Make saemix and corresponding tests optional

Address release critical check and test issues

7 files changed, 71 insertions, 50 deletions

diff --git a/tests/testthat/print_mmkin_biphasic_mixed.txt b/tests/testthat/print_mmkin_biphasic_mixed.txt
index 3d92b120..11e11bfc 100644
--- a/tests/testthat/print_mmkin_biphasic_mixed.txt
+++ b/tests/testthat/print_mmkin_biphasic_mixed.txt
@@ -21,6 +21,6 @@ OK: No warnings
 
 Mean fitted parameters:
        parent_0        log_k_m1 f_parent_qlogis          log_k1          log_k2 
-        100.700          -6.299          -0.078          -3.094          -3.954 
+        100.702          -5.347          -0.078          -2.681          -4.366 
        g_qlogis 
-          0.027 
+         -0.335 
diff --git a/tests/testthat/print_nlme_biphasic.txt b/tests/testthat/print_nlme_biphasic.txt
index 98895d3a..f86bda76 100644
--- a/tests/testthat/print_nlme_biphasic.txt
+++ b/tests/testthat/print_nlme_biphasic.txt
@@ -11,19 +11,19 @@ d_m1/dt = + f_parent_to_m1 * ((k1 * g * exp(-k1 * time) + k2 * (1 - g)
 Data:
 509 observations of 2 variable(s) grouped in 15 datasets
 
-Log-likelihood: -1343
+Log-likelihood: -1329
 
 Fixed effects:
  list(parent_0 ~ 1, log_k_m1 ~ 1, f_parent_qlogis ~ 1, log_k1 ~ 1,      log_k2 ~ 1, g_qlogis ~ 1) 
        parent_0        log_k_m1 f_parent_qlogis          log_k1          log_k2 
-         100.37           -6.23           -0.08           -3.22           -4.10 
+         100.43           -5.34           -0.08           -2.90           -4.34 
        g_qlogis 
-          -0.10 
+          -0.19 
 
 Random effects:
  Formula: list(parent_0 ~ 1, log_k_m1 ~ 1, f_parent_qlogis ~ 1, log_k1 ~ 1,      log_k2 ~ 1, g_qlogis ~ 1)
  Level: ds
  Structure: Diagonal
         parent_0 log_k_m1 f_parent_qlogis log_k1 log_k2 g_qlogis Residual
-StdDev:        1    2e-04             0.3    0.7    0.8      0.3        3
+StdDev:        1      0.1             0.3    0.6    0.5      0.3        3
 
diff --git a/tests/testthat/setup_script.R b/tests/testthat/setup_script.R
index fd9635d1..2071e05c 100644
--- a/tests/testthat/setup_script.R
+++ b/tests/testthat/setup_script.R
@@ -156,7 +156,7 @@ DFOP_SFO <- mkinmod(
   m1 = mkinsub("SFO"),
   quiet = TRUE)
 dfop_sfo_pop <- list(parent_0 = 100,
-  k_m1 = 0.002, f_parent_to_m1 = 0.5,
+  k_m1 = 0.005, f_parent_to_m1 = 0.5,
   k1 = 0.05, k2 = 0.01, g = 0.5)
 syn_biphasic_parms <- as.matrix(data.frame(
   k1 = rlnorm(n_biphasic, log(dfop_sfo_pop$k1), log_sd),
@@ -178,19 +178,27 @@ ds_biphasic <- lapply(ds_biphasic_mean, function(ds) {
 })
 
 # Mixed model fits
-mmkin_sfo_1 <- mmkin("SFO", ds_sfo, quiet = TRUE, error_model = "tc")
-sfo_saem_1 <- saem(mmkin_sfo_1, quiet = TRUE, transformations = "saemix")
+saemix_available <- FALSE
+if (requireNamespace("saemix", quietly = TRUE)) {
+  if(packageVersion("saemix") > "3.1.9000") saemix_available <- TRUE
+}
+mmkin_sfo_1 <- mmkin("SFO", ds_sfo, quiet = TRUE, error_model = "tc", cores = n_cores)
+mmkin_dfop_1 <- mmkin("DFOP", ds_dfop, quiet = TRUE, cores = n_cores)
+mmkin_biphasic <- mmkin(list("DFOP-SFO" = DFOP_SFO), ds_biphasic, quiet = TRUE, cores = n_cores)
+mmkin_biphasic_mixed <- mixed(mmkin_biphasic)
 
