diff options
Diffstat (limited to 'tests/testthat')
| -rw-r--r-- | tests/testthat/setup_script.R | 18 | ||||
| -rw-r--r-- | tests/testthat/summary_saem_biphasic_s.txt | 77 | ||||
| -rw-r--r-- | tests/testthat/test_mixed.R | 131 | ||||
| -rw-r--r-- | tests/testthat/test_plot.R | 11 |
4 files changed, 0 insertions, 237 deletions
diff --git a/tests/testthat/setup_script.R b/tests/testthat/setup_script.R index 2071e05c..547b2d6c 100644 --- a/tests/testthat/setup_script.R +++ b/tests/testthat/setup_script.R @@ -178,10 +178,6 @@ ds_biphasic <- lapply(ds_biphasic_mean, function(ds) { }) # Mixed model fits -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) @@ -190,16 +186,6 @@ mmkin_biphasic_mixed <- mixed(mmkin_biphasic) dfop_nlme_1 <- nlme(mmkin_dfop_1) nlme_biphasic <- nlme(mmkin_biphasic) -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")])) names(ds_uba) <- paste("Dataset", 6:10) @@ -211,7 +197,3 @@ f_uba_mmkin <- mmkin(list("SFO-SFO" = sfo_sfo_uba, "DFOP-SFO" = dfop_sfo_uba), ds_uba, quiet = TRUE, cores = n_cores) f_uba_dfop_sfo_mixed <- mixed(f_uba_mmkin[2, ]) -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_saem_biphasic_s.txt b/tests/testthat/summary_saem_biphasic_s.txt deleted file mode 100644 index b5777ce1..00000000 --- a/tests/testthat/summary_saem_biphasic_s.txt +++ /dev/null @@ -1,77 +0,0 @@ -saemix version used for fitting: Dummy 0.0 for testing -mkin version used for pre-fitting: Dummy 0.0 for testing -R version used for fitting: Dummy R version for testing -Date of fit: Dummy date for testing -Date of summary: Dummy date for testing - -Equations: -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: -509 observations of 2 variable(s) grouped in 15 datasets - -Model predictions using solution type analytical - -Fitted in test time 0 s using 300, 100 iterations - -Variance model: Constant variance - -Mean of starting values for individual parameters: - parent_0 k_m1 f_parent_to_m1 k1 k2 - 1.0e+02 1.8e-03 4.8e-01 4.5e-02 1.9e-02 - g - 5.1e-01 - -Fixed degradation parameter values: -None - -Results: - -Likelihood computed by importance sampling - AIC BIC logLik - 2692 2702 -1333 - -Optimised parameters: - est. lower upper -parent_0 1.0e+02 99.3030 1.0e+02 -k_m1 2.2e-03 0.0016 2.8e-03 -f_parent_to_m1 4.9e-01 0.4477 5.3e-01 -k1 4.0e-02 0.0239 5.6e-02 -k2 1.5e-02 0.0085 2.2e-02 -g 5.0e-01 0.3805 6.2e-01 - -Correlation: - prnt_0 k_m1 f_p__1 k1 k2 -k_m1 -0.152 -f_parent_to_m1 -0.138 0.396 -k1 0.085 -0.036 -0.026 -k2 0.005 0.067 0.018 -0.043 -g -0.075 -0.113 -0.029 -0.248 -0.263 - -Random effects: - est. lower upper -SD.parent_0 1.23 0.39 2.07 -SD.k_m1 0.14 -0.48 0.75 -SD.f_parent_to_m1 0.28 0.17 0.39 -SD.k1 0.71 0.42 1.00 -SD.k2 0.78 0.47 1.09 -SD.g 0.27 -0.33 0.86 - -Variance model: - est. lower upper -a.1 2.7 2.6 2.9 - -Resulting formation fractions: - ff -parent_m1 0.49 -parent_sink 0.51 - -Estimated disappearance times: - DT50 DT90 DT50back DT50_k1 DT50_k2 -parent 27 110 33 17 46 -m1 318 1055 NA NA NA diff --git a/tests/testthat/test_mixed.R b/tests/testthat/test_mixed.R index e9af10e6..ca0072ef 100644 --- a/tests/testthat/test_mixed.R +++ b/tests/testthat/test_mixed.R @@ -1,98 +1,9 @@ context("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)) - expect_error(update(mmkin_sfo_1, models = c("SFOOO")), "Please supply models.