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_saem.R | 133 --------------------------------------------- 1 file changed, 133 deletions(-) delete mode 100644 tests/testthat/test_saem.R (limited to 'tests/testthat/test_saem.R') diff --git a/tests/testthat/test_saem.R b/tests/testthat/test_saem.R deleted file mode 100644 index aa32d0b5..00000000 --- a/tests/testthat/test_saem.R +++ /dev/null @@ -1,133 +0,0 @@ -context("Nonlinear mixed effects models fitted with SAEM from saemix") - -set.seed(123456) -sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120) -n <- n_biphasic <- 15 -log_sd <- 0.3 -err_1 = list(const = 1, prop = 0.05) -tc <- function(value) sigma_twocomp(value, err_1$const, err_1$prop) -const <- function(value) 2 - -SFO <- mkinmod(parent = mkinsub("SFO")) -k_parent = rlnorm(n, log(0.03), log_sd) -ds_sfo <- lapply(1:n, function(i) { - ds_mean <- mkinpredict(SFO, c(k_parent = k_parent[i]), - c(parent = 100), sampling_times) - add_err(ds_mean, tc, n = 1)[[1]] -}) - -DFOP <- mkinmod(parent = mkinsub("DFOP")) -dfop_pop <- list(parent_0 = 100, k1 = 0.06, k2 = 0.015, g = 0.4) -dfop_parms <- as.matrix(data.frame( - k1 = rlnorm(n, log(dfop_pop$k1), log_sd), - k2 = rlnorm(n, log(dfop_pop$k2), log_sd), - g = plogis(rnorm(n, qlogis(dfop_pop$g), log_sd)))) -ds_dfop <- lapply(1:n, function(i) { - ds_mean <- mkinpredict(DFOP, dfop_parms[i, ], - c(parent = dfop_pop$parent_0), sampling_times) - add_err(ds_mean, const, n = 1)[[1]] -}) - -set.seed(123456) -DFOP_SFO <- mkinmod( - parent = mkinsub("DFOP", "m1"), - m1 = mkinsub("SFO"), - quiet = TRUE) -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) - } -) -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]] -}) - -test_that("Parent only models can be fitted with saemix", { - # 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$confint_back["k_parent", "est."], 3)) - - mmkin_dfop_1 <- mmkin("DFOP", ds_dfop, quiet = TRUE) - - dfop_saemix_1 <- saem(mmkin_dfop_1, quiet = TRUE, transformations = "mkin") - dfop_saemix_2 <- saem(mmkin_dfop_1, quiet = TRUE, transformations = "saemix") - dfop_nlme_1 <- nlme(mmkin_dfop_1) - s_dfop_s1 <- summary(dfop_saemix_1) - s_dfop_s2 <- summary(dfop_saemix_2) - s_dfop_n <- summary(dfop_nlme_1) - - dfop_pop <- as.numeric(dfop_pop) - expect_true(all(s_dfop_s1$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$confint_back[, "est."] - dfop_pop) / dfop_pop - expect_true(all(rel_diff_2 < 0.08)) -}) - -test_that("Print methods work", { - expect_known_output(print(sfo_saemix_1, digits = 1), "print_sfo_saemix_1.txt") - expect_known_output(print(mmkin_biphasic_mixed, digits = 2), "print_mmkin_biphasic_mixed.txt") -}) - -test_that("Saemix results are reproducible", { - - test_summary <- summary(saem_biphasic_s) - test_summary$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) - -}) -- cgit v1.2.1