Increase test coverage

Also, using mkin analytical solutions for more than one observed
variable is not supported (but could be if out_values would be
reordered).

6 files changed, 92 insertions, 20 deletions

diff --git a/R/saem.R b/R/saem.R
index 83de97b0..a9f97d23 100644
--- a/R/saem.R
+++ b/R/saem.R
@@ -307,6 +307,10 @@ saemix_model <- function(object, solution_type = "auto",
 
   mkin_model <- object[[1]]$mkinmod
 
+  if (length(mkin_model$spec) > 1 & solution_type[1] == "analytical") {
+    stop("mkin analytical solutions not supported for more thane one observed variable")
+  }
+
   degparms_optim <-  mean_degparms(object, test_log_parms = test_log_parms)
   na_degparms <- names(which(is.na(degparms_optim)))
   if (length(na_degparms) > 0) {
diff --git a/inst/rmarkdown/templates/hierarchical_kinetics/skeleton/skeleton.Rmd b/inst/rmarkdown/templates/hierarchical_kinetics/skeleton/skeleton.Rmd
index cb328308..71d62677 100644
--- a/inst/rmarkdown/templates/hierarchical_kinetics/skeleton/skeleton.Rmd
+++ b/inst/rmarkdown/templates/hierarchical_kinetics/skeleton/skeleton.Rmd
@@ -15,7 +15,6 @@ library(mkin)
 library(knitr)
 library(saemix)
 library(parallel)
-library(readxl)
 ```
 
 ```{r n_cores, cache = FALSE}
@@ -186,6 +185,13 @@ illparms(parent_best_pH_2)
 parms(parent_best_pH_2, ci = TRUE) |> kable(digits = 3)
 ```
 
+The endpoints corresponding to the median pH in the tested soils
+are shown below.
+
+```{r dependson = "parent-best-pH"}
+endpoints(parent_best_pH_2)
+```
+
 ```{r}
 stopCluster(cl)
 ```
@@ -280,6 +286,13 @@ plot(path_1_refined)
 parms(path_1_refined, ci = TRUE) |> kable(digits = 3)
 ```
 
+The pathway endpoints corresponding to the median pH in the tested soils
+are shown below.
+
+```{r dependson = "parent-best-pH"}
+endpoints(parent_best_pH_2)
+```
+
 ```{r}
 stopCluster(cl)
 ```
@@ -324,7 +337,6 @@ tex_listing(path_1_refined,
 ## Session info
 
 ```{r echo = FALSE, cache = FALSE}
-parallel::stopCluster(cl)
 sessionInfo()
 ```
 
diff --git a/log/check.log b/log/check.log
index b7f6068c..b58119ef 100644
--- a/log/check.log
+++ b/log/check.log
@@ -21,7 +21,8 @@ Maintainer: ‘Johannes Ranke <johannes.ranke@jrwb.de>’
 * checking whether package ‘mkin’ can be installed ... OK
 * checking installed package size ... OK
 * checking package directory ... OK
-* checking for future file timestamps ... OK
+* checking for future file timestamps ... NOTE
+unable to verify current time
 * checking ‘build’ directory ... OK
 * checking DESCRIPTION meta-information ... OK
 * checking top-level files ... OK
@@ -70,5 +71,9 @@ Maintainer: ‘Johannes Ranke <johannes.ranke@jrwb.de>’
 * checking for detritus in the temp directory ... OK
 * DONE
 
-Status: OK
+Status: 1 NOTE
+See
+  ‘/home/jranke/git/mkin/mkin.Rcheck/00check.log’
+for details.
+
 
diff --git a/log/test.log b/log/test.log
index fa808f22..cec5e7ed 100644
--- a/log/test.log
+++ b/log/test.log
@@ -1,39 +1,39 @@
 ℹ Testing mkin
 ✔ | F W S  OK | Context
 ✔ |         5 | AIC calculation
-✔ |         5 | Analytical solutions for coupled models [1.6s]
+✔ |         5 | Analytical solutions for coupled models [1.5s]
 ✔ |         5 | Calculation of Akaike weights
 ✔ |         3 | Export dataset for reading into CAKE
-✔ |         7 | Use of precompiled symbols in mkinpredict [3.3s]
+✔ |         6 | Use of precompiled symbols in mkinpredict [3.2s]
 ✔ |        12 | Confidence intervals and p-values [0.4s]
-✔ |     1  12 | Dimethenamid data from 2018 [13.4s]
+✔ |     1  12 | Dimethenamid data from 2018 [12.5s]
 ────────────────────────────────────────────────────────────────────────────────
 Skip ('test_dmta.R:88'): 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 [2.5s]
+✔ |        14 | Error model fitting [2.4s]
 ✔ |         5 | Time step normalisation
 ✔ |         4 | Calculation of FOCUS chi2 error levels [0.3s]
-✔ |        14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [0.5s]
-✔ |         4 | Test fitting the decline of metabolites from their maximum [0.3s]
+✔ |        14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [0.4s]
+✔ |         4 | Test fitting the decline of metabolites from their maximum [0.2s]
 ✔ |         1 | Fitting the logistic model [0.1s]
-✔ |        10 | Batch fitting and diagnosing hierarchical kinetic models [19.8s]
-✔ |     1  11 | Nonlinear mixed-effects models [6.1s]
+✔ |        10 | Batch fitting and diagnosing hierarchical kinetic models [19.1s]
+✔ |     1  17 | Nonlinear mixed-effects models [294.0s]
 ────────────────────────────────────────────────────────────────────────────────
 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 [0.4s]
+✔ |        10 | Special cases of mkinfit calls [0.3s]
 ✔ |         3 | mkinfit features [0.5s]
 ✔ |         8 | mkinmod model generation and printing
 ✔ |         3 | Model predictions with mkinpredict [0.1s]
-✔ |        12 | Multistart method for saem.mmkin models [21.7s]
+✔ |        12 | Multistart method for saem.mmkin models [23.2s]
 ✔ |        16 | Evaluations according to 2015 NAFTA guidance [1.5s]
 ✔ |         9 | Nonlinear mixed-effects models with nlme [3.8s]
-✔ |        15 | Plotting [4.7s]
+✔ |        15 | Plotting [4.8s]
 ✔ |         4 | Residuals extracted from mkinfit models
-✔ |     1  36 | saemix parent models [32.0s]
+✔ |     1  36 | saemix parent models [30.7s]
 ────────────────────────────────────────────────────────────────────────────────
 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
@@ -44,15 +44,15 @@ Reason: This still takes almost 2.5 minutes although we do not solve ODEs
 ✔ |         1 | Summaries of old mkinfit objects
 ✔ |         5 | Summary
 ✔ |         4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [0.8s]
-✔ |         9 | Hypothesis tests [3.0s]
+✔ |         9 | Hypothesis tests [2.9s]
 ✔ |         4 | Calculation of maximum time weighted average concentrations (TWAs) [0.7s]
 
