From 3b15daaf373ebc36da2eb92f2e37ed569731f07d Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 9 Dec 2020 13:08:01 +0100 Subject: More tests --- tests/testthat/test_mixed.R | 128 ++++++++++++++++++++++++++++++++------------ 1 file changed, 95 insertions(+), 33 deletions(-) (limited to 'tests/testthat/test_mixed.R') diff --git a/tests/testthat/test_mixed.R b/tests/testthat/test_mixed.R index 2d69e13e..b9713c6e 100644 --- a/tests/testthat/test_mixed.R +++ b/tests/testthat/test_mixed.R @@ -1,35 +1,97 @@ -context("Fitting of nonlinear mixed effects models") - -sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120) -n_biphasic <- 8 -err_1 = list(const = 1, prop = 0.07) - -DFOP_SFO <- mkinmod( - parent = mkinsub("DFOP", "m1"), - m1 = mkinsub("SFO"), - quiet = TRUE) - -set.seed(123456) -log_sd <- 0.3 -syn_biphasic_parms <- as.matrix(data.frame( - k1 = rlnorm(n_biphasic, log(0.05), log_sd), - k2 = rlnorm(n_biphasic, log(0.01), log_sd), - g = plogis(rnorm(n_biphasic, 0, log_sd)), - f_parent_to_m1 = plogis(rnorm(n_biphasic, 0, log_sd)), - k_m1 = rlnorm(n_biphasic, log(0.002), log_sd))) - -ds_biphasic_mean <- lapply(1:n_biphasic, - function(i) { - mkinpredict(DFOP_SFO, syn_biphasic_parms[i, ], - c(parent = 100, m1 = 0), sampling_times) - } -) - -set.seed(123456L) -ds_biphasic <- lapply(ds_biphasic_mean, function(ds) { - add_err(ds, - sdfunc = function(value) sqrt(err_1$const^2 + value^2 * err_1$prop^2), - n = 1, secondary = "m1")[[1]] +context("Nonlinear mixed effects models") + +test_that("Parent only models can be fitted using nonlinear mixed effects models", { + # Some fits were done in the setup script + mmkin_sfo_2 <- mmkin("SFO", ds_sfo, fixed_initials = c(parent = 100), quiet = TRUE) + + sfo_saemix_2 <- saem(mmkin_sfo_1, quiet = TRUE, transformations = "mkin") + sfo_saemix_3 <- expect_error(saem(mmkin_sfo_2, quiet = TRUE), "at least two parameters") + s_sfo_s1 <- summary(sfo_saemix_1) + s_sfo_s2 <- summary(sfo_saemix_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$confint_back["k_parent", "est."], 3)) + + s_dfop_s1 <- summary(dfop_saemix_1) + s_dfop_s2 <- summary(dfop_saemix_2) + s_dfop_n <- summary(dfop_nlme_1) + + dfop_pop <- as.numeric(dfop_pop) + expect_true(all(s_dfop_s1$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$confint_back[, "upper"] > dfop_pop)) + + + # We get < 20% deviations with transformations made in mkin + rel_diff_1 <- (s_dfop_s1$confint_back[, "est."] - dfop_pop) / dfop_pop + expect_true(all(rel_diff_1 < 0.2)) + + # We get < 8% deviations with transformations made in saemix + rel_diff_2 <- (s_dfop_s2$confint_back[, "est."] - dfop_pop) / dfop_pop + expect_true(all(rel_diff_2 < 0.08)) +}) + +test_that("Print methods work", { + expect_known_output(print(mmkin_biphasic_mixed, digits = 2), "print_mmkin_biphasic_mixed.txt") + expect_known_output(print(nlme_biphasic, digits = 2), "print_nlme_biphasic.txt") + expect_known_output(print(sfo_saemix_1, digits = 1), "print_sfo_saemix_1.txt") +}) + +test_that("nlme results are reproducible", { + + test_summary <- summary(nlme_biphasic) + test_summary$nlmeversion <- "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$time <- c(elapsed = "test time 0") + + expect_known_output(print(test_summary, digits = 2), "summary_nlme_biphasic_s.txt") + + dfop_sfo_pop <- as.numeric(dfop_sfo_pop) + ci_dfop_sfo_n <- summary(nlme_biphasic)$confint_back + # 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", { + + 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) + ci_dfop_sfo_s_s <- summary(saem_biphasic_s)$confint_back + expect_true(all(ci_dfop_sfo_s_s[, "lower"] < dfop_sfo_pop)) + expect_true(all(ci_dfop_sfo_s_s[, "upper"] > dfop_sfo_pop)) + + # The following does not work, as k1 and k2 are not fitted well + ci_dfop_sfo_s_m <- summary(saem_biphasic_m)$confint_back + # expect_true(all(ci_dfop_sfo_s_m[, "lower"] < dfop_sfo_pop)) + # expect_true(all(ci_dfop_sfo_s_m[, "upper"] > dfop_sfo_pop)) + + # Somehow this does not work at the moment. But it took forever (~ 10 min) anyways... + #saem_biphasic_2 <- saem(mmkin_biphasic, solution_type = "deSolve", quiet = TRUE) + }) -f_mmkin <- mmkin(list("DFOP-SFO" = DFOP_SFO), ds_biphasic, quiet = TRUE) -- cgit v1.2.1