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authorJohannes Ranke <jranke@uni-bremen.de>2020-12-09 19:12:38 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2020-12-09 19:12:38 +0100
commita5746dcc0e5a018548bf977f4ac61f0ad2a4dd2d (patch)
treeb3d9e3820368b7470ca0388ebdc5fb1b380fd8a6
parentb0341af402271a1339308ba930c12530f62d4cf8 (diff)
Some test fixes
-rw-r--r--test.log45
-rw-r--r--tests/testthat/print_sfo_saem_1.txt (renamed from tests/testthat/print_sfo_saemix_1.txt)2
-rw-r--r--tests/testthat/test_mixed.R2
-rw-r--r--tests/testthat/test_plot.R6
4 files changed, 11 insertions, 44 deletions
diff --git a/test.log b/test.log
index f39791ae..6105128f 100644
--- a/test.log
+++ b/test.log
@@ -6,7 +6,7 @@ Testing mkin
✔ | 2 | Export dataset for reading into CAKE
✔ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [1.0 s]
✔ | 4 | Calculation of FOCUS chi2 error levels [0.5 s]
-✔ | 7 | Fitting the SFORB model [3.6 s]
+✔ | 7 | Fitting the SFORB model [3.5 s]
✔ | 5 | Analytical solutions for coupled models [3.2 s]
✔ | 5 | Calculation of Akaike weights
✔ | 14 | Confidence intervals and p-values [1.2 s]
@@ -14,33 +14,7 @@ Testing mkin
✔ | 3 | Time step normalisation
✔ | 4 | Test fitting the decline of metabolites from their maximum [0.3 s]
✔ | 1 | Fitting the logistic model [0.2 s]
-⠏ | 8 2 | Nonlinear mixed effects models
-LL by is "-1333.17 (df=13)"
-
-LL by is "-1333.17 (df=13)"
-
-LL by is "-1336.30 (df=13)"
- ✖ | 11 2 | Nonlinear mixed effects models [6.4 s]
-────────────────────────────────────────────────────────────────────────────────
-ERROR (test_mixed.R:11:3): Parent only models can be fitted using nonlinear mixed effects models
-Error: object 'sfo_saem_1' not found
-Backtrace:
- 1. base::summary(sfo_saem_1) test_mixed.R:11:2
-
-FAILURE (test_mixed.R:91:3): Print methods work
-Results have changed from known value recorded in 'print_sfo_saemix_1.txt'.
-
-old[6:11] vs new[6:13]
- "Data:"
- "264 observations of 1 variable(s) grouped in 15 datasets"
- ""
- "Likelihood computed by importance sampling"
-+ " "
-+ "LL by is \"-653.97 (df=6)\""
- " AIC BIC logLik"
- " 1320 1324 -654"
- ""
-────────────────────────────────────────────────────────────────────────────────
+✔ | 31 | Nonlinear mixed effects models [27.5 s]
✔ | 2 | Test dataset classes mkinds and mkindsg
✔ | 1 | mkinfit features [0.3 s]
✔ | 12 | Special cases of mkinfit calls [0.8 s]
@@ -48,21 +22,16 @@ old[6:11] vs new[6:13]
✔ | 3 | Model predictions with mkinpredict [0.4 s]
✔ | 16 | Evaluations according to 2015 NAFTA guidance [1.6 s]
✔ | 9 | Nonlinear mixed-effects models [7.8 s]
-✖ | 15 1 | Plotting [1.9 s]
-────────────────────────────────────────────────────────────────────────────────
-FAILURE (test_plot.R:39:3): Plotting mkinfit and mmkin objects is reproducible
-Figures don't match: mixed-model-fit-for-nlme-object.svg
-
-────────────────────────────────────────────────────────────────────────────────
+✔ | 16 | Plotting [1.9 s]
✔ | 4 | Residuals extracted from mkinfit models
-✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.6 s]
+✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.5 s]
✔ | 4 | Summary [0.1 s]
✔ | 1 | Summaries of old mkinfit objects
✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.3 s]
✔ | 9 | Hypothesis tests [7.3 s]
-✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.3 s]
+✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.4 s]
══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 48.1 s
+Duration: 69.3 s
-[ FAIL 3 | WARN 0 | SKIP 0 | PASS 183 ]
+[ FAIL 0 | WARN 0 | SKIP 0 | PASS 204 ]
diff --git a/tests/testthat/print_sfo_saemix_1.txt b/tests/testthat/print_sfo_saem_1.txt
index 9dd4f175..d341e9e7 100644
--- a/tests/testthat/print_sfo_saemix_1.txt
+++ b/tests/testthat/print_sfo_saem_1.txt
@@ -6,8 +6,6 @@ Data:
264 observations of 1 variable(s) grouped in 15 datasets
Likelihood computed by importance sampling
-
-LL by is "-653.97 (df=6)"
AIC BIC logLik
1320 1324 -654
diff --git a/tests/testthat/test_mixed.R b/tests/testthat/test_mixed.R
index 6fc6c2f0..7798be8a 100644
--- a/tests/testthat/test_mixed.R
+++ b/tests/testthat/test_mixed.R
@@ -88,7 +88,7 @@ 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")
- expect_known_output(print(sfo_saemix_1, digits = 1), "print_sfo_saemix_1.txt")
+ expect_known_output(print(sfo_saem_1, digits = 1), "print_sfo_saem_1.txt")
})
test_that("nlme results are reproducible", {
diff --git a/tests/testthat/test_plot.R b/tests/testthat/test_plot.R
index b0bf2c8f..22f4307f 100644
--- a/tests/testthat/test_plot.R
+++ b/tests/testthat/test_plot.R
@@ -35,14 +35,14 @@ test_that("Plotting mkinfit and mmkin 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)
- plot_biphasic_nlme <- function() plot(dfop_nlme_1)
- vdiffr::expect_doppelganger("mixed model fit for nlme object", plot_biphasic_nlme)
-
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)
+ vdiffr::expect_doppelganger("mixed model fit for nlme object", plot_biphasic_nlme)
+
#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)

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