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authorJohannes Ranke <jranke@uni-bremen.de>2021-02-03 16:41:31 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2021-02-03 18:18:19 +0100
commitf0ef23a7598e5d19648ae4edc2b74e0fba27a41c (patch)
tree03af20e730330e148acf3a7c008d82387dbe52eb /tests/testthat
parent82814b17ec182467c25325d747fffa8ffbe4bb33 (diff)
Prepare for v1.0.0v1.0.0
- Improve authorship and copyright information - Prepare pkgdown config - Remove dependence on saemix as we need the development version which is not ready for CRAN - Temporarily remove saemix interface to check code coverage of the rest
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.R131
-rw-r--r--tests/testthat/test_plot.R11
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)

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