Merge branch 'main' into dev

9 files changed, 228 insertions, 174 deletions

diff --git a/tests/testthat/Rplots.pdf b/tests/testthat/Rplots.pdf
new file mode 100644
index 00000000..2638aff8
--- /dev/null
+++ b/tests/testthat/Rplots.pdf
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 ed9168fb..c733f84f 100644
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diff --git a/tests/testthat/print_dfop_saem_1.txt b/tests/testthat/print_dfop_saem_1.txt
index f7354320..3a1f1667 100644
--- a/tests/testthat/print_dfop_saem_1.txt
+++ b/tests/testthat/print_dfop_saem_1.txt
@@ -18,6 +18,6 @@ log_k1       -2.71 -2.94  -2.49
 log_k2       -4.14 -4.26  -4.01
 g_qlogis     -0.36 -0.54  -0.17
 a.1           0.93  0.69   1.17
-b.1           0.05  0.04   0.06
+b.1           0.05  0.04   0.05
 SD.log_k1     0.37  0.23   0.51
 SD.log_k2     0.23  0.14   0.31
diff --git a/tests/testthat/summary_hfit_sfo_tc.txt b/tests/testthat/summary_hfit_sfo_tc.txt
index 0618c715..ba7d1362 100644
--- a/tests/testthat/summary_hfit_sfo_tc.txt
+++ b/tests/testthat/summary_hfit_sfo_tc.txt
@@ -43,7 +43,7 @@ Optimised parameters:
                  est. lower upper
 parent_0        92.52 89.11  95.9
 log_k_parent    -1.66 -2.07  -1.3
-a.1              2.03  1.60   2.5
+a.1              2.03  1.61   2.5
 b.1              0.09  0.07   0.1
 SD.log_k_parent  0.51  0.22   0.8
 
@@ -57,7 +57,7 @@ SD.log_k_parent  0.5   0.2   0.8
 
 Variance model:
     est. lower upper
-a.1 2.03  1.60   2.5
+a.1 2.03  1.61   2.5
 b.1 0.09  0.07   0.1
 
 Backtransformed parameters:
diff --git a/tests/testthat/summary_saem_dfop_sfo_s.txt b/tests/testthat/summary_saem_dfop_sfo_s.txt
index 6468ff17..a19824ce 100644
--- a/tests/testthat/summary_saem_dfop_sfo_s.txt
+++ b/tests/testthat/summary_saem_dfop_sfo_s.txt
@@ -86,7 +86,7 @@ SD.g              0.21   0.06   0.4
 
 Variance model:
     est. lower upper
-a.1 0.93  0.79  1.06
+a.1 0.93  0.80  1.06
 b.1 0.05  0.05  0.06
 
 Resulting formation fractions:
diff --git a/tests/testthat/test_mixed.R b/tests/testthat/test_mixed.R
index d8ad4417..b9715096 100644
--- a/tests/testthat/test_mixed.R
+++ b/tests/testthat/test_mixed.R
@@ -89,6 +89,7 @@ test_that("saemix results are reproducible for biphasic fits", {
 test_that("Reading spreadsheets, finding ill-defined parameters and covariate modelling", {
 
   skip_on_cran()
+  skip_on_travis()
 
   data_path <- system.file(
     "testdata", "lambda-cyhalothrin_soil_efsa_2014.xlsx",
@@ -115,6 +116,7 @@ test_that("Reading spreadsheets, finding ill-defined parameters and covariate mo
 test_that("SFO-SFO saemix specific analytical solution work", {
 
   skip_on_cran()
+  skip_on_travis()
 
   SFO_SFO <- mkinmod(DMTA = mkinsub("SFO", "M23"),
     M23 = mkinsub("SFO"), quiet = TRUE)
diff --git a/tests/testthat/test_multistart.R b/tests/testthat/test_multistart.R
index dda0ea23..36aa63f7 100644
--- a/tests/testthat/test_multistart.R
+++ b/tests/testthat/test_multistart.R
@@ -44,13 +44,16 @@ test_that("multistart works for saem.mmkin models", {
   vdiffr::expect_doppelganger("mixed model fit for saem object with mkin transformations", plot_dfop_sfo_saem_m)
 
