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authorJohannes Ranke <jranke@uni-bremen.de>2020-05-10 21:53:00 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2020-05-10 21:53:00 +0200
commitd113cd79b178fdc91aecb894707ed356129dfb75 (patch)
treedc28e049e94eb3ee9745f9cd86387de96a894c93 /tests/testthat
parentefab37957381919c21d874906ce870f4941c760a (diff)
Default to analytical for coupled models if available
This revealed that transforming rates is necessary for fitting the analytical solution of the SFO-SFO model to the FOCUS D dataset. Benchmarks show that fitting coupled models with deSolve got a bit slower through the latest changes
Diffstat (limited to 'tests/testthat')
-rw-r--r--tests/testthat/FOCUS_2006_D.csf2
-rw-r--r--tests/testthat/test_FOCUS_D_UBA_expertise.R21
2 files changed, 16 insertions, 7 deletions
diff --git a/tests/testthat/FOCUS_2006_D.csf b/tests/testthat/FOCUS_2006_D.csf
index f113a668..d41f0a9f 100644
--- a/tests/testthat/FOCUS_2006_D.csf
+++ b/tests/testthat/FOCUS_2006_D.csf
@@ -5,7 +5,7 @@ Description:
MeasurementUnits: % AR
TimeUnits: days
Comments: Created using mkin::CAKE_export
-Date: 2020-05-09
+Date: 2020-05-10
Optimiser: IRLS
[Data]
diff --git a/tests/testthat/test_FOCUS_D_UBA_expertise.R b/tests/testthat/test_FOCUS_D_UBA_expertise.R
index f3b12bd9..be2806de 100644
--- a/tests/testthat/test_FOCUS_D_UBA_expertise.R
+++ b/tests/testthat/test_FOCUS_D_UBA_expertise.R
@@ -2,19 +2,22 @@ context("Results for FOCUS D established in expertise for UBA (Ranke 2014)")
# Results are from p. 40
+# Avoid warnings due to the zero value in the data for m1 at time zero
+FOCUS_D <- subset(FOCUS_2006_D, value != 0)
+
test_that("Fits without formation fractions are correct for FOCUS D", {
- fit.default <- expect_warning(mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE), "value of zero")
+ fit.noff <- mkinfit(SFO_SFO, FOCUS_D, quiet = TRUE)
- expect_equal(round(as.numeric(endpoints(fit.default)$distimes["parent", ]), 2),
+ expect_equal(round(as.numeric(endpoints(fit.noff)$distimes["parent", ]), 2),
c(7.02, 23.33))
- expect_equal(round(as.numeric(endpoints(fit.default)$distimes["m1", ]), 1),
+ expect_equal(round(as.numeric(endpoints(fit.noff)$distimes["m1", ]), 1),
c(131.8, 437.7))
})
test_that("Fits with formation fractions are correct for FOCUS D", {
skip_on_cran()
- fit.ff <- expect_warning(mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE), "value of zero")
+ fit.ff <- mkinfit(SFO_SFO.ff, FOCUS_D, quiet = TRUE)
expect_equivalent(round(fit.ff$bparms.optim, c(2, 4, 4, 4)),
c(99.60, 0.0987, 0.0053, 0.5145))
@@ -30,8 +33,15 @@ test_that("Fits with formation fractions are correct for FOCUS D", {
test_that("Fits without internal transformations are correct for FOCUS D", {
skip_on_cran()
expect_warning(
+ # Analytical solutions (now the default for SFO_SFO with formation fractions)
+ # return NA at some point not internally transforming rates
+ expect_error(fit.ff.notrans <- mkinfit(SFO_SFO.ff, FOCUS_D,
+ transform_fractions = FALSE, transform_rates = FALSE, quiet = TRUE)))
+
+ expect_warning(
fit.ff.notrans <- mkinfit(SFO_SFO.ff, FOCUS_2006_D,
- transform_fractions = FALSE, transform_rates = FALSE, quiet = TRUE),
+ transform_fractions = FALSE, transform_rates = FALSE,
+ quiet = TRUE, solution_type = "deSolve"),
"sum of formation fractions")
expect_equivalent(round(fit.ff.notrans$bparms.optim, c(2, 4, 4, 4)),
@@ -40,7 +50,6 @@ test_that("Fits without internal transformations are correct for FOCUS D", {
expect_equivalent(round(100 * mkinerrmin(fit.ff.notrans)$err.min, 2),
c(6.40, 6.46, 4.69))
-
expect_equal(round(as.numeric(endpoints(fit.ff.notrans)$distimes["parent", ]), 2),
c(7.02, 23.33))
expect_equal(round(as.numeric(endpoints(fit.ff.notrans)$distimes["m1", ]), 1),

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