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authorJohannes Ranke <jranke@uni-bremen.de>2021-02-06 18:30:32 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2021-02-06 18:30:32 +0100
commit48c463680b51fa767b4cd7bd62865f192d0354ac (patch)
tree5b66eb08a7fd5e29fb7e6d3a9a8258ccdcaea73e /tests/testthat
parent2ee20b257e34210e2d1f044431f3bfe059c9c5e7 (diff)
Reintroduce interface to saemix
Also after the upgrade from buster to bullseye of my local system, some test results for saemix have changed.
Diffstat (limited to 'tests/testthat')
-rw-r--r--tests/testthat/setup_script.R18
-rw-r--r--tests/testthat/summary_saem_biphasic_s.txt77
-rw-r--r--tests/testthat/test_mixed.R135
-rw-r--r--tests/testthat/test_plot.R11
4 files changed, 240 insertions, 1 deletions
diff --git a/tests/testthat/setup_script.R b/tests/testthat/setup_script.R
index 547b2d6c..9229c198 100644
--- a/tests/testthat/setup_script.R
+++ b/tests/testthat/setup_script.R
@@ -178,6 +178,10 @@ 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)
@@ -186,6 +190,16 @@ 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)
@@ -197,3 +211,7 @@ 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
new file mode 100644
index 00000000..1e0f1ccc
--- /dev/null
+++ b/tests/testthat/summary_saem_biphasic_s.txt
@@ -0,0 +1,77 @@
+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 4.8e-03 4.8e-01 6.8e-02 1.3e-02
+ g
+ 4.2e-01
+
+Fixed degradation parameter values:
+None
+
+Results:
+
+Likelihood computed by importance sampling
+ AIC BIC logLik
+ 2645 2654 -1310
+
+Optimised parameters:
+ est. lower upper
+parent_0 1.0e+02 99.627 1.0e+02
+k_m1 4.8e-03 0.004 5.6e-03
+f_parent_to_m1 4.8e-01 0.437 5.2e-01
+k1 6.5e-02 0.051 8.0e-02
+k2 1.2e-02 0.010 1.4e-02
+g 4.3e-01 0.362 5.0e-01
+
+Correlation:
+ prnt_0 k_m1 f_p__1 k1 k2
+k_m1 -0.156
+f_parent_to_m1 -0.157 0.372
+k1 0.159 0.000 -0.029
+k2 0.074 0.145 0.032 0.332
+g -0.072 -0.142 -0.044 -0.422 -0.570
+
+Random effects:
+ est. lower upper
+SD.parent_0 1.14 0.251 2.03
+SD.k_m1 0.14 -0.073 0.35
+SD.f_parent_to_m1 0.29 0.176 0.41
+SD.k1 0.36 0.211 0.52
+SD.k2 0.18 0.089 0.27
+SD.g 0.32 0.098 0.53
+
+Variance model:
+ est. lower upper
+a.1 2.7 2.5 2.9
+
+Resulting formation fractions:
+ ff
+parent_m1 0.48
+parent_sink 0.52
+
+Estimated disappearance times:
+ DT50 DT90 DT50back DT50_k1 DT50_k2
+parent 25 145 44 11 58
+m1 145 481 NA NA NA
diff --git a/tests/testthat/test_mixed.R b/tests/testthat/test_mixed.R
index 6f28d0c3..0eb1f0d5 100644
--- a/tests/testthat/test_mixed.R
+++ b/tests/testthat/test_mixed.R
@@ -1,9 +1,98 @@
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)$confint_back
+
+ #expect_true(all(ci_hs_s2[, "lower"] < hs_pop[2:4])) # k1 again overestimated
+ expect_true(all(ci_hs_s2[, "upper"] > hs_pop[2:4]))
+
+ # HS would likely benefit from implemenation of transformations = "saemix"
+})
+
test_that("Print methods work", {
expect_known_output(print(fits[, 2:3], digits = 2), "print_mmkin_parent.txt")
expect_known_output(print(mmkin_biphasic_mixed, digits = 2), "print_mmkin_biphasic_mixed.txt")
expect_known_output(print(nlme_biphasic, digits = 1), "print_nlme_biphasic.txt")
+
+ skip_if(!saemix_available)
+ expect_known_output(print(sfo_saem_1, digits = 1), "print_sfo_saem_1.txt")
})
test_that("nlme results are reproducible to some degree", {
@@ -20,6 +109,50 @@ test_that("nlme results are reproducible to some degree", {
dfop_sfo_pop <- as.numeric(dfop_sfo_pop)
ci_dfop_sfo_n <- summary(nlme_biphasic)$confint_back
- # expect_true(all(ci_dfop_sfo_n[, "lower"] < dfop_sfo_pop)) # k2 is overestimated
+ expect_true(all(ci_dfop_sfo_n[, "lower"] < dfop_sfo_pop))
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)
+ no_k1_k2 <- c(1, 2, 3, 6)
+
+ ci_dfop_sfo_s_s <- summary(saem_biphasic_s)$confint_back
+ # k1 and k2 are overestimated
+ expect_true(all(ci_dfop_sfo_s_s[no_k1_k2, "lower"] < dfop_sfo_pop[no_k1_k2]))
+ expect_true(all(ci_dfop_sfo_s_s[, "upper"] > dfop_sfo_pop))
+
+ # k1 and k2 are not fitted well
+ ci_dfop_sfo_s_m <- summary(saem_biphasic_m)$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 0bf3ee66..1c95d069 100644
--- a/tests/testthat/test_plot.R
+++ b/tests/testthat/test_plot.R
@@ -35,6 +35,11 @@ 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)
@@ -43,6 +48,12 @@ 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)

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