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2023-08-07TyposRanke Johannes1-2/+2
2023-08-04Mesotrione data and vignetteJohannes Ranke15-703/+1318
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 Ranke185-5978/+3258
- 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
2023-05-08Fix obtaining endpoints for user defined covariate valuesJohannes Ranke2-3/+6
2023-04-20Update vignettes in dev docsJohannes Ranke31-260/+341
After the post-release fixes to the release version online docs
2023-04-20Switch docs back to devel modeJohannes Ranke1-2/+2
2023-04-20Merge branch 'v1.2.3_pkgdown'Johannes Ranke272-1788/+15228
2023-04-20Fix and rebuild documentation, see NEWSJohannes Ranke269-1784/+15174
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.
2023-04-20Small changes to the multistart vignetteJohannes Ranke1-16/+11
- Fix legend positions and y axis scaling - Include two more variants in the model comparison at the end, and fix the logic of the discussion
2023-04-17Post release changes to the docsJohannes Ranke4-17/+54
The cyantraniliprole and dmta pathway vignettes were not working any more with the latest changes in deSolve and mkin. All docs need a rebuild.
2023-04-17Bump version, add release date of v1.2.3Johannes Ranke2-3/+3
2023-04-17Improve docs of multistart methodJohannes Ranke22-186/+99
2023-04-16Bump datev1.2.3Johannes Ranke1-1/+1
2023-04-16Suppress a warning about a path "(embedding)"Johannes Ranke1-2/+4
2023-04-16Skip another test on CRAN to save CPU cyclesJohannes Ranke1-0/+2
2023-04-16Complete rebuild of static docsJohannes Ranke213-1253/+3513
2023-04-16Add coverage target for local coverage reportJohannes Ranke3-0/+6
I get almost 90% when testing locally
2023-04-16Make travis wait longer also for codecov coverageJohannes Ranke1-1/+1
2023-04-16Make the template work on Windows (with RStudio)Johannes Ranke1-4/+8
It seems that we cannot use stored DLLs (for pathway fits) on clusters when using Windows, where we use PSOCK clusters. Although it works on winbuilder in the tests in tests/testthat/test_compiled.R. Maybe it is something RStudio specific.
2023-04-16Skip the Eigenvalue based saem testJohannes Ranke2-13/+18
It took too long, and this solution method is not recommended. We are saving 140 seconds here on my system, so more time is saved on travis.
2023-04-15Need even more time for tests nowJohannes Ranke1-1/+1
2023-04-15Fix the travis_wait commandJohannes Ranke1-1/+1
2023-04-15The tests run longer now, so make travis waitJohannes Ranke1-1/+1
2023-04-15Increase test coverageJohannes Ranke6-20/+92
Also, using mkin analytical solutions for more than one observed variable is not supported (but could be if out_values would be reordered).
2023-04-15Update description and newsJohannes Ranke2-3/+7
2023-04-15Fix logic in testJohannes Ranke1-1/+1
2023-04-15Merge branch 'codecov'Johannes Ranke1-0/+1
2023-04-15Fix platform dependence in testJohannes Ranke1-1/+5
2023-04-15Make predefined symbols saferJohannes Ranke9-28/+113
We still need to create a parallel processing cluster _after_ creating a compiled model that is moved to a user defined location, at least I did not find another way to make it work. This is not a problem with parallel processing without a cluster, which is not available on Windows.
2023-04-15Don't try(mkinpredict), it would still error laterJohannes Ranke1-3/+2
2023-04-15Move preprocessing of DMTA data to the test setupJohannes Ranke2-11/+12
2023-04-15Make using predefined symbols optionalJohannes Ranke1-2/+11
I got crashes under some circumstances when using symbols stored in the mkinmod object. One such circumstance was the use of a moved DLL in combination with parallel computing on a cluster. As I cannot exactly define at the moment when this happens, it is better to make this an opt in.
2023-04-14Dont fix mean_degparms if it does not existJohannes Ranke1-4/+6
2023-04-14Reintroduce codecov badge with correct linkJohannes Ranke1-0/+1
2023-04-06Remove codecov badge, as the link does not workJohannes Ranke2-2/+1
Also, every time I would like to log in to codecov.io with my github account, it tells me that it wants complete read and write access to all my repositories, which I do not want to grant for obvious reasons.
2023-04-06Fix a bug with moved DLLs and current deSolveJohannes Ranke3-24/+18
In mkinmod, dll_info was not included in the returned model object in the case that the DLL was moved to a user defined directory. This is now fixed.
2023-04-06Check notes on winbuilderJohannes Ranke3-6/+6
- The CRAN spell check does not like 'backend', using 'back end' now - URL updates in README
2023-04-02Bump dateJohannes Ranke1-1/+1
2023-04-02Deal with covariates in summary for saem.mmkin objectsJohannes Ranke5-20/+49
2023-04-01Update tests on 5950xJohannes Ranke7-166/+159
Update platform dependent test plots
2023-03-23Support covariates in endpoints()Johannes Ranke12-49/+100
2023-03-22Merge branch 'main' into covariate_parms_and_endpointsJohannes Ranke10-160/+169
2023-03-22Fix typo in mkinerrminJohannes Ranke10-160/+169
Thanks to Sebastian Meyer for spotting it.
2023-03-22Fix plotting saemix without covariates, polishJohannes Ranke1-4/+11
Better linetypes and labels
2023-03-20Support covariates in parms and plot.saem.mmkinJohannes Ranke3-53/+113
2023-03-15Start parms and endpoints for covariatesJohannes Ranke2-3/+13
2023-03-14deSolve 1.35 is on CRAN now, thanks Thomas!Johannes Ranke1-1/+0
2023-02-26Improve documentation of the formatJohannes Ranke2-3/+38
2023-02-23Basic check if covariate data are usableJohannes Ranke1-4/+11
2023-02-18Tell travis to take deSolve from drat repoJohannes Ranke1-0/+1
It seems that eddelbuettel/r-ci#10 is still bugging me

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