hypothesis tests [36.9 s]
 
 ══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 130.9 s
+Duration: 132.2 s
 
-OK:       150
+OK:       153
 Failed:   0
 Warnings: 0
 Skipped:  0
diff --git a/tests/testthat/FOCUS_2006_D.csf b/tests/testthat/FOCUS_2006_D.csf
index de5ee0a4..dfccc13f 100644
--- a/tests/testthat/FOCUS_2006_D.csf
+++ b/tests/testthat/FOCUS_2006_D.csf
@@ -5,7 +5,7 @@ Description:
 MeasurementUnits: % AR
 TimeUnits: days
 Comments: Created using mkin::CAKE_export
-Date: 2020-04-09
+Date: 2020-04-16
 Optimiser: IRLS
 
 [Data]
diff --git a/tests/testthat/test_nlme.R b/tests/testthat/test_nlme.R
index efbc231a..d272af38 100644
--- a/tests/testthat/test_nlme.R
+++ b/tests/testthat/test_nlme.R
@@ -1,5 +1,7 @@
 context("Nonlinear mixed-effects models")
 
+library(nlme)
+
 test_that("nlme_function works correctly", {
 
   sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120)
@@ -47,8 +49,27 @@ test_that("nlme_function works correctly", {
 
   expect_equal(m_nlme_raw$coefficients, m_nlme_mkin$coefficients)
 
+  m_nlme_mmkin <- nlme(f)
+
+  m_nlme_raw_2 <- nlme(value ~ SSasymp(time, 0, parent_0, log_k_parent_sink),
+    data = grouped_data,
+    fixed = parent_0 + log_k_parent_sink ~ 1,
+    random = pdDiag(parent_0 + log_k_parent_sink ~ 1),
+    start = mean_degparms(f, random = TRUE))
+
+  expect_equal(m_nlme_raw_2$coefficients, m_nlme_mmkin$coefficients)
+
+  anova_nlme <- anova(m_nlme_mmkin, m_nlme_raw) # mmkin needs to go first as we had
+  # to adapt the method due to
+  # https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17761
+
+  # We get a slightly lower AIC with the improved starting values used within
+  # nlme.mmkin
+  expect_lt(anova_nlme["m_nlme_mmkin", "AIC"],
+    anova_nlme["m_nlme_raw", "AIC"])
+
   m_nlme_raw_up_1 <- update(m_nlme_raw, random = log_k_parent_sink ~ 1)
-  # The following two calls give an error although they should
+  # The following three calls give an error although they should
   # do the same as the call above
   # The error occurs in the evaluation of the modelExpression in the
   # call to .C(fit_nlme, ...)
@@ -58,16 +79,20 @@ test_that("nlme_function works correctly", {
   #   fixed = parent_0 + log_k_parent_sink ~ 1,
   #   random = log_k_parent_sink ~ 1,
   #   start = mean_dp)
+  # update(m_nlme_mmkin, random = pdDiag(log_k_parent_sink ~ 1),
+  #   start = c(parent_0 = 100, log_k_parent_sink = 0.1))
 
   m_nlme_raw_up_2 <- update(m_nlme_raw, random = parent_0 ~ 1)
   m_nlme_mkin_up_2 <- update(m_nlme_mkin, random = parent_0 ~ 1)
   expect_equal(m_nlme_raw_up_2$coefficients, m_nlme_mkin_up_2$coefficients)
 
   expect_silent(tmp <- update(m_nlme_mkin))
+  expect_silent(tmp <- update(m_nlme_mmkin))
 })
 
 test_that("nlme_function works correctly in other cases", {
 
+  skip_on_cran()
   dt50_in <- c(400, 800, 1200, 1600, 2000)
   k_in <- log(2) / dt50_in
   SFO <- mkinmod(parent = mkinsub("SFO"))