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2022-07-21Remove platform sensitive convergence testsJohannes Ranke2-11/+11
2022-07-21Summary method for mmkin objectsJohannes Ranke6-5038/+1195
Also, add a method for gathering convergence information and a method for gathering information on ill-defined parameters
2022-07-12Tests before releasev1.1.1Johannes Ranke3-1/+3870
2022-07-12Avoid spawning multiple cores in tests on CRANJohannes Ranke1-2/+2
2022-07-08Store DLL info in mkinmod objects for performanceJohannes Ranke2-1169/+1169
Thanks to Tomas Kalibera for his analysis of the problem on the r-package-devel mailing list and for the suggestion on how to fix it. See the current benchmark vignette for the new data on mkin 1.1.1 with R 4.2.1, with unprecedented performance.
2022-04-13More control of y axes in plot.mkinfit, updatesJohannes Ranke4-7/+7
Documentation and test results were updated, the latter with regard to the previous work on plot.mixed.mmkin.
2022-03-19Test saemix without special analytical solutionsJohannes Ranke1-0/+12
Also increase the performance a bit (from about 210 s to about 140 s in the case of DFOP with four chains and 300, 100 iterations).
2022-03-19Improvements to CAKE_export()Johannes Ranke3-9/+18
2022-03-14Reduce check time for CRAN, releasev1.1.0Johannes Ranke4-19/+17
2022-03-08Avoid using multiple processes on CRAN check machinesJohannes Ranke1-3/+3
2022-03-07Remove nlmixr interface for release of mkin 1.1.0Johannes Ranke8-2421/+2231
I am postponing my attempts to get the nlmixr interface to CRAN, given some problems with nlmixr using R-devel under Windows, see https://github.com/nlmixrdevelopment/nlmixr/issues/596 and https://github.com/r-hub/rhub/issues/512, which is fixed by the removal of nlmixr from the testsuite. For the tests to be more platform independent, the biphasic mixed effects models test dataset was defined in a way that fitting should be more robust (less ill-defined).
2022-03-03Reintroduce the skipped test, with a workaroundJohannes Ranke1-8/+15
2022-03-03Skip a test that assigns to the global environmentJohannes Ranke1-0/+1
2022-03-03More work to try to pass tests on R-devel winbuilderJohannes Ranke5-30/+24
2022-03-02Skip some tests on CRAN to reduce loadJohannes Ranke1-0/+2
In the hope that winbuilder will cope better then
2022-03-02Make tests more platform independent, update docsJohannes Ranke14-1393/+1343
2022-03-02Fix nlmixr fits with parallel metabolitesJohannes Ranke1-3/+14
2022-03-02Add a test for tffm0()Johannes Ranke1-0/+10
2022-03-01Avoid using cat() for default output, testsJohannes Ranke2-4/+13
2022-03-01Add some more testsJohannes Ranke7-35/+137
2022-03-01Some more tests for nlmixr.mmkinJohannes Ranke2-0/+6
2022-03-01Add a test for the DMTA dataJohannes Ranke1-39/+41
comparing nlme and saemix. This test shows a reasonable evaluation of the DMTA data with nlme and saemix, which was missing, as the data used in the paper are flawed.
2022-02-28Add test for summary.nlmixr.mmkinJohannes Ranke3-0/+118
2022-02-28Relax a test for travisJohannes Ranke2-27/+27
2022-02-28Improve tests, skip some on TravisJohannes Ranke3-13/+60
Respect digits argument when printing correlations in summaries
2022-02-28Add nlmixr tests, reorganize, test intervals()Johannes Ranke5-157/+214
2022-02-28With saemix 3.0 on CRAN there's no need to check for it in testsJohannes Ranke5-126/+79
2022-02-09Adapt saemix interface to saemix 3.0 on CRANJohannes Ranke6-1481/+1471
2021-11-17Update required saemix version, update testsJohannes Ranke5-1463/+1463
2021-09-16Merge branch 'master' into nlmixrJohannes Ranke1-1/+1
2021-09-15Update test result to corrected data, version bumpJohannes Ranke1-1/+1
2021-07-23Merge branch 'master' into nlmixrJohannes Ranke42-9122/+8461
After the merge, run make test and accept the new snapshot for the mixed model fit for an nlme object
2021-07-23Update vdiffr tests for version 1.0Johannes Ranke40-9110/+5248
2021-06-17Let backtransform_odeparms handle nlmixr formation fractionsJohannes Ranke1-97/+97
Also adapt summary.nlmixr.mmkin to correctly handle the way formation fractions are translated to nlmixr
2021-06-16Translate formation fractions to nlmixr languageJohannes Ranke1-0/+99
Works for the dimethenamid data, at least for FOCEI. Very little testing yet. The summary function does not yet handle the new transformations of formation fractions (that are in fact very old, as they were used in the very first version of mkin). The test file has no tests yet, just some code that may be used for testing.
2021-06-12Small cosmeticsJohannes Ranke1-1/+1
2021-04-21Merge branch 'master' into saemixJohannes Ranke4-112/+112
2021-04-21Version 1.0.4 published yesterdayv1.0.4Johannes Ranke4-112/+112
2021-03-09Some improvements for borderline casesJohannes Ranke11-3534/+3571
- fit_with_errors for saem() - test_log_parms for mean_degparms() and saem()
2021-02-24Merge branch 'master' into saemixJohannes Ranke2-0/+10
2021-02-24Reset graphical parameters with on.exit()Johannes Ranke2-0/+10
plot.mixed.mmkin did not reset graphical parameters at all. The other plotting functions did not use on.exit, so this change should make the use of the plotting functions safer.
2021-02-06Reintroduce interface to saemixJohannes Ranke6-3009/+3248
Also after the upgrade from buster to bullseye of my local system, some test results for saemix have changed.
2021-02-06Increase test tolerance for parameter comparisonsv1.0.1Johannes Ranke1-4/+4
Platform dependence also revealed after upgrade to bullseye
2021-02-06Address issue revealed by additional tests on CRANJohannes Ranke3-17/+6
Remove tests relying on non-convergence of the FOMC fit to the FOCUS A dataset, as this is platform dependent. After the upgrade, the fit converges on this system as well, although neither ATLAS is used, nor R was configured disabling long doubles (these were the conditions under which the tests failed on CRAN).
2021-02-03Prepare for v1.0.0v1.0.0Johannes Ranke4-237/+0
- Improve authorship and copyright information - Prepare pkgdown config - Remove dependence on saemix as we need the development version which is not ready for CRAN - Temporarily remove saemix interface to check code coverage of the rest
2021-01-25Update visual testsJohannes Ranke3-1895/+1895
2021-01-25Change default ylab in plot.mkinfit, explicit ylab for plot.mmkinJohannes Ranke12-20/+20
See NEWS.md. Closes #12
2021-01-06Make saemix and corresponding tests optionalJohannes Ranke7-50/+71
Address release critical check and test issues
2020-12-19Dimethenamid data, normalisation optionsJohannes Ranke3-2/+11
2020-12-17Remove two skipped (on Travis) tests to reduce noiseJohannes Ranke3-217/+1

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