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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
2020-04-10Improve nlme function docsJohannes Ranke12-31/+119
2020-04-04Static documentation rebuilt by pkgdownJohannes Ranke6-11/+221
2020-04-03Compiled models article, reduce distractionsJohannes Ranke4-115/+85
- Added a section with platform specific notes on getting compiled models to work to the compiled models article - Don't return empty SFORB parameter list from endpoints() if there is no SFORB model - Avoid warnings when using standardized = TRUE in plot.mmkin()
2020-03-31Update NEWS, static documentation rebuilt by pkgdownv0.9.49.9Johannes Ranke1-1/+2
2020-03-31Use inline documentation for R6 class mkindsJohannes Ranke2-26/+44
2020-03-30Static documentation rebuilt by pkgdownJohannes Ranke23-217/+365
2020-01-09Remove unused FME package from DESCRIPTION textJohannes Ranke7-12/+11
2020-01-08Typos in NEWS, update static docsJohannes Ranke1-1/+1
2019-12-16Argument ymax for plot.mmkinJohannes Ranke1-2/+6
2019-12-10More additions to the READMEJohannes Ranke1-1/+1
2019-12-10Update and amend the READMEJohannes Ranke1-2/+20
2019-12-09Consistently use "two-component error model"Johannes Ranke2-5/+5
instead of "two component error model"
2019-11-13Improve formatting using markdownJohannes Ranke1-6/+6
2019-11-13Improve READMEJohannes Ranke1-3/+3
2019-11-13Calculate Akaike weightsJohannes Ranke4-0/+224
2019-11-13Likelihood ratio test for mmkin columns with two fitsJohannes Ranke2-3/+7
2019-11-09Add a lack-of-fit testJohannes Ranke9-0/+353
- Switch an example dataset in the test setup to a dataset with replicates, adapt tests - Skip the test for lrtest with an update specification as it does not only fail when pkgdown generates static help pages, but also in testthat
2019-11-05Fix standardized residual plots in 'plot_res'Johannes Ranke2-4/+5

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