More tests

1 files changed, 95 insertions, 33 deletions

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)