diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2020-12-10 10:14:07 +0100 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2020-12-10 10:14:07 +0100 |
| commit | 9c87bd68e2eb0342bc53d11fe2c3920a2e903d16 (patch) | |
| tree | d88fdec4b95b6aa9be4ab97d7abcd5b483a795de | |
| parent | c58c14078f6a30c22863b7b9730f4afc39db4577 (diff) | |
Tried to find a fast test for deSolve in saemix
But could not find one.
| -rw-r--r-- | tests/testthat/setup_script.R | 3 | ||||
| -rw-r--r-- | tests/testthat/test_mixed.R | 6 |
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) |