aboutsummaryrefslogtreecommitdiff
path: root/tests
diff options
context:
space:
mode:
authorJohannes Ranke <jranke@uni-bremen.de>2020-12-10 10:14:07 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2020-12-10 10:14:07 +0100
commit9c87bd68e2eb0342bc53d11fe2c3920a2e903d16 (patch)
treed88fdec4b95b6aa9be4ab97d7abcd5b483a795de /tests
parentc58c14078f6a30c22863b7b9730f4afc39db4577 (diff)
Tried to find a fast test for deSolve in saemix
But could not find one.
Diffstat (limited to 'tests')
-rw-r--r--tests/testthat/setup_script.R3
-rw-r--r--tests/testthat/test_mixed.R6
2 files changed, 7 insertions, 2 deletions
diff --git a/tests/testthat/setup_script.R b/tests/testthat/setup_script.R
index cfdc9277..fd9635d1 100644
--- a/tests/testthat/setup_script.R
+++ b/tests/testthat/setup_script.R
@@ -95,7 +95,7 @@ fit_obs_1 <- mkinfit(m_synth_SFO_lin, SFO_lin_a, error_model = "obs", quiet = TR
fit_tc_1 <- mkinfit(m_synth_SFO_lin, SFO_lin_a, error_model = "tc", quiet = TRUE,
error_model_algorithm = "threestep")
-# Mixed models data and
+# Mixed models data and fits
sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120)
n <- n_biphasic <- 15
log_sd <- 0.3
@@ -203,5 +203,4 @@ f_uba_mmkin <- mmkin(list("SFO-SFO" = sfo_sfo_uba, "DFOP-SFO" = dfop_sfo_uba),
ds_uba, quiet = TRUE)
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_sfo_sfo_saem <- saem(f_uba_mmkin["SFO-SFO", ], solution_type = "deSolve", quiet = TRUE) # currently fails
f_uba_dfop_sfo_saem <- saem(f_uba_mmkin["DFOP-SFO", ], quiet = TRUE, transformations = "saemix")
diff --git a/tests/testthat/test_mixed.R b/tests/testthat/test_mixed.R
index 05632c6f..41e8160a 100644
--- a/tests/testthat/test_mixed.R
+++ b/tests/testthat/test_mixed.R
@@ -134,6 +134,12 @@ test_that("saem results are reproducible for biphasic fits", {
expect_true(all(ci_dfop_sfo_s_m[no_k2, "lower"] < dfop_sfo_pop[no_k2]))
expect_true(all(ci_dfop_sfo_s_m[no_k1, "upper"] > dfop_sfo_pop[no_k1]))
+ # I tried to only do few iterations in routine tests as this is so slow
+ # but then deSolve fails at some point (presumably at the switch between
+ # the two types of iterations)
+ #saem_biphasic_2 <- saem(mmkin_biphasic, solution_type = "deSolve",
+ # control = list(nbiter.saemix = c(10, 5), nbiter.burn = 5), quiet = TRUE)
+
skip("Fitting with saemix takes around 10 minutes when using deSolve")
saem_biphasic_2 <- saem(mmkin_biphasic, solution_type = "deSolve", quiet = TRUE)

Contact - Imprint