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2022-03-08Avoid using multiple processes on CRAN check machinesJohannes Ranke1-5/+5
2022-03-07Remove nlmixr interface for release of mkin 1.1.0Johannes Ranke1-24/+21
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).
2022-03-03R-devel with openblasJohannes Ranke1-13/+13
2022-03-03More work to try to pass tests on R-devel winbuilderJohannes Ranke1-10/+10
2022-03-02Make tests more platform independent, update docsJohannes Ranke1-17/+17
2022-03-02Fix nlmixr fits with parallel metabolitesJohannes Ranke1-13/+13
2022-03-02Add a test for tffm0()Johannes Ranke1-7/+8
2022-03-01Avoid using cat() for default output, testsJohannes Ranke1-13/+13
2022-03-01Add some more testsJohannes Ranke1-11/+17
2022-02-28Improve tests, skip some on TravisJohannes Ranke1-10/+10
Respect digits argument when printing correlations in summaries
2022-02-28Add nlmixr tests, reorganize, test intervals()Johannes Ranke1-19/+22
2022-02-10GNUMakefile: Convince testthat to give dynamic outputJohannes Ranke1-156/+7
This means that we still get the \r in the test logs so so the postprocessing with sed works unmodified
2022-02-09Adapt saemix interface to saemix 3.0 on CRANJohannes Ranke1-8/+157
2021-11-17Update required saemix version, update testsJohannes Ranke1-30/+30
2021-09-16Adapt and improve the dimethenamid vignetteJohannes Ranke1-3/+3
Adapt to the corrected data and unify control parameters for saemix and nlmixr with saem. Update docs
2021-09-16Merge branch 'master' into nlmixrJohannes Ranke1-27/+13
2021-09-15Fix Open EFSA URL, changelog for 1.0.5v1.0.5Johannes Ranke1-4/+4
The EFSA URL failed on winbuilder because some cookie sets a different domain, so I am now using \href{} with the full link as link text instead of \url{}
2021-09-15Update test result to corrected data, version bumpJohannes Ranke1-8/+8
2021-07-23Merge branch 'master' into nlmixrJohannes Ranke1-20/+22
After the merge, run make test and accept the new snapshot for the mixed model fit for an nlme object
2021-07-23Rerun tests, use current vdiffr on travisJohannes Ranke1-33/+9
2021-06-17Let backtransform_odeparms handle nlmixr formation fractionsJohannes Ranke1-21/+24
Also adapt summary.nlmixr.mmkin to correctly handle the way formation fractions are translated to nlmixr
2021-04-21Merge branch 'master' into saemixJohannes Ranke1-20/+29
2021-04-21Version 1.0.4 published yesterdayv1.0.4Johannes Ranke1-18/+25
2021-03-31Bug fix in plot.mkinfitJohannes Ranke1-8/+25
In residual plots, use xlab and xlim if appropriate
2021-03-09Some improvements for borderline casesJohannes Ranke1-18/+18
- fit_with_errors for saem() - test_log_parms for mean_degparms() and saem()
2021-02-15Fully rebuild docs, rerun tests and checkJohannes Ranke1-14/+14
2021-02-15Merge branch 'master' into saemixJohannes Ranke1-1/+1
2021-02-15Improve README, introductory vignette and some other docsv1.0.3Johannes Ranke1-2/+2
Also bump version to 1.0.3.
2021-02-13Merge branch 'master' into saemixJohannes Ranke1-10/+10
Run make testcheck to regenerate logs with merge conflicts
2021-02-13Update for gmkin 0.6.12v1.0.2Johannes Ranke1-8/+8
mkinfit: Keep model names stored in mkinmod objects, avoiding their loss in gmkin
2021-02-06Reintroduce interface to saemixJohannes Ranke1-10/+17
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 Ranke1-10/+10
Platform dependence also revealed after upgrade to bullseye
2021-02-04Documentation improvements, mainly fixing example codeJohannes Ranke1-2/+2
The errors in the example code were in the \dontrun sections, so they were not caught by CRAN checks. In addition, the static help files generated with pkgdown were cached, so I noticed the errors only after completely regenerating the documentation for version 1.0.0.
2021-02-03Prepare for v1.0.0v1.0.0Johannes Ranke1-33/+20
- 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
2021-01-06Make saemix and corresponding tests optionalJohannes Ranke1-23/+29
Address release critical check and test issues
2020-12-19Dimethenamid data, normalisation optionsJohannes Ranke1-8/+8
2020-12-10Add a test for saemix with deSolveJohannes Ranke1-9/+16
But skip the test as it takes too long to always run
2020-12-09Make saem using mkinpredict work againJohannes Ranke1-7/+7
I threw out mclapply as it did not play well with the linear algebra routines used in the saemix code. Most of the change is actually indentation in the code creating the model function. But there is an important fix in mkinpredict which I had broken.
2020-12-09Some test fixesJohannes Ranke1-38/+7
2020-12-09Add more tests and fix HS in saemJohannes Ranke1-9/+40
2020-12-09Fix a test I accidentally brokeJohannes Ranke1-17/+12
2020-12-09Any yet more testsJohannes Ranke1-14/+19
2020-12-09Fix tests and rerunJohannes Ranke1-28/+10
2020-12-08mixed.mmkin and test coverageJohannes Ranke1-17/+23
2020-12-02Possibility to specify random effects structuresJohannes Ranke1-13/+9
The default is pdDiag again, as we often have a small number of datasets in degradation kinetics.
2020-11-30Log-Cholesky parameterisation as default in nlme.mmkinJohannes Ranke1-9/+13
2020-11-27Improved way to have persistent DLLs for mkinmodJohannes Ranke1-6/+6
Depends on inline >= 0.16.2 (including the bug fixes from eddelbuettel/inline#18), which provides 'moveDLL' to store the DLL for a compiled function in a safe place in case the argument 'dll_dir' is specified in the call to 'mkinmod'. Huge thanks to Dirk @eddelbuettel for his review and support for the work on the inline package.
2020-11-24Support storing mkinmod compiled code as CFunc objectsJohannes Ranke1-8/+8
With automatic reloading in mkinfit and mkinpredict in case the DLL is not loaded and the original DLL path has been cleaned up. Depends on jranke/inline@974bdea04fcedfafaab231e6f359c88270b56cb9 See inline#13
2020-11-19Update tests, improve CAKE_export testJohannes Ranke1-20/+21
2020-11-08Improve saem method, add summaryJohannes Ranke1-3/+3
Also make the endpoints function work for saem objects.

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