-mmkin_dfop_1 <- mmkin("DFOP", ds_dfop, quiet = TRUE)
-dfop_saemix_1 <- saem(mmkin_dfop_1, quiet = TRUE, transformations = "mkin")
-dfop_saemix_2 <- saem(mmkin_dfop_1, quiet = TRUE, transformations = "saemix")
 dfop_nlme_1 <- nlme(mmkin_dfop_1)
-
-mmkin_biphasic <- mmkin(list("DFOP-SFO" = DFOP_SFO), ds_biphasic, quiet = TRUE)
-mmkin_biphasic_mixed <- mixed(mmkin_biphasic)
 nlme_biphasic <- nlme(mmkin_biphasic)
-saem_biphasic_m <- saem(mmkin_biphasic, transformations = "mkin", quiet = TRUE)
-saem_biphasic_s <- saem(mmkin_biphasic, transformations = "saemix", quiet = TRUE)
+
+if (saemix_available) {
+  sfo_saem_1 <- saem(mmkin_sfo_1, quiet = TRUE, transformations = "saemix")
+
+  dfop_saemix_1 <- saem(mmkin_dfop_1, quiet = TRUE, transformations = "mkin")
+  dfop_saemix_2 <- saem(mmkin_dfop_1, quiet = TRUE, transformations = "saemix")
+
+  saem_biphasic_m <- saem(mmkin_biphasic, transformations = "mkin", quiet = TRUE)
+  saem_biphasic_s <- saem(mmkin_biphasic, transformations = "saemix", quiet = TRUE)
+}
 
 ds_uba <- lapply(experimental_data_for_UBA_2019[6:10],
   function(x) subset(x$data[c("name", "time", "value")]))
@@ -200,7 +208,10 @@ sfo_sfo_uba <- mkinmod(parent = mkinsub("SFO", "A1"),
 dfop_sfo_uba <- mkinmod(parent = mkinsub("DFOP", "A1"),
   A1 = mkinsub("SFO"), quiet = TRUE)
 f_uba_mmkin <- mmkin(list("SFO-SFO" = sfo_sfo_uba, "DFOP-SFO" = dfop_sfo_uba),
-  ds_uba, quiet = TRUE)
+  ds_uba, quiet = TRUE, cores = n_cores)
 f_uba_dfop_sfo_mixed <- mixed(f_uba_mmkin[2, ])
-f_uba_sfo_sfo_saem <- saem(f_uba_mmkin["SFO-SFO", ], quiet = TRUE, transformations = "saemix")
-f_uba_dfop_sfo_saem <- saem(f_uba_mmkin["DFOP-SFO", ], quiet = TRUE, transformations = "saemix")
+
+if (saemix_available) {
+  f_uba_sfo_sfo_saem <- saem(f_uba_mmkin["SFO-SFO", ], quiet = TRUE, transformations = "saemix")
+  f_uba_dfop_sfo_saem <- saem(f_uba_mmkin["DFOP-SFO", ], quiet = TRUE, transformations = "saemix")
+}
diff --git a/tests/testthat/summary_nlme_biphasic_s.txt b/tests/testthat/summary_nlme_biphasic_s.txt
index f9171748..65aead62 100644
--- a/tests/testthat/summary_nlme_biphasic_s.txt
+++ b/tests/testthat/summary_nlme_biphasic_s.txt
@@ -17,15 +17,15 @@ Data:
 
 Model predictions using solution type analytical 
 
-Fitted in test time 0 s using 2 iterations
+Fitted in test time 0 s using 3 iterations
 
 Variance model: Constant variance 
 
 Mean of starting values for individual parameters:
        parent_0        log_k_m1 f_parent_qlogis          log_k1          log_k2 
-         100.70           -6.30           -0.08           -3.09           -3.95 
+         100.70           -5.35           -0.08           -2.68           -4.37 
        g_qlogis 
-           0.03 
+          -0.33 
 
 Fixed degradation parameter values:
      value  type
@@ -34,40 +34,40 @@ m1_0     0 state
 Results:
 
