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2021-03-31Bug fix in plot.mkinfitJohannes Ranke120-109/+213
In residual plots, use xlab and xlim if appropriate
2021-02-24Clarify version status in NEWSJohannes Ranke2-3/+3
2021-02-24Rebuild docsJohannes Ranke13-9/+17
2021-02-15Don't let pkgdown add release datesJohannes Ranke2-95/+50
It didn't pick up the release of 1.0.3, and most of the other release dates were duplicated.
2021-02-15Correct grant numbers in README, update docsJohannes Ranke7-33/+34
2021-02-15Improve README, introductory vignette and some other docsv1.0.3Johannes Ranke177-567/+815
Also bump version to 1.0.3.
2021-02-13Update for gmkin 0.6.12v1.0.2Johannes Ranke13-10/+18
mkinfit: Keep model names stored in mkinmod objects, avoiding their loss in gmkin
2021-02-06Increase test tolerance for parameter comparisonsv1.0.1Johannes Ranke2-1/+2
Platform dependence also revealed after upgrade to bullseye
2021-02-06Update static docsJohannes Ranke2-90/+91
2021-02-04Documentation improvements, mainly fixing example codeJohannes Ranke21-127/+166
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 Ranke177-1690/+4908
- 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
2021-01-25Change default ylab in plot.mkinfit, explicit ylab for plot.mmkinJohannes Ranke19-34/+28
See NEWS.md. Closes #12
2021-01-11Rebuild docsJohannes Ranke8-64/+86
2020-12-21plot.mixed: Possibility to overlay predictionsJohannes Ranke6-35/+47
2020-12-19Update docsJohannes Ranke5-17/+262
2020-12-16And add the second candidate modelJohannes Ranke2-1/+22
2020-12-16and update docsJohannes Ranke3-21/+18
2020-12-16Add printout of d24 model and update docsJohannes Ranke9-28/+47
2020-12-11Update static docsJohannes Ranke18-137/+405
2020-11-30Complete rebuild of static docs of dev versionJohannes Ranke117-2652/+949
2020-11-27Update static docsJohannes Ranke4-6/+7
2020-11-19Depend on parallel, doc improvementsJohannes Ranke132-1357/+3369
By depending on parallel instead of importing it, functions to set up and stop a cluster are always available when mkin is loaded. The use of multicore processing in mmkin on Windows is now documented in the help file, which brings mkin closer to a version 1.0 #9.
2020-11-11Update static docsJohannes Ranke6-264/+297
2020-11-11Add print and plot calls to the saem example codeJohannes Ranke12-60/+102
2020-11-10Digits for summary methods, print.saem.mmkinJohannes Ranke5-61/+76
2020-11-09saemix.mmkin and nlme.mmkin inherit from mixed.mmkinJohannes Ranke16-60/+375
With a plot method. The class mixed.mmkin is currently only a virtual class created to unify the plotting method.
2020-11-09Merge plot methods for nlme.mmkin and saem.mmkinJohannes Ranke12-23/+557
This avoids code duplication
2020-11-09Add plot method for saem.mmkin objectsJohannes Ranke9-9/+320
2020-11-09Remove outdated doc pageJohannes Ranke1-1202/+0
2020-11-09Doc improvementsJohannes Ranke2-6/+7
2020-11-09Some work on example code, pkgdown updateJohannes Ranke10-178/+389
2020-11-09Custom analytical solutions for saemixJohannes Ranke3-23/+59
Currently SFO-SFO and DFOP-SFO. Speed increase factor about 60
2020-11-08The call to saemix.predict fails with DFOP-SFOJohannes Ranke3-3/+3
2020-11-08Update static docsJohannes Ranke7-24/+482
2020-11-07Update static docs for dev versionJohannes Ranke9-121/+450
2020-11-07Create saem generic for fitting saemix modelsJohannes Ranke2-2/+2
The reasons for this decision were - Creating an saemix generic in the saemix package caused problems with roxygen, because functions like saemix.plot.xy were documented in their help files as S3 methods, although explicitly exported with @export - Creating an saemix generic in this package is possible, but would make it necessary to load samix with exclude = "saemix" in order to avoid overwriting the generic when loading saemix. - The return object of such an saemix generic in this package cannot be an S3 class with class attribute c("saemix.mmkin", "SaemixObject") similar to nlme.mmkin, as saemix returns an S4 class. - Extending the S4 class SaemixObject using simple inheritance to a class SaemixMmkinObject with additional slots did not work as expected. When the initialize method was left untouched, it prevented creation of an SaemixMmkinObject even if it was based on an initialised SaemixObject, as the initialize method seems to always be called by new(). This could potentially be circumvented by a coerce method. If an alternative initialize method was used, an SaemixMmkinObject could be created. However, the methods written for SaemixObjects only worked in some instances, either because they checked for the class, and not for class inheritance (like compare.saemix), or because the initialize method was called for some reason. Therefore, the idea of creating a derived S4 class was abandoned. - A side effect of this decision is that the introduction of the saem generic opens the possibility to use the same generic also for other backends like nlmixr with the SAEM algorithm.
2020-11-06Update benchmarks for dev versionJohannes Ranke4-69/+129
2020-11-06Fast analytical solutions for saemix, update.mmkinJohannes Ranke40-406/+972
Also, use logit transformation for g and for solitary formation fractions, addressing #10.
2020-11-05Fix link and update docsJohannes Ranke8-93/+117
2020-10-27Add summary method for nlme.mmkin objectsJohannes Ranke9-48/+535
Improve and update docs
2020-10-26Put the legend in its own area for plot.nlme.mmkinJohannes Ranke15-80/+74
2020-10-24Fix a bug for nlme with parent only, improve examplesJohannes Ranke10-89/+14
2020-10-24Improve plot layoutJohannes Ranke4-17/+6
2020-10-24Plot method for nlme.mmkin objectsJohannes Ranke11-76/+351
Update docs
2020-10-22Really fix check for nlme::varConstPropJohannes Ranke2-4/+49
And add output for nlme fit translating the mkinfit error model "obs" into nlme::varIdent().
2020-10-22Fix check for nlme::varConstPropJohannes Ranke2-1/+1
2020-10-22Update pkgdown docsJohannes Ranke22-113/+201
2020-10-15More gentle example for saemix with combined error modelJohannes Ranke9-47/+43
2020-10-15Update online docs for release versionJohannes Ranke140-2295/+2725
2020-10-15Updating docs of current dev versionJohannes Ranke34-154/+456

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