*") - - sfo_saem_2 <- saem(mmkin_sfo_1, quiet = TRUE, transformations = "mkin") - sfo_saem_3 <- expect_error(saem(mmkin_sfo_2, quiet = TRUE), "at least two parameters") - s_sfo_s1 <- summary(sfo_saem_1) - s_sfo_s2 <- summary(sfo_saem_2) - - sfo_nlme_1 <- expect_warning(nlme(mmkin_sfo_1), "not converge") - s_sfo_n <- summary(sfo_nlme_1) - - # Compare with input - expect_equal(round(s_sfo_s2$confint_ranef["SD.log_k_parent", "est."], 1), 0.3) - # k_parent is a bit different from input 0.03 here - expect_equal(round(s_sfo_s1$confint_back["k_parent", "est."], 3), 0.035) - expect_equal(round(s_sfo_s2$confint_back["k_parent", "est."], 3), 0.035) - - # But the result is pretty unanimous between methods - expect_equal(round(s_sfo_s1$confint_back["k_parent", "est."], 3), - round(s_sfo_s2$confint_back["k_parent", "est."], 3)) - 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", cores = n_cores) - fomc_saem_1 <- saem(mmkin_fomc_1, quiet = TRUE) - ci_fomc_s1 <- summary(fomc_saem_1)$confint_back - - fomc_pop <- as.numeric(fomc_pop) - expect_true(all(ci_fomc_s1[, "lower"] < fomc_pop)) - expect_true(all(ci_fomc_s1[, "upper"] > fomc_pop)) - - mmkin_fomc_2 <- update(mmkin_fomc_1, state.ini = 100, fixed_initials = "parent") - fomc_saem_2 <- saem(mmkin_fomc_2, quiet = TRUE, transformations = "mkin") - ci_fomc_s2 <- summary(fomc_saem_2)$confint_back - - expect_true(all(ci_fomc_s2[, "lower"] < fomc_pop[2:3])) - expect_true(all(ci_fomc_s2[, "upper"] > fomc_pop[2:3])) - - s_dfop_s1 <- summary(dfop_saemix_1) - s_dfop_s2 <- summary(dfop_saemix_2) - s_dfop_n <- summary(dfop_nlme_1) - - dfop_pop <- as.numeric(dfop_pop) - expect_true(all(s_dfop_s1$confint_back[, "lower"] < dfop_pop)) - expect_true(all(s_dfop_s1$confint_back[, "upper"] > dfop_pop)) - expect_true(all(s_dfop_s2$confint_back[, "lower"] < dfop_pop)) - expect_true(all(s_dfop_s2$confint_back[, "upper"] > dfop_pop)) - - dfop_mmkin_means_trans <- apply(parms(mmkin_dfop_1, transformed = TRUE), 1, mean) - dfop_mmkin_means <- backtransform_odeparms(dfop_mmkin_means_trans, mmkin_dfop_1$mkinmod) - - # We get < 22% deviations by averaging the transformed parameters - rel_diff_mmkin <- (dfop_mmkin_means - dfop_pop) / dfop_pop - expect_true(all(rel_diff_mmkin < 0.22)) - - # We get < 50% deviations with transformations made in mkin - rel_diff_1 <- (s_dfop_s1$confint_back[, "est."] - dfop_pop) / dfop_pop - expect_true(all(rel_diff_1 < 0.5)) - - # We get < 12% deviations with transformations made in saemix - rel_diff_2 <- (s_dfop_s2$confint_back[, "est."] - dfop_pop) / dfop_pop - expect_true(all(rel_diff_2 < 0.12)) - - mmkin_hs_1 <- mmkin("HS", ds_hs, quiet = TRUE, error_model = "const", cores = n_cores) - hs_saem_1 <- saem(mmkin_hs_1, quiet = TRUE) - ci_hs_s1 <- summary(hs_saem_1)$confint_back - - hs_pop <- as.numeric(hs_pop) - # expect_true(all(ci_hs_s1[, "lower"] < hs_pop)) # k1 is overestimated - expect_true(all(ci_hs_s1[, "upper"] > hs_pop)) - - mmkin_hs_2 <- update(mmkin_hs_1, state.ini = 100, fixed_initials = "parent") - hs_saem_2 <- saem(mmkin_hs_2, quiet = TRUE) - ci_hs_s2 <- summary(hs_saem_2)$confint_back - - #expect_true(all(ci_hs_s2[, "lower"] < hs_pop[2:4])) # k1 