    AIC  BIC logLik
-  2711 2766  -1343
+  2683 2738  -1329
 
 Optimised, transformed parameters with symmetric confidence intervals:
                 lower   est.  upper
-parent_0         99.5 100.37 101.23
-log_k_m1         -6.5  -6.23  -5.94
-f_parent_qlogis  -0.2  -0.08   0.08
-log_k1           -3.6  -3.22  -2.84
-log_k2           -4.5  -4.10  -3.68
-g_qlogis         -0.4  -0.10   0.17
+parent_0         99.6 100.43 101.26
+log_k_m1         -5.5  -5.34  -5.18
+f_parent_qlogis  -0.3  -0.08   0.09
+log_k1           -3.2  -2.90  -2.60
+log_k2           -4.6  -4.34  -4.07
+g_qlogis         -0.5  -0.19   0.08
 
 Correlation: 
                 prnt_0 lg_k_1 f_prn_ log_k1 log_k2
-log_k_m1        -0.185                            
-f_parent_qlogis -0.161  0.405                     
-log_k1           0.056 -0.014 -0.016              
-log_k2           0.025  0.011 -0.004  0.026       
-g_qlogis        -0.032 -0.046 -0.012 -0.109 -0.103
+log_k_m1        -0.177                            
+f_parent_qlogis -0.164  0.385                     
+log_k1           0.108 -0.017 -0.025              
+log_k2           0.036  0.054  0.008  0.096       
+g_qlogis        -0.068 -0.110 -0.030 -0.269 -0.267
 
 Random effects:
  Formula: list(parent_0 ~ 1, log_k_m1 ~ 1, f_parent_qlogis ~ 1, log_k1 ~ 1,      log_k2 ~ 1, g_qlogis ~ 1)
  Level: ds
  Structure: Diagonal
         parent_0 log_k_m1 f_parent_qlogis log_k1 log_k2 g_qlogis Residual
-StdDev:        1    2e-04             0.3    0.7    0.8      0.3        3
+StdDev:        1      0.1             0.3    0.6    0.5      0.3        3
 
 
 Backtransformed parameters with asymmetric confidence intervals:
                lower  est. upper
 parent_0       1e+02 1e+02 1e+02
-k_m1           1e-03 2e-03 3e-03
+k_m1           4e-03 5e-03 6e-03
 f_parent_to_m1 4e-01 5e-01 5e-01
-k1             3e-02 4e-02 6e-02
-k2             1e-02 2e-02 3e-02
+k1             4e-02 6e-02 7e-02
+k2             1e-02 1e-02 2e-02
 g              4e-01 5e-01 5e-01
 
 Resulting formation fractions:
@@ -77,5 +77,5 @@ parent_sink 0.5
 
 Estimated disappearance times:
        DT50 DT90 DT50back DT50_k1 DT50_k2
-parent   27  105       31      17      42
-m1      352 1171       NA      NA      NA
+parent   26  131       39      13      53
+m1      144  479       NA      NA      NA
diff --git a/tests/testthat/test_error_models.R b/tests/testthat/test_error_models.R
index 2a1ffcc1..c11f6712 100644
--- a/tests/testthat/test_error_models.R
+++ b/tests/testthat/test_error_models.R
@@ -56,6 +56,7 @@ test_that("The default error model algorithm finds the best known AIC values for
   f_tc_exp_d_3 <- mmkin(c("SFO", "DFOP", "HS"),
     lapply(experimental_data_for_UBA_2019, function(x) x$data),
     error_model = "tc",
+    cores = n_cores,
     quiet = TRUE)
 
   AIC_exp_d_3 <- lapply(f_tc_exp_d_3, AIC)
diff --git a/tests/testthat/test_mixed.R b/tests/testthat/test_mixed.R
index 1e96c338..e9af10e6 100644
--- a/tests/testthat/test_mixed.R
+++ b/tests/testthat/test_mixed.R
@@ -1,6 +1,8 @@
 context("Nonlinear mixed-effects models")
 
-test_that("Parent only models can be fitted using nonlinear mixed effects models", {
+test_that("Parent fits using saemix are correctly implemented", {
+  skip_if(!saemix_available)
+
   expect_error(saem(fits), "Only row objects")
   # Some fits were done in the setup script
   mmkin_sfo_2 <- update(mmkin_sfo_1, fixed_initials = c(parent = 100))
@@ -26,7 +28,7 @@ test_that("Parent only models can be fitted using nonlinear mixed effects models
   expect_equal(round(s_sfo_s1$confint_back["k_parent", "est."], 3),
     round(s_sfo_n$confint_back["k_parent", "est."], 3))
 
