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2021-09-27intervals() methods, more DFOP/tc variantsJohannes Ranke1-0/+2
2021-09-16Merge branch 'master' into nlmixrJohannes Ranke1-1/+5
2021-09-15Fix Open EFSA URL, changelog for 1.0.5v1.0.5Johannes Ranke1-0/+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{}
2021-07-29Go back to 1.0.x version, update docsJohannes Ranke1-0/+2
2021-07-27Publication date for 1.0.4 in NEWS, update docsJohannes Ranke1-1/+1
2021-06-11Finished 'summary.nlmixr.mmkin', checks, docsJohannes Ranke1-1/+1
2021-06-09Rudimentary support for setting up nlmixr modelsJohannes Ranke1-10/+4
- All degradation models are specified as ODE models. This appears to be fast enough - Error models are being translated to nlmixr as close to the mkin error model as possible. When using the 'saem' backend, it appears not to be possible to use the same error model for more than one observed variable - No support yet for models with parallel formation of metabolites, where the ilr transformation is used in mkin per default - There is a bug in nlmixr which appears to be triggered if the data are not balanced, see nlmixrdevelopment/nlmixr#530 - There is a print and a plot method, the summary method is not finished
2021-04-21Merge branch 'master' into saemixJohannes Ranke1-3/+5
2021-04-21Version 1.0.4 published yesterdayv1.0.4Johannes Ranke1-0/+2
2021-03-31Bug fix in plot.mkinfitJohannes Ranke1-2/+2
In residual plots, use xlab and xlim if appropriate
2021-03-19test_log_parms for plot.mixed.mmkin, roxygen runJohannes Ranke1-1/+3
2021-03-09Some improvements for borderline casesJohannes Ranke1-0/+2
- fit_with_errors for saem() - test_log_parms for mean_degparms() and saem()
2021-02-24Clarify version status in NEWSJohannes Ranke1-1/+1
2021-02-24Merge branch 'master' into saemixJohannes Ranke1-1/+7
2021-02-24Rebuild docsJohannes Ranke1-0/+6
2021-02-18Merge branch 'master' into saemixJohannes Ranke1-4/+4
2021-02-15Don't let pkgdown add release datesJohannes Ranke1-4/+4
It didn't pick up the release of 1.0.3, and most of the other release dates were duplicated.
2021-02-15Merge branch 'master' into saemixJohannes Ranke1-1/+5
2021-02-15Improve README, introductory vignette and some other docsv1.0.3Johannes Ranke1-0/+4
Also bump version to 1.0.3.
2021-02-13Structure NEWS entryJohannes Ranke1-0/+4
2021-02-13Merge branch 'master' into saemixJohannes Ranke1-1/+5
Run make testcheck to regenerate logs with merge conflicts
2021-02-13Update for gmkin 0.6.12v1.0.2Johannes Ranke1-0/+4
mkinfit: Keep model names stored in mkinmod objects, avoiding their loss in gmkin
2021-02-06Reintroduce interface to saemixJohannes Ranke1-0/+10
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 Ranke1-0/+2
Platform dependence also revealed after upgrade to bullseye
2021-02-06Address issue revealed by additional tests on CRANJohannes Ranke1-0/+2
Remove tests relying on non-convergence of the FOMC fit to the FOCUS A dataset, as this is platform dependent. After the upgrade, the fit converges on this system as well, although neither ATLAS is used, nor R was configured disabling long doubles (these were the conditions under which the tests failed on CRAN).
2021-02-04Documentation improvements, mainly fixing example codeJohannes Ranke1-0/+8
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 Ranke1-12/+3
- 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
2021-01-25Some more plotting improvementsJohannes Ranke1-2/+2
2021-01-25Change default ylab in plot.mkinfit, explicit ylab for plot.mmkinJohannes Ranke1-0/+5
See NEWS.md. Closes #12
2021-01-06Make saemix and corresponding tests optionalJohannes Ranke1-9/+17
Address release critical check and test issues
2020-12-08mixed.mmkin and test coverageJohannes Ranke1-0/+2
2020-12-07Updates after inline 0.3.17 has been releasedJohannes Ranke1-1/+1
2020-11-27Closes #11Johannes Ranke1-0/+2
2020-11-12mkindsg class to hold groups of datasetsJohannes Ranke1-0/+8
- D24_2014 dataset on aerobic soil degradation of 2,4-D from the EU assessment as mkindsg object with metadata - f_time_norm_focus() to do time-step normalisation using the FOCUS method - focus_soil_moisture data with default moisture contents at pF1, pF 2 and pF 2.5 for USDA soil types from FOCUS GW guidance - Dataset generation scripts in inst/dataset_generation - Depend on R >= 2.15.1 in order to facilitate the use of utils::globalVariables()
2020-11-09saemix.mmkin and nlme.mmkin inherit from mixed.mmkinJohannes Ranke1-1/+3
With a plot method. The class mixed.mmkin is currently only a virtual class created to unify the plotting method.
2020-11-08Improve saem method, add summaryJohannes Ranke1-0/+2
Also make the endpoints function work for saem objects.
2020-11-06Fast analytical solutions for saemix, update.mmkinJohannes Ranke1-0/+4
Also, use logit transformation for g and for solitary formation fractions, addressing #10.
2020-10-27Add summary method for nlme.mmkin objectsJohannes Ranke1-3/+1
Improve and update docs
2020-10-24Plot method for nlme.mmkin objectsJohannes Ranke1-0/+2
Update docs
2020-10-24Printing method for mmkin objectsJohannes Ranke1-0/+2
2020-10-15Reintroduce saemix helper functionsJohannes Ranke1-1/+5
2020-10-08Fix issues for releaseJohannes Ranke1-1/+1
2020-10-08Avoid dep on dev version of saemix for releaseJohannes Ranke1-3/+1
2020-09-01Back-calculated DT50 values for biphasic modelsJohannes Ranke1-0/+2
2020-07-17mkinfit: Ignore unused components of state.iniJohannes Ranke1-0/+2
2020-07-15Improve handling of (partially) failing fitsJohannes Ranke1-0/+4
2020-05-29Warn if standardized residuals are unlikely normalJohannes Ranke1-0/+2
This revealed a bug in the data returned in mkinfit$data in the case of the d_3 algorithm, which also affected the residual plot - the data from the direct fitting was not returned even if this was the better method.
2020-05-28use_of_ff = "max" for shorthand models like "SFO"Johannes Ranke1-0/+2
2020-05-26Use all cores per default, confint toleranceJohannes Ranke1-0/+4
Also, use more intelligent starting values for the variance of the random effects for saemix. While this does not appear to speed up the convergence, it shows where this variance is greatly reduced by using mixed-effects models as opposed to the separate independent fits.
2020-05-25First working version of saemix helper functionsJohannes Ranke1-0/+2
saemix_data depends on a development version of saemix, see pull request saemixdevelopment/saemixextension#2

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