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2022-09-16Improve multistart documentation, bugfixJohannes Ranke26-101/+1319
- Split out llhist and parhist documentation - Add example code for multistart - Create a multistart vignette, because the example code fails when run by pkgdown - Fix multistart for the case of mkin transformations in the saem fit
2022-09-16Tell travis to wait for coverage reportJohannes Ranke1-1/+1
2022-09-16Rerun test with saemix 3.1 from CRANJohannes Ranke3-14/+14
Apparently, the change I introduced into saemix saemixdevelopment/saemixextension#34 to fix error model parameters to positive values slightly influences the results. So this is now with the CRAN version to keep test results in sync with Travis
2022-09-16Improve docs and update pkgdownJohannes Ranke22-445/+560
2022-09-16Diagnostic plots for multistart methodJohannes Ranke13-111/+223
2022-09-14Remove purrr dependencyJohannes Ranke6-8/+11
We now directly import from rlang and vctrs, which were indirect dependencies anyways. purrr::map_dfr is deprecated in the upcoming purrr 1.0, and depends on dplyr (since when?) which is only suggested by purrr. This would lead new installations of mkin to fail if dplyr is not installed as well.
2022-09-13More work on multistartJohannes Ranke5-2/+18
2022-08-31Some more work on multistartJohannes Ranke2-5/+33
2022-08-14Basic multistart method for saem.mmkin objectsJohannes Ranke6-23/+99
2022-08-11Start a multistart methodJohannes Ranke2-0/+26
2022-08-10Update dev docsJohannes Ranke2-2/+2
2022-08-10Merge branch 'v1.1.2'Johannes Ranke75-4158/+5580
2022-08-10Remove codemeta file to avoid the maintenanceJohannes Ranke1-322/+0
2022-08-10Change dev branch used for docs, update static docsJohannes Ranke75-4158/+5580
2022-08-10Update docsJohannes Ranke4-263/+354
2022-08-10Naming of random effects for reduced parameter modelsJohannes Ranke4-6/+81
2022-08-10Increase test coverage, require saemix version 3.1Johannes Ranke7-6/+35
2022-08-10Update static docsJohannes Ranke16-282/+664
2022-08-10Batch processing for hierarchical fitsJohannes Ranke14-24/+460
- 'R/mhmkin.R': New method for performing multiple hierarchical mkin fits in one function call, optionally in parallel. - 'R/saem.R': 'logLik' and 'update' methods for 'saem.mmkin' objects. - 'R/illparms.R': Add methods for 'saem.mmkin' and 'mhmkin' objects. tests: Use 2 cores on travis, should work according to docs
2022-08-09Update docs for saemJohannes Ranke1-3/+3
2022-08-08Error on unsupported saemix transformationsJohannes Ranke4-13/+26
Also, support FOMC with saemix transformations
2022-08-08Fix fitting HS with saemix transformationsJohannes Ranke4-27/+39
2022-07-26Import parallel instead of depending on itJohannes Ranke3-6/+7
This cleans up the startup message. Loading parallel is not that important, users wanting to use it will know what to do. Also, add codemeta.json to .Rbuildignore
2022-07-23r-universe badge, release date of v1.1.1 in NEWSJohannes Ranke4-12/+11
Also skip complete log directory in .Rbuildignore and reorganize that file to improve readability
2022-07-22Update MakefileJohannes Ranke1-2/+1
2022-07-22Add codemeta file as created by R package codemetaJohannes Ranke1-0/+322
2022-07-22Remove TODO file as I hardly ever look at itJohannes Ranke1-7/+0
2022-07-22Move logs into own directory to clean rootJohannes Ranke8-15/+10
2022-07-22Update static docsJohannes Ranke15-50/+651
2022-07-21Try to tell covr that Travis is not CRANJohannes Ranke1-1/+1
2022-07-21Try coverage from r-ci, re-add badgesJohannes Ranke2-4/+6
2022-07-21Remove platform sensitive convergence testsJohannes Ranke4-40/+20
2022-07-21Try to explicitly install nlme from CRANJohannes Ranke1-0/+1
to get the current version
2022-07-21Try the r2u variantJohannes Ranke1-5/+4
2022-07-21Don't use BSPM as it fails due to low nlme versionJohannes Ranke1-3/+4
2022-07-21Try Travis with Dirks run.sh from eddelbuettel/r-ciJohannes Ranke3-5/+36
2022-07-21Remove travis config as R seems to be unmaintained thereJohannes Ranke3-29/+7
See https://travis-ci.community/t/please-update-the-r-version-used-for-r-release-to-r-4-1-0/11886 and the Pull request referenced there, and the message by Gabor which I found today: https://travis-ci.community/t/about-the-r-category/748/2
2022-07-21Update Travis configJohannes Ranke1-1/+3
- Use current R release - Add system libraries used by textshaping, pulled in by pkgdown
2022-07-21Summary method for mmkin objectsJohannes Ranke21-5117/+1574
Also, add a method for gathering convergence information and a method for gathering information on ill-defined parameters
2022-07-21Updates to summary.mkinfitJohannes Ranke1-2/+2
2022-07-14Improve readability of benchmark code shown in vignetteJohannes Ranke3-29/+44
2022-07-12Tests before releasev1.1.1Johannes Ranke5-132/+3906
2022-07-12Avoid spawning multiple cores in tests on CRANJohannes Ranke1-2/+2
2022-07-12Rerun benchmarks on desktop computerJohannes Ranke6-15/+193
2022-07-08Use inherits() instead of comparing class to stringJohannes Ranke1-1/+1
2022-07-08Store DLL info in mkinmod objects for performanceJohannes Ranke25-2157/+1952
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.
2022-07-01Sensitivity of AIC values in DMTA vignette to BLAS versionJohannes Ranke17-147/+2399
2022-07-01Rerun benchmarks with R 4.2.1 and openblas-serialJohannes Ranke2-11/+11
After confirming that lapack versus atlas versus openblas results are quite similar, and therefore not responsible for the differences between R 4.1.3 and R 4.2.1
2022-07-01Update benchmark article in online docsJohannes Ranke3-65/+65
2022-07-01Add benchmarks on laptop with R 4.1.3 and 4.2.1Johannes Ranke3-46/+75

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