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authorJohannes Ranke <jranke@uni-bremen.de>2022-07-21 20:12:35 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2022-07-21 20:12:35 +0200
commitec151046007d1fc57585e0a4fee8fb41300611e3 (patch)
tree7856fa22812d7311f792d4da8095c552f8d07794
parentd1ae627e78579716e32fec8c22627b722a654675 (diff)
Remove platform sensitive convergence tests
-rw-r--r--summary_parent_FOCUS_2006.txt20
-rw-r--r--test.log18
-rw-r--r--tests/testthat/summary_parent_FOCUS_2006.txt20
-rw-r--r--tests/testthat/test_summary.R2
4 files changed, 20 insertions, 40 deletions
diff --git a/summary_parent_FOCUS_2006.txt b/summary_parent_FOCUS_2006.txt
deleted file mode 100644
index d31bd869..00000000
--- a/summary_parent_FOCUS_2006.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-Error model: Constant variance
-Fitted in test time 0 s
-
-Convergence:
- dataset
-model FOCUS_A FOCUS_C FOCUS_D
- SFO OK OK OK
- FOMC OK OK OK
- DFOP OK OK OK
- HS OK OK OK
-
-OK: No warnings
-
-Ill-defined parameters:
- dataset
-model FOCUS_A FOCUS_C FOCUS_D
- SFO
- FOMC parent_0, alpha, beta, sigma alpha, beta
- DFOP g g
- HS k2
diff --git a/test.log b/test.log
index 03755ce5..266a566f 100644
--- a/test.log
+++ b/test.log
@@ -3,11 +3,11 @@ Loading required package: parallel
ℹ Testing mkin
✔ | F W S OK | Context
✔ | 5 | AIC calculation
-✔ | 5 | Analytical solutions for coupled models [3.4s]
+✔ | 5 | Analytical solutions for coupled models [3.2s]
✔ | 5 | Calculation of Akaike weights
✔ | 3 | Export dataset for reading into CAKE
✔ | 12 | Confidence intervals and p-values [1.0s]
-✔ | 1 12 | Dimethenamid data from 2018 [34.2s]
+✔ | 1 12 | Dimethenamid data from 2018 [31.6s]
────────────────────────────────────────────────────────────────────────────────
Skip (test_dmta.R:98:3): Different backends get consistent results for SFO-SFO3+, dimethenamid data
Reason: Fitting this ODE model with saemix takes about 15 minutes on my system
@@ -16,7 +16,7 @@ Reason: Fitting this ODE model with saemix takes about 15 minutes on my system
✔ | 5 | Time step normalisation
✔ | 4 | Calculation of FOCUS chi2 error levels [0.6s]
✔ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [0.8s]
-✔ | 4 | Test fitting the decline of metabolites from their maximum [0.4s]
+✔ | 4 | Test fitting the decline of metabolites from their maximum [0.3s]
✔ | 1 | Fitting the logistic model [0.2s]
✔ | 1 12 | Nonlinear mixed-effects models [0.2s]
────────────────────────────────────────────────────────────────────────────────
@@ -27,14 +27,14 @@ Reason: Fitting with saemix takes around 10 minutes when using deSolve
✔ | 10 | Special cases of mkinfit calls [0.4s]
✔ | 3 | mkinfit features [0.7s]
✔ | 8 | mkinmod model generation and printing [0.2s]
-✔ | 3 | Model predictions with mkinpredict [0.3s]
+✔ | 3 | Model predictions with mkinpredict [0.4s]
✔ | 16 | Evaluations according to 2015 NAFTA guidance [1.7s]
-✔ | 9 | Nonlinear mixed-effects models with nlme [8.5s]
-✔ | 16 | Plotting [10.2s]
+✔ | 9 | Nonlinear mixed-effects models with nlme [8.3s]
+✔ | 16 | Plotting [10.6s]
✔ | 4 | Residuals extracted from mkinfit models
-✔ | 25 | saemix parent models [175.0s]
+✔ | 25 | saemix parent models [172.9s]
✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.4s]
-✔ | 7 | Fitting the SFORB model [3.6s]
+✔ | 7 | Fitting the SFORB model [3.7s]
✔ | 1 | Summaries of old mkinfit objects
✔ | 5 | Summary [0.2s]
✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.1s]
@@ -42,7 +42,7 @@ Reason: Fitting with saemix takes around 10 minutes when using deSolve
✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.2s]
══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 260.5 s
+Duration: 255.9 s
── Skipped tests ──────────────────────────────────────────────────────────────
• Fitting this ODE model with saemix takes about 15 minutes on my system (1)
diff --git a/tests/testthat/summary_parent_FOCUS_2006.txt b/tests/testthat/summary_parent_FOCUS_2006.txt
index d31bd869..60a36b67 100644
--- a/tests/testthat/summary_parent_FOCUS_2006.txt
+++ b/tests/testthat/summary_parent_FOCUS_2006.txt
@@ -3,18 +3,18 @@ Fitted in test time 0 s
Convergence:
dataset
-model FOCUS_A FOCUS_C FOCUS_D
- SFO OK OK OK
- FOMC OK OK OK
- DFOP OK OK OK
- HS OK OK OK
+model FOCUS_C FOCUS_D
+ SFO OK OK
+ FOMC OK OK
+ DFOP OK OK
+ HS OK OK
OK: No warnings
Ill-defined parameters:
dataset
-model FOCUS_A FOCUS_C FOCUS_D
- SFO
- FOMC parent_0, alpha, beta, sigma alpha, beta
- DFOP g g
- HS k2
+model FOCUS_C FOCUS_D
+ SFO
+ FOMC alpha, beta
+ DFOP g
+ HS k2
diff --git a/tests/testthat/test_summary.R b/tests/testthat/test_summary.R
index a31d3bae..87dc7de2 100644
--- a/tests/testthat/test_summary.R
+++ b/tests/testthat/test_summary.R
@@ -47,7 +47,7 @@ test_that("Summaries are reproducible", {
})
test_that("Summaries of mmkin objects are reproducible", {
- test_summary <- summary(fits)
+ test_summary <- summary(fits[ , 2:3])
test_summary$time <- c(elapsed = "test time 0")
expect_known_output(print(test_summary), "summary_parent_FOCUS_2006.txt")
})

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