again overestimated - expect_true(all(ci_hs_s2[, "upper"] > hs_pop[2:4])) - - # HS would likely benefit from implemenation of transformations = "saemix" -}) - test_that("Print methods work", { expect_known_output(print(fits, digits = 2), "print_mmkin_parent.txt") expect_known_output(print(mmkin_biphasic_mixed, digits = 2), "print_mmkin_biphasic_mixed.txt") expect_known_output(print(nlme_biphasic, digits = 1), "print_nlme_biphasic.txt") - - skip_if(!saemix_available) - expect_known_output(print(sfo_saem_1, digits = 1), "print_sfo_saem_1.txt") }) test_that("nlme results are reproducible to some degree", { @@ -112,45 +23,3 @@ test_that("nlme results are reproducible to some degree", { # expect_true(all(ci_dfop_sfo_n[, "lower"] < dfop_sfo_pop)) # k2 is overestimated expect_true(all(ci_dfop_sfo_n[, "upper"] > dfop_sfo_pop)) }) - -test_that("saem results are reproducible for biphasic fits", { - - skip_if(!saemix_available) - test_summary <- summary(saem_biphasic_s) - test_summary$saemixversion <- "Dummy 0.0 for testing" - test_summary$mkinversion <- "Dummy 0.0 for testing" - test_summary$Rversion <- "Dummy R version for testing" - test_summary$date.fit <- "Dummy date for testing" - test_summary$date.summary <- "Dummy date for testing" - test_summary$time <- c(elapsed = "test time 0") - - expect_known_output(print(test_summary, digits = 2), "summary_saem_biphasic_s.txt") - - dfop_sfo_pop <- as.numeric(dfop_sfo_pop) - no_k1 <- c(1, 2, 3, 5, 6) - no_k2 <- c(1, 2, 3, 4, 6) - - ci_dfop_sfo_s_s <- summary(saem_biphasic_s)$confint_back - expect_true(all(ci_dfop_sfo_s_s[, "lower"] < dfop_sfo_pop)) - expect_true(all(ci_dfop_sfo_s_s[, "upper"] > dfop_sfo_pop)) - - # k1 and k2 are not fitted well - ci_dfop_sfo_s_m <- summary(saem_biphasic_m)$confint_back - expect_true(all(ci_dfop_sfo_s_m[no_k2, "lower"] < dfop_sfo_pop[no_k2])) - expect_true(all(ci_dfop_sfo_s_m[no_k1, "upper"] > dfop_sfo_pop[no_k1])) - - # I tried to only do few iterations in routine tests as this is so slow - # but then deSolve fails at some point (presumably at the switch between - # the two types of iterations) - #saem_biphasic_2 <- saem(mmkin_biphasic, solution_type = "deSolve", - # control = list(nbiter.saemix = c(10, 5), nbiter.burn = 5), quiet = TRUE) - - skip("Fitting with saemix takes around 10 minutes when using deSolve") - saem_biphasic_2 <- saem(mmkin_biphasic, solution_type = "deSolve", quiet = TRUE) - - # As with the analytical solution, k1 and k2 are not fitted well - ci_dfop_sfo_s_d <- summary(saem_biphasic_2)$confint_back - 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])) -}) - diff --git a/tests/testthat/test_plot.R b/tests/testthat/test_plot.R index 1c95d069..0bf3ee66 100644 --- a/tests/testthat/test_plot.R +++ b/tests/testthat/test_plot.R @@ -35,11 +35,6 @@ 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) - 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() plot_biphasic_nlme <- function() plot(dfop_nlme_1) @@ -48,12 +43,6 @@ 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) - 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) - } # different results when working with eigenvalues plot_errmod_fit_D_obs_eigen <- function() plot_err(fit_D_obs_eigen, sep_obs = FALSE) |