   llhist_sfo <- function() llhist(saem_sfo_s_multi)
-  parplot_sfo <- function() parplot(saem_sfo_s_multi, ylim = c(0.5, 2))
+  parplot_sfo <- function() parplot(saem_sfo_s_multi, ylim = c(0.5, 2), las = 1)
   vdiffr::expect_doppelganger("llhist for sfo fit", llhist_sfo)
   vdiffr::expect_doppelganger("parplot for sfo fit", parplot_sfo)
 
   llhist_dfop_sfo <- function() llhist(saem_dfop_sfo_m_multi)
-  parplot_dfop_sfo <- function() parplot(saem_dfop_sfo_m_multi,
-    ylim = c(0.5, 2), llquant = 0.5)
+  parplot_dfop_sfo <- function() {
+    par(mar = c(10.1, 4.1, 2.1, 2.1))
+    parplot(saem_dfop_sfo_m_multi,
+      ylim = c(0.5, 2), llquant = 0.5, las = 2)
+  }
 
   vdiffr::expect_doppelganger("llhist for dfop sfo fit", llhist_dfop_sfo)
   vdiffr::expect_doppelganger("parplot for dfop sfo fit", parplot_dfop_sfo)
diff --git a/tests/testthat/test_saemix_parent.R b/tests/testthat/test_saemix_parent.R
index 7fbecd0c..8ac04614 100644
--- a/tests/testthat/test_saemix_parent.R
+++ b/tests/testthat/test_saemix_parent.R
@@ -148,3 +148,30 @@ test_that("We can also use mkin solution methods for saem", {
   rel_diff <- abs(distimes_dfop_analytical - distimes_dfop) / distimes_dfop
   expect_true(all(rel_diff < 0.01))
 })
+
+test_that("illparms finds a single random effect that is ill-defined", {
+  set.seed(123456)
+  n <- 4
+  SFO <- mkinmod(parent = mkinsub("SFO"))
+  sfo_pop <- list(parent_0 = 100, k_parent = 0.03)
+  sfo_parms <- as.matrix(data.frame(
+      k_parent = rlnorm(n, log(sfo_pop$k_parent), 0.001)))
+  sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120)
+  err_1 = list(const = 1, prop = 0.05)
+  tc <- function(value) sigma_twocomp(value, err_1$const, err_1$prop)
+  set.seed(123456)
+  ds_sfo <- lapply(1:n, function(i) {
+    ds_mean <- mkinpredict(SFO, sfo_parms[i, ],
+      c(parent = sfo_pop$parent_0), sampling_times)
+    add_err(ds_mean, tc, n = 1)[[1]]
+  })
+  m_mmkin <- mmkin("SFO", ds_sfo, error_model = "tc", quiet = TRUE, cores = n_cores)
+  m_saem_1 <- saem(m_mmkin)
+  expect_equal(
+    as.character(illparms(m_saem_1)),
+    c("sd(parent_0)", "sd(log_k_parent)"))
+  m_saem_2 <- saem(m_mmkin, no_random_effect = "parent_0")
+  expect_equal(
+    as.character(illparms(m_saem_2)),
+    "sd(log_k_parent)")
+})
diff --git a/tests/testthat/test_water-sediment.R b/tests/testthat/test_water-sediment.R
new file mode 100644
index 00000000..6d5693c9
--- /dev/null
+++ b/tests/testthat/test_water-sediment.R
@@ -0,0 +1,17 @@
+# Issue #13 on github
+water_sed_no_sed_sink <- mkinmod(
+  use_of_ff = "min",
+  water = mkinsub("SFO", "sediment"),
+  sediment = mkinsub("SFO", "water", sink = FALSE))
+
+ws_data <- FOCUS_D
+levels(ws_data$name) <- c("water", "sediment")
+
+test_that("An reversible reaction with the sink turned off in the second compartment works", {
+  # Solution method "analytical" was previously available, but erroneous
+  expect_error(
+    ws_fit_no_sed_sink <- mkinfit(water_sed_no_sed_sink, ws_data, quiet = TRUE, solution_type = "analytical"),
+    "Analytical solution not implemented")
+  ws_fit_no_sed_sink_default <- mkinfit(water_sed_no_sed_sink, ws_data, quiet = TRUE)
+  expect_equal(ws_fit_no_sed_sink_default$solution_type, "deSolve")
+})