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authorJohannes Ranke <jranke@uni-bremen.de>2020-11-19 16:03:38 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2020-11-19 16:03:38 +0100
commit300c0fccf327b9959db39c256bae0974908e59b2 (patch)
treea1b461ad04e63aa8d0463f2b468ee873ddb1b383
parentdb9ae6a0c9cecb92048fde6f06af1da183c09b5f (diff)
Update tests, improve CAKE_export test
-rw-r--r--build.log1
-rw-r--r--test.log41
-rw-r--r--tests/testthat/FOCUS_2006_D.csf2
-rw-r--r--tests/testthat/test_CAKE_export.R5
4 files changed, 25 insertions, 24 deletions
diff --git a/build.log b/build.log
index d101d06b..13905abe 100644
--- a/build.log
+++ b/build.log
@@ -5,5 +5,6 @@
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
+Removed empty directory ‘mkin/tests/testthat/_snaps’
* building ‘mkin_0.9.50.4.tar.gz’
diff --git a/test.log b/test.log
index 32d12209..957a3e87 100644
--- a/test.log
+++ b/test.log
@@ -1,48 +1,49 @@
Loading mkin
+Loading required package: parallel
Testing mkin
✔ | OK F W S | Context
✔ | 4 | AIC calculation
✔ | 2 | Export dataset for reading into CAKE
✔ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [0.9 s]
✔ | 4 | Calculation of FOCUS chi2 error levels [0.4 s]
-✔ | 7 | Fitting the SFORB model [3.4 s]
-✔ | 5 | Analytical solutions for coupled models [3.0 s]
+✔ | 7 | Fitting the SFORB model [3.5 s]
+✔ | 5 | Analytical solutions for coupled models [3.1 s]
✔ | 5 | Calculation of Akaike weights
✔ | 10 | Confidence intervals and p-values [1.0 s]
-✔ | 14 | Error model fitting [4.1 s]
+✔ | 14 | Error model fitting [4.6 s]
✔ | 4 | Test fitting the decline of metabolites from their maximum [0.3 s]
✔ | 1 | Fitting the logistic model [0.2 s]
✔ | 1 | Test dataset class mkinds used in gmkin
-✔ | 1 | mkinfit features [0.2 s]
-✔ | 12 | Special cases of mkinfit calls [0.6 s]
-✔ | 8 | mkinmod model generation and printing [0.2 s]
+✔ | 1 | mkinfit features [0.3 s]
+✔ | 12 | Special cases of mkinfit calls [0.7 s]
+✔ | 8 | mkinmod model generation and printing [0.3 s]
✔ | 3 | Model predictions with mkinpredict [0.4 s]
-✔ | 14 2 | Evaluations according to 2015 NAFTA guidance [1.1 s]
+✔ | 14 2 | Evaluations according to 2015 NAFTA guidance [1.2 s]
────────────────────────────────────────────────────────────────────────────────
-test_nafta.R:25: skip: Test data from Appendix B are correctly evaluated
+Skip (test_nafta.R:26:5): Test data from Appendix B are correctly evaluated
Reason: getRversion() < "4.1.0" is TRUE
-test_nafta.R:53: skip: Test data from Appendix D are correctly evaluated
+Skip (test_nafta.R:55:5): Test data from Appendix D are correctly evaluated
Reason: getRversion() < "4.1.0" is TRUE
────────────────────────────────────────────────────────────────────────────────
-✔ | 9 | Nonlinear mixed-effects models [7.8 s]
+✔ | 9 | Nonlinear mixed-effects models [8.2 s]
✔ | 0 1 | Plotting [0.7 s]
────────────────────────────────────────────────────────────────────────────────
-test_plot.R:24: skip: Plotting mkinfit and mmkin objects is reproducible
+Skip (test_plot.R:25:3): Plotting mkinfit and mmkin objects is reproducible
Reason: getRversion() < "4.1.0" is TRUE
────────────────────────────────────────────────────────────────────────────────
✔ | 4 | Residuals extracted from mkinfit models
-✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.5 s]
+✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.6 s]
✔ | 4 | Summary [0.1 s]
✔ | 1 | Summaries of old mkinfit objects
-✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.2 s]
-✔ | 9 | Hypothesis tests [7.0 s]
-✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.5 s]
+✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.3 s]
+✔ | 9 | Hypothesis tests [7.2 s]
+✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.4 s]
══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 37.8 s
+Duration: 39.5 s
-OK: 146
-Failed: 0
-Warnings: 0
-Skipped: 3
+── Skipped tests ──────────────────────────────────────────────────────────────
+● getRversion() < "4.1.0" is TRUE (3)
+
+[ FAIL 0 | WARN 0 | SKIP 3 | PASS 146 ]
diff --git a/tests/testthat/FOCUS_2006_D.csf b/tests/testthat/FOCUS_2006_D.csf
index 7d562426..5969712b 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: 2020-11-11
+Date: Dummy date 0000-00-00
Optimiser: IRLS
[Data]
diff --git a/tests/testthat/test_CAKE_export.R b/tests/testthat/test_CAKE_export.R
index 8445b69a..b3941f1b 100644
--- a/tests/testthat/test_CAKE_export.R
+++ b/tests/testthat/test_CAKE_export.R
@@ -6,10 +6,9 @@ test_that("Exporting is reproducible", {
"FOCUS D" = FOCUS_2006_D),
map = c(parent = "Parent", m1 = "M1"),
links = c(parent = "m1"),
- filename = "FOCUS_2006_D.csf", overwrite = TRUE,
- study = "FOCUS 2006 D")
+ filename = "FOCUS_2006_D.csf", overwrite = TRUE,
+ study = "FOCUS 2006 D", date = "Dummy date 0000-00-00")
csf <- readLines(con = "FOCUS_2006_D.csf")
- csf[8] <- "Date: Dummy date 0000-00-00"
expect_known_value(csf, file = "FOCUS_2006_D.rds")
expect_error(CAKE_export(ds = list("FOCUS C" = FOCUS_2006_C),
filename = "FOCUS_2006_D.csf", overwrite = FALSE),

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