-  mmkin_fomc_1 <- mmkin("FOMC", ds_fomc, quiet = TRUE, error_model = "tc")
+  mmkin_fomc_1 <- mmkin("FOMC", ds_fomc, quiet = TRUE, error_model = "tc", cores = n_cores)
   fomc_saem_1 <- saem(mmkin_fomc_1, quiet = TRUE)
   ci_fomc_s1 <- summary(fomc_saem_1)$confint_back
 
@@ -66,7 +68,7 @@ test_that("Parent only models can be fitted using nonlinear mixed effects models
   rel_diff_2 <- (s_dfop_s2$confint_back[, "est."] - dfop_pop) / dfop_pop
   expect_true(all(rel_diff_2 < 0.12))
 
-  mmkin_hs_1 <- mmkin("HS", ds_hs, quiet = TRUE, error_model = "const")
+  mmkin_hs_1 <- mmkin("HS", ds_hs, quiet = TRUE, error_model = "const", cores = n_cores)
   hs_saem_1 <- saem(mmkin_hs_1, quiet = TRUE)
   ci_hs_s1 <- summary(hs_saem_1)$confint_back
 
@@ -88,10 +90,12 @@ test_that("Print methods work", {
   expect_known_output(print(fits, digits = 2), "print_mmkin_parent.txt")
   expect_known_output(print(mmkin_biphasic_mixed, digits = 2), "print_mmkin_biphasic_mixed.txt")
   expect_known_output(print(nlme_biphasic, digits = 1), "print_nlme_biphasic.txt")
+
+  skip_if(!saemix_available)
   expect_known_output(print(sfo_saem_1, digits = 1), "print_sfo_saem_1.txt")
 })
 
-test_that("nlme results are reproducible", {
+test_that("nlme results are reproducible to some degree", {
 
   test_summary <- summary(nlme_biphasic)
   test_summary$nlmeversion <- "Dummy 0.0 for testing"
@@ -111,6 +115,7 @@ test_that("nlme results are reproducible", {
 
 test_that("saem results are reproducible for biphasic fits", {
 
+  skip_if(!saemix_available)
   test_summary <- summary(saem_biphasic_s)
   test_summary$saemixversion <- "Dummy 0.0 for testing"
   test_summary$mkinversion <- "Dummy 0.0 for testing"
diff --git a/tests/testthat/test_plot.R b/tests/testthat/test_plot.R
index 75d401a3..1c95d069 100644
--- a/tests/testthat/test_plot.R
+++ b/tests/testthat/test_plot.R
@@ -35,8 +35,10 @@ test_that("Plotting mkinfit, mmkin and mixed model objects is reproducible", {
   plot_biphasic_mmkin <- function() plot(f_uba_dfop_sfo_mixed)
   vdiffr::expect_doppelganger("mixed model fit for mmkin object", plot_biphasic_mmkin)
 
-  plot_biphasic_saem_s <- function() plot(f_uba_dfop_sfo_saem)
-  vdiffr::expect_doppelganger("mixed model fit for saem object with saemix transformations", plot_biphasic_saem_s)
+  if (saemix_available) {
+    plot_biphasic_saem_s <- function() plot(f_uba_dfop_sfo_saem)
+    vdiffr::expect_doppelganger("mixed model fit for saem object with saemix transformations", plot_biphasic_saem_s)
+  }
 
   skip_on_travis()
 
@@ -46,10 +48,12 @@ test_that("Plotting mkinfit, mmkin and mixed model objects is reproducible", {
   #plot_biphasic_mmkin <- function() plot(mixed(mmkin_biphasic))
   # Biphasic fits with lots of data and fits have lots of potential for differences
   plot_biphasic_nlme <- function() plot(nlme_biphasic)
-  #plot_biphasic_saem_s <- function() plot(saem_biphasic_s)
-  plot_biphasic_saem_m <- function() plot(saem_biphasic_m)
+  if (saemix_available) {
+    #plot_biphasic_saem_s <- function() plot(saem_biphasic_s)
+    plot_biphasic_saem_m <- function() plot(saem_biphasic_m)
 
-  vdiffr::expect_doppelganger("mixed model fit for saem object with mkin transformations", plot_biphasic_saem_m)
+    vdiffr::expect_doppelganger("mixed model fit for saem object with mkin transformations", plot_biphasic_saem_m)
+  }
 
   # different results when working with eigenvalues
   plot_errmod_fit_D_obs_eigen <- function() plot_err(fit_D_obs_eigen, sep_obs = FALSE)