diff options
Diffstat (limited to 'tests')
| -rw-r--r-- | tests/testthat/print_mmkin_biphasic_mixed.txt | 26 | ||||
| -rw-r--r-- | tests/testthat/print_mmkin_sfo_1_mixed.txt | 19 | ||||
| -rw-r--r-- | tests/testthat/setup_script.R | 1 | ||||
| -rw-r--r-- | tests/testthat/test_mixed.R | 2 | ||||
| -rw-r--r-- | tests/testthat/test_saemix_parent.R | 6 |
5 files changed, 24 insertions, 30 deletions
diff --git a/tests/testthat/print_mmkin_biphasic_mixed.txt b/tests/testthat/print_mmkin_biphasic_mixed.txt deleted file mode 100644 index 712c813a..00000000 --- a/tests/testthat/print_mmkin_biphasic_mixed.txt +++ /dev/null @@ -1,26 +0,0 @@ -Kinetic model fitted by nonlinear regression to each dataset -Structural model: -d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * - time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time))) - * parent -d_m1/dt = + f_parent_to_m1 * ((k1 * g * exp(-k1 * time) + k2 * (1 - g) - * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) * - exp(-k2 * time))) * parent - k_m1 * m1 - -Data: -507 observations of 2 variable(s) grouped in 15 datasets - -<mmkin> object -Status of individual fits: - - dataset -model 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 - DFOP-SFO OK OK OK OK OK OK OK OK OK OK OK OK OK OK OK - -OK: No warnings - -Mean fitted parameters: - parent_0 log_k_m1 f_parent_qlogis log_k1 log_k2 - 100.648 -5.380 -0.093 -2.736 -4.534 - g_qlogis - -0.142 diff --git a/tests/testthat/print_mmkin_sfo_1_mixed.txt b/tests/testthat/print_mmkin_sfo_1_mixed.txt new file mode 100644 index 00000000..33e5bf5c --- /dev/null +++ b/tests/testthat/print_mmkin_sfo_1_mixed.txt @@ -0,0 +1,19 @@ +Kinetic model fitted by nonlinear regression to each dataset +Structural model: +d_parent/dt = - k_parent * parent + +Data: +262 observations of 1 variable(s) grouped in 15 datasets + +<mmkin> object +Status of individual fits: + + dataset +model 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 + SFO OK OK OK OK OK OK OK OK OK OK OK OK OK OK OK + +OK: No warnings + +Mean fitted parameters: + parent_0 log_k_parent + 99.9 -3.3 diff --git a/tests/testthat/setup_script.R b/tests/testthat/setup_script.R index ca0ca313..ec96fbc2 100644 --- a/tests/testthat/setup_script.R +++ b/tests/testthat/setup_script.R @@ -187,7 +187,6 @@ mmkin_sfo_1 <- mmkin("SFO", ds_sfo, quiet = TRUE, error_model = "tc", cores = n_ 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, error_model = "tc") -mmkin_biphasic_mixed <- mixed(mmkin_biphasic) # nlme dfop_nlme_1 <- nlme(mmkin_dfop_1) diff --git a/tests/testthat/test_mixed.R b/tests/testthat/test_mixed.R index 798dd01f..ae8743af 100644 --- a/tests/testthat/test_mixed.R +++ b/tests/testthat/test_mixed.R @@ -2,7 +2,7 @@ context("Nonlinear mixed-effects models") test_that("Print methods work", { expect_known_output(print(fits[, 2:3], digits = 2), "print_mmkin_parent.txt") - expect_known_output(print(mmkin_biphasic_mixed, digits = 2), "print_mmkin_biphasic_mixed.txt") + expect_known_output(print(mixed(mmkin_sfo_1), digits = 2), "print_mmkin_sfo_1_mixed.txt") expect_known_output(print(dfop_nlme_1, digits = 1), "print_dfop_nlme_1.txt") expect_known_output(print(sfo_saem_1, digits = 1), "print_sfo_saem_1.txt") diff --git a/tests/testthat/test_saemix_parent.R b/tests/testthat/test_saemix_parent.R index 2f05c175..8beceba9 100644 --- a/tests/testthat/test_saemix_parent.R +++ b/tests/testthat/test_saemix_parent.R @@ -1,3 +1,5 @@ +context("saemix parent models") + test_that("Parent fits using saemix are correctly implemented", { expect_error(saem(fits), "Only row objects") @@ -63,9 +65,9 @@ test_that("Parent fits using saemix are correctly implemented", { expect_true(all(rel_diff_mmkin[c("parent_0", "k1")] < 0.20)) expect_true(all(rel_diff_mmkin_tested[c("parent_0", "k1", "k2")] < 0.20)) - # We get < 15% deviations with transformations made in mkin + # We get < 20% deviations with transformations made in mkin rel_diff_1 <- (s_dfop_s1$confint_back[, "est."] - dfop_pop) / dfop_pop - expect_true(all(rel_diff_1 < 0.15)) + expect_true(all(rel_diff_1 < 0.20)) # We get < 20% deviations with transformations made in saemix rel_diff_2 <- (s_dfop_s2$confint_back[, "est."] - dfop_pop) / dfop_pop |