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6 daysAxis legend formatting, update vignettesJohannes Ranke1-2/+2
6 daysMerge branch 'devel'Johannes Ranke2-3/+3
6 daysUpdate wordlist, bump date and simplify DESCRIPTIONJohannes Ranke2-3/+3
Also, the R-Universe URL that the badge points to is updated
2024-12-19Skip small symbols in plot.mixed()Ranke Johannes1-1/+1
2024-12-19Plot mixed models with more than 25 datasetsRanke Johannes1-1/+1
Closes #15
2024-12-19Support observed data as tibbleRanke Johannes1-1/+5
Closes #14
2024-09-06Support covariate models in parplot.multistartRanke Johannes1-7/+12
Also, filter negative scaled parameter values for plotting, with a warning.
2024-04-27Fix bug in R/create_deg_func.RJohannes Ranke1-11/+27
Closes #13
2023-11-26Deal with 'saem' fits failing when updating an 'mhmkin' objectJohannes Ranke2-14/+32
2023-11-23fix: 'R/illparms.R': An ill-defined random effect is now also found if there ↵Johannes Ranke1-4/+6
is only one random effect in the model. Also add a test for this.
2023-08-07TyposRanke Johannes1-2/+2
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 Ranke2-2/+2
- 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 Ranke1-1/+4
2023-04-20Merge branch 'v1.2.3_pkgdown'Johannes Ranke1-1/+3
2023-04-17Post release changes to the docsJohannes Ranke1-1/+3
The cyantraniliprole and dmta pathway vignettes were not working any more with the latest changes in deSolve and mkin. All docs need a rebuild.
2023-04-17Improve docs of multistart methodJohannes Ranke1-7/+4
2023-04-16Suppress a warning about a path "(embedding)"Johannes Ranke1-2/+4
2023-04-15Increase test coverageJohannes Ranke1-0/+4
Also, using mkin analytical solutions for more than one observed variable is not supported (but could be if out_values would be reordered).
2023-04-15Make predefined symbols saferJohannes Ranke4-10/+20
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
2023-04-15Make 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
2023-04-06Fix a bug with moved DLLs and current deSolveJohannes Ranke1-4/+3
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.
2023-04-02Deal with covariates in summary for saem.mmkin objectsJohannes Ranke1-1/+10
2023-03-23Support covariates in endpoints()Johannes Ranke2-8/+29
2023-03-22Merge branch 'main' into covariate_parms_and_endpointsJohannes Ranke1-1/+1
2023-03-22Fix typo in mkinerrminJohannes Ranke1-1/+1
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
2023-02-26Improve documentation of the formatJohannes Ranke1-2/+19
2023-02-23Basic check if covariate data are usableJohannes Ranke1-4/+11
2023-02-17Update online docs, fix bug that surfacedJohannes Ranke1-5/+6
2023-02-17Finish adapting to upcoming deSolveJohannes Ranke4-24/+19
2023-02-17Merge remote-tracking branch 'origin/main' into faster_lsodaJohannes Ranke1-4/+3
2023-02-13Update mmkin docs, parallel is not loaded any moreJohannes Ranke1-4/+3
2023-02-13WIP adapting to new deSolve with faster lsodaJohannes Ranke2-83/+20
2023-02-13Merge branch 'main' into custom_lsoda_callJohannes Ranke15-78/+277
2023-01-09Prebuilt PDF vignettes, summary_listingJohannes Ranke3-33/+60
2023-01-05Don't preschedule multistart runsJohannes Ranke1-2/+5
Sometimes a lot of them fail, so we were wasting time
2023-01-04Update documentation of 'use_of_ff' argumentJohannes Ranke1-1/+1
2023-01-03Improved skeleton for hierarchical fitsJohannes Ranke1-0/+1
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.
2023-01-02Fix no_random_effect with character vectorJohannes Ranke1-1/+1
2023-01-02Echo R code per default in markdown templateJohannes Ranke1-1/+1
2022-12-19Rename template folder, create formatJohannes Ranke2-1/+40
Instead of rmarkdown::pdf_document, mkin::hierarchical_kinetics is used as a document format in the template. In this way, the template file can be freed from some R code and yaml options that the average user does not have to be aware of.
2022-12-15List random effects correlations in output if anyJohannes Ranke2-4/+20
Update docs
2022-12-07Fix parplot for the case of failed multistart runsJohannes Ranke2-2/+2
2022-12-07Check slopes in saemix covariate modelsJohannes Ranke1-1/+13
2022-12-06Some parplot improvementsJohannes Ranke1-4/+12
llquant argument, improved legend text, tests

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