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2025-05-12Check and test locallyJohannes Ranke1-1/+1
2025-02-16Fix solution type "deSolve" for a special caseJohannes Ranke1-1/+1
The special case occurs if not observed data for time zero are available. Fixes #16. Write NEWS and update docs. A lot of html was regenerated, because I had checked out the main branch in between, which made pkgdown believe that I have changed the help files.
2025-02-14Initialize dev docsJohannes Ranke1-2/+2
2025-02-13Avoid note about spellingJohannes Ranke1-1/+1
2025-02-13Update wordlist, bump date and simplify DESCRIPTIONJohannes Ranke1-8/+7
Also, the R-Universe URL that the badge points to is updated
2024-07-28Make sure test work on my desktop, skip more tests on travisJohannes Ranke1-1/+1
2024-04-27Fix bug in R/create_deg_func.RJohannes Ranke1-3/+3
Closes #13
2023-11-26Deal with 'saem' fits failing when updating an 'mhmkin' objectJohannes Ranke1-2/+2
2023-11-25Bump the date to trigger build on TravisJohannes Ranke1-1/+1
They refilled my credits, thanks for that!
2023-11-23Bump version, fix test from last commit, check and testJohannes Ranke1-2/+2
2023-10-13Update DESCRIPTION und NEWSJohannes Ranke1-2/+2
2023-08-09Depend on saemix 3.2 to control test resultsRanke Johannes1-1/+1
2023-08-09Don't install saemix 3.2 from github any moreRanke Johannes1-1/+1
Emmanuelle has made an official release to CRAN in June
2023-08-04Mesotrione data and vignetteJohannes Ranke1-2/+2
The vignette illustrates pH dependent degradation (covariate modelling) with some detail for the parent compound. Also, a bug in the saem method of the illparms function was fixed, which prevented to find ill-defined parameters in cases where e.g. slopes of covariate models have a negative estimate.
2023-05-19Prepare release of v1.2.4v1.2.4Johannes Ranke1-1/+1
- Update DESCRIPTION - Update Makefile to document how to use R-patched - Remove markup from two URLs to avoid CRAN NOTE - Switch two vignettes from html_document to html_vignette to save space in the docs directory, also avoiding a CRAN NOTE - Complete rebuild of pkgdown docs for release
2023-04-20Merge branch 'v1.2.3_pkgdown'Johannes Ranke1-1/+1
2023-04-20Fix and rebuild documentation, see NEWSJohannes Ranke1-2/+2
I had to fix the two pathway vignettes, as they did not work with the released version any more. So they and the multistart vignette which got some small fixes as well were rebuilt. Complete rebuild of the online docs with the released version. The documentation of the 'hierarchial_kinetics' format had to be fixed as well.
2023-04-17Bump version, add release date of v1.2.3Johannes Ranke1-2/+2
2023-04-16Bump datev1.2.3Johannes Ranke1-1/+1
2023-04-15Update description and newsJohannes Ranke1-1/+1
2023-04-06Check notes on winbuilderJohannes Ranke1-2/+2
- The CRAN spell check does not like 'backend', using 'back end' now - URL updates in README
2023-04-02Bump dateJohannes Ranke1-1/+1
2023-03-23Support covariates in endpoints()Johannes Ranke1-1/+1
2023-02-17Rethink versioning and remove 7950X benchmarksJohannes Ranke1-1/+1
I will add benchmark data for 1.2.0, 1.2.2 and 1.2.3 for better comparison
2023-02-17Finish adapting to upcoming deSolveJohannes Ranke1-1/+1
2023-02-13WIP adapting to new deSolve with faster lsodaJohannes Ranke1-1/+1
2023-02-13Merge branch 'main' into custom_lsoda_callJohannes Ranke1-9/+9
2023-01-09Prebuilt PDF vignettes, summary_listingJohannes Ranke1-1/+1
2023-01-03Improved skeleton for hierarchical fitsJohannes Ranke1-7/+7
Now with working pathway fits using SFORB-SFO2 (only two parallel metabolites instead of three) as the data for compound Ia was not sufficient for a reliable fit.
2022-11-24Start online docs of the development versionJohannes Ranke1-1/+1
2022-11-22Start new development versionJohannes Ranke1-2/+2
2022-11-18Prepare follow-up release to fix CRAN checksJohannes Ranke1-2/+2
2022-11-16Update DESCRIPTION and NEWS, check and testJohannes Ranke1-1/+1
2022-11-16We get about 25% performance gainJohannes Ranke1-4/+4
with the custom lsoda call, avoiding repeated getNativeSymbolInfo calls. It's just that we should not be calling foreign functions from different packages, because the may change without notice. Using getNativeSymbolInfo for "call_lsoda" avoids the CRAN note, and a similar call could probably be used for "unlock_solver", avoiding the NOTE in checks for cran, but we should not do this in a CRAN package.
2022-11-01Add tex_listing()Johannes Ranke1-1/+1
2022-11-01Add read_spreadsheetJohannes Ranke1-1/+1
2022-10-29Next version will be 1.2.0, complete NEWSJohannes Ranke1-1/+1
2022-10-26We don't use KernSmooth any moreJohannes Ranke1-2/+1
2022-09-16Diagnostic plots for multistart methodJohannes Ranke1-2/+3
2022-09-14Remove purrr dependencyJohannes Ranke1-2/+2
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.
2022-08-10Increase test coverage, require saemix version 3.1Johannes Ranke1-1/+1
2022-07-26Import parallel instead of depending on itJohannes Ranke1-4/+4
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
2022-07-21Summary method for mmkin objectsJohannes Ranke1-2/+2
Also, add a method for gathering convergence information and a method for gathering information on ill-defined parameters
2022-07-08Store DLL info in mkinmod objects for performanceJohannes Ranke1-2/+2
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.
2022-05-18Remove outdated comment in FOCUS L vignette, update docsJohannes Ranke1-1/+1
This also adds the first benchmark results obtained on my laptop system
2022-04-09Improvements to mean_degparms() and plot.mixed.mmkin()Johannes Ranke1-1/+1
- New argument 'default_log_parms' for mean_degparms() - 'plot.mixed.mmkin': Pass the frame argument also to residual plots, take the 'default_log_parms' argument for 'mean_degparms' used for constructing approximate population curves, plot population curve last to avoid that it is covered by data
2022-03-07Update maintainer e-mail addressJohannes Ranke1-1/+1
2022-03-07Remove nlmixr interface for release of mkin 1.1.0Johannes Ranke1-2/+2
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).
2022-03-03More work to try to pass tests on R-devel winbuilderJohannes Ranke1-1/+1
2022-03-02Make tests more platform independent, update docsJohannes Ranke1-1/+1

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