From 2ee20b257e34210e2d1f044431f3bfe059c9c5e7 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Sat, 6 Feb 2021 09:46:53 +0100 Subject: Increase test tolerance for parameter comparisons Platform dependence also revealed after upgrade to bullseye --- NEWS.md | 2 ++ docs/news/index.html | 1 + docs/pkgdown.yml | 2 +- test.log | 20 ++++++++++---------- tests/testthat/test_error_models.R | 8 ++++---- 5 files changed, 18 insertions(+), 15 deletions(-) diff --git a/NEWS.md b/NEWS.md index a7f52b88..124111d6 100644 --- a/NEWS.md +++ b/NEWS.md @@ -8,6 +8,8 @@ - Remove tests relying on non-convergence of the FOMC fit to the FOCUS A dataset as this is platform dependent (revealed by the new additional tests on CRAN, thanks!) +- Increase test tolerance for some parameter comparisons that also proved to be platform dependent + # mkin 1.0.0 ## General diff --git a/docs/news/index.html b/docs/news/index.html index c568202b..5b24742f 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -150,6 +150,7 @@

  • ‘logLik.mkinfit’: Improve example code to avoid warnings and show convenient syntax

  • ‘mkinresplot’: Re-add Katrin Lindenberger as coauthor who was accidentally removed long ago

  • Remove tests relying on non-convergence of the FOMC fit to the FOCUS A dataset as this is platform dependent (revealed by the new additional tests on CRAN, thanks!)

    • +

  • Increase test tolerance for some parameter comparisons that also proved to be platform dependent

    • diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 463d6e59..4100aea3 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -10,7 +10,7 @@ articles: web_only/NAFTA_examples: NAFTA_examples.html web_only/benchmarks: benchmarks.html web_only/compiled_models: compiled_models.html -last_built: 2021-02-06T08:30Z +last_built: 2021-02-06T08:46Z urls: reference: https://pkgdown.jrwb.de/mkin/reference article: https://pkgdown.jrwb.de/mkin/articles diff --git a/test.log b/test.log index 9c075726..d609022b 100644 --- a/test.log +++ b/test.log @@ -6,11 +6,11 @@ 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 [3.5 s] +✔ | 7 | Fitting the SFORB model [3.4 s] ✔ | 5 | Analytical solutions for coupled models [3.3 s] ✔ | 5 | Calculation of Akaike weights -✔ | 14 | Confidence intervals and p-values [1.2 s] -✔ | 14 | Error model fitting [4.4 s] +✔ | 12 | Confidence intervals and p-values [1.0 s] +✔ | 14 | Error model fitting [4.2 s] ✔ | 5 | Time step normalisation ✔ | 4 | Test fitting the decline of metabolites from their maximum [0.3 s] ✔ | 1 | Fitting the logistic model [0.2 s] @@ -19,19 +19,19 @@ Testing mkin ✔ | 1 | mkinfit features [0.3 s] ✔ | 10 | Special cases of mkinfit calls [0.3 s] ✔ | 8 | mkinmod model generation and printing [0.2 s] -✔ | 3 | Model predictions with mkinpredict [0.4 s] +✔ | 3 | Model predictions with mkinpredict [0.3 s] ✔ | 16 | Evaluations according to 2015 NAFTA guidance [1.6 s] -✔ | 9 | Nonlinear mixed-effects models [7.8 s] +✔ | 9 | Nonlinear mixed-effects models [8.0 s] ✔ | 14 | Plotting [1.7 s] ✔ | 4 | Residuals extracted from mkinfit models ✔ | 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 [7.2 s] -✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.4 s] +✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.2 s] +✔ | 9 | Hypothesis tests [8.1 s] +✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.6 s] ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 40.6 s +Duration: 41.3 s -[ FAIL 0 | WARN 0 | SKIP 0 | PASS 176 ] +[ FAIL 0 | WARN 0 | SKIP 0 | PASS 174 ] diff --git a/tests/testthat/test_error_models.R b/tests/testthat/test_error_models.R index c11f6712..fee29d2c 100644 --- a/tests/testthat/test_error_models.R +++ b/tests/testthat/test_error_models.R @@ -33,22 +33,22 @@ test_that("The different error model fitting methods work for parent fits", { f_9_threestep <- mkinfit("SFO", test_9, error_model = "tc", error_model_algorithm = "threestep", quiet = TRUE) expect_equivalent(round(AIC(f_9_threestep), 2), 139.43) - expect_equivalent(parms(f_9_threestep)[1:3], f_9_parms_const) + expect_equivalent(parms(f_9_threestep)[1:3], f_9_parms_const, tolerance = 1e-5) f_9_fourstep <- mkinfit("SFO", test_9, error_model = "tc", error_model_algorithm = "fourstep", quiet = TRUE) expect_equivalent(round(AIC(f_9_fourstep), 2), 139.43) - expect_equivalent(parms(f_9_fourstep)[1:3], f_9_parms_const) + expect_equivalent(parms(f_9_fourstep)[1:3], f_9_parms_const, tolerance = 1e-5) f_9_IRLS <- mkinfit("SFO", test_9, error_model = "tc", error_model_algorithm = "IRLS", quiet = TRUE) expect_equivalent(round(AIC(f_9_IRLS), 2), 139.43) - expect_equivalent(parms(f_9_IRLS)[1:3], f_9_parms_const) + expect_equivalent(parms(f_9_IRLS)[1:3], f_9_parms_const, tolerance = 1e-5) f_9_d_3 <- mkinfit("SFO", test_9, error_model = "tc", error_model_algorithm = "d_3", quiet = TRUE) expect_equivalent(round(AIC(f_9_d_3), 2), 134.94) - expect_equivalent(parms(f_9_d_3), f_9_parms_tc_direct) + expect_equivalent(parms(f_9_d_3), f_9_parms_tc_direct, tolerance = 1e-5) }) test_that("The default error model algorithm finds the best known AIC values for parent fits", { -- cgit v1.2.1