 ══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 120.2 s
+Duration: 406.1 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 277 ]
+[ FAIL 0 | WARN 0 | SKIP 3 | PASS 282 ]
diff --git a/tests/testthat/test_compiled_symbols.R b/tests/testthat/test_compiled_symbols.R
index 0c8aff99..740781cf 100644
--- a/tests/testthat/test_compiled_symbols.R
+++ b/tests/testthat/test_compiled_symbols.R
@@ -53,6 +53,6 @@ test_that("We can safely use compiled code", {
   } else {
     expect_true(file.remove("test_dlls/sfo_sfo.so"))
   }
-  expect_true(file.remove("test_dlls"))
+  suppressWarnings(file.remove("test_dlls"))
 })
 
diff --git a/tests/testthat/test_mixed.R b/tests/testthat/test_mixed.R
index 39a332f5..c60d1421 100644
--- a/tests/testthat/test_mixed.R
+++ b/tests/testthat/test_mixed.R
@@ -83,3 +83,54 @@ test_that("saemix results are reproducible for biphasic fits", {
   expect_true(all(ci_dfop_sfo_s_d[no_k2, "lower"] < dfop_sfo_pop[no_k2]))
   expect_true(all(ci_dfop_sfo_s_d[no_k1, "upper"] > dfop_sfo_pop[no_k1]))
 })
+
+test_that("Reading spreadsheets, finding ill-defined parameters and covariate modelling", {
+
+  skip_on_cran()
+
+  data_path <- system.file(
+    "testdata", "lambda-cyhalothrin_soil_efsa_2014.xlsx",
+    package = "mkin")
+  ds_lambda <- read_spreadsheet(data_path, valid_datasets = c(1:4, 7:13))
+  covariates <- attr(ds_lambda, "covariates")
+
+  lambda_sforb <- mmkin("SFORB", ds_lambda, quiet = TRUE,
+    cores = n_cores,
+    error_model = "const")
+  lambda_sforb_saem_pH <- saem(lambda_sforb, covariates = covariates,
+    covariate_models = list(log_k_lambda_bound_free ~ pH))
+  expect_equal(
+    as.character(illparms(lambda_sforb_saem_pH)),
+    c("sd(lambda_free_0)", "sd(log_k_lambda_free_bound)"))
+
+  lambda_endpoints <- endpoints(lambda_sforb_saem_pH)
+  expect_equal(lambda_endpoints$covariates$pH, 6.45)
+  expect_equal(
+    round(as.numeric(lambda_endpoints$distimes), 0),
+    c(47, 422, 127, 7, 162))
+})
+
+test_that("SFO-SFO saemix specific analytical solution work", {
+
+  skip_on_cran()
+
+  SFO_SFO <- mkinmod(DMTA = mkinsub("SFO", "M23"),
+    M23 = mkinsub("SFO"), quiet = TRUE)
+  mmkin_sfo_sfo <- mmkin(list("SFO-SFO" = SFO_SFO), dmta_ds, quiet = TRUE,
+    cores = n_cores,
+    error_model = "const")
+  saem_sfo_sfo_saemix_analytical <- saem(mmkin_sfo_sfo)
+
+  expect_error(saem(mmkin_sfo_sfo, solution_type = "analytical"), "not supported")
+
+  saem_sfo_sfo_mkin_eigen<- saem(mmkin_sfo_sfo, solution_type = "eigen")
+  expect_equal(
+    endpoints(saem_sfo_sfo_saemix_analytical),
+    endpoints(saem_sfo_sfo_mkin_eigen))
+
+  saem_sfo_sfo_mkin_desolve <- saem(mmkin_sfo_sfo, solution_type = "deSolve")
+  expect_equal(
+    endpoints(saem_sfo_sfo_saemix_analytical),
+    endpoints(saem_sfo_sfo_mkin_desolve))
+
+})