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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
2020-10-08Fix another URL, add devcheck targetv0.9.50.3Johannes Ranke7-10/+10
2020-10-08Fix issues for releaseJohannes Ranke69-1129/+799
2020-05-27Improve mkinmod docsJohannes Ranke2-33/+57
2020-05-27Change dev version label to info colorJohannes Ranke24-94/+94
instead of the orange danger color.
2020-05-27Add docs generated using released version 0.9.52Johannes Ranke63-1348/+660
2020-05-27Create up to date pkgdown docs in development modeJohannes Ranke184-0/+24656
2020-05-26Use all cores per default, confint toleranceJohannes Ranke9-105/+80
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 Ranke14-25/+526
saemix_data depends on a development version of saemix, see pull request saemixdevelopment/saemixextension#2
2020-05-15Use markdown links in mkinfit documentationJohannes Ranke2-47/+49
2020-05-14Update version number, better example formattingJohannes Ranke8-22/+14
2020-05-14Add a parms method for mmkin objectsJohannes Ranke3-4/+89
2020-05-14Test markdown link, article update due to .rmd extensionJohannes Ranke11-72/+96
2020-05-13Further formatting improvement of benchmark vignetteJohannes Ranke2-86/+62
Also, use .rmd extension instead of .Rmd for vignettes.
2020-05-12Another documentation updateJohannes Ranke2-23/+23
2020-05-12Update pkgdownJohannes Ranke2-31/+166
2020-05-12Add a link to the benchmark vignette to the docsJohannes Ranke7-1/+19
2020-05-12Update vignettes and docsJohannes Ranke91-1474/+1537
2020-05-12Rerun tests and checks, CRAN commentsJohannes Ranke1-1/+1
2020-05-12Improve documentation, now using a spell checkerJohannes Ranke15-120/+114
2020-05-12Documentation improvements, rebuild static docsJohannes Ranke51-872/+908
2020-05-11Add analytical solution for DFOP-SFOJohannes Ranke8-10/+21
This is about twice as fast as deSolve compiled in the case of FOCUS D
2020-05-11Avoid merge() and data.frame() in cost functionJohannes Ranke21-535/+607
also for deSolve and eigenvalue based solutions. This noticeably increases performance for these methods, see test.log and benchmark vignette.
2020-05-07Another overhaul of analytical solutionsJohannes Ranke19-125/+359
Still in preparation for analytical solutions of coupled models
2020-05-07Merge parent solutions to one fileJohannes Ranke7-7/+47
- Combine R/*.solution.R into R/parent_solutions.R - Create a roxygen family of related functions - Reduce redundancy by using the inherit tag - Change the parent.0 argument to parent_0 to match the corresponding parameter name used in mkinfit
2020-05-07Static documentation rebuilt by pkgdownJohannes Ranke26-798/+1157
2020-04-20Prepare release to address failed CRAN checkJohannes Ranke8-35/+38
2020-04-18Avoid assignment to .GlobalEnv for CRANJohannes Ranke4-6/+191
2020-04-17Advertise nlme related functionalityJohannes Ranke1-0/+1
2020-04-17News entry, static documentation rebuilt by pkgdownJohannes Ranke1-0/+1
2020-04-15Adapt endpoint() to also work for nlme.mmkin objectsJohannes Ranke3-11/+49
2020-04-15Include random effects in starting parametersJohannes Ranke17-84/+200
- mean_degparms() now optionally returns starting values for fixed and random effects, which makes it possible to obtain acceptable fits also in more difficult cases (with more parameters) - Fix the anova method, as it is currently not enough to inherit from lme: https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17761 - Show fit information, and per default also errmin information in plot.nlme.mmkin() - Examples for nlme.mmkin: Decrease tolerance and increase the number of iterations in the PNLS step in order to be able to fit FOMC-SFO and DFOP-SFO
2020-04-15A plot method for nlme.mmkin fitsJohannes Ranke7-16/+599
2020-04-14Keep order of datasets in nlme_data, add a plotJohannes Ranke2-2/+34

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