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2021-02-04Documentation improvements, mainly fixing example codeJohannes Ranke1-2/+12
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 Ranke1-6/+35
- 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
2020-10-15Update online docs for release versionJohannes Ranke1-5/+24
2020-05-27Add docs generated using released version 0.9.52Johannes Ranke1-15/+1
2020-05-26Use all cores per default, confint toleranceJohannes Ranke1-0/+2
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 Ranke1-1/+2
saemix_data depends on a development version of saemix, see pull request saemixdevelopment/saemixextension#2
2020-05-14Update version number, better example formattingJohannes Ranke1-1/+1
2020-05-14Add a parms method for mmkin objectsJohannes Ranke1-0/+8
2020-05-12Add a link to the benchmark vignette to the docsJohannes Ranke1-0/+3
2020-05-12Update vignettes and docsJohannes Ranke1-1/+1
2020-05-12Improve documentation, now using a spell checkerJohannes Ranke1-6/+15
2020-05-12Documentation improvements, rebuild static docsJohannes Ranke1-1/+1
2020-05-11Add analytical solution for DFOP-SFOJohannes Ranke1-1/+2
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 Ranke1-1/+0
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 Ranke1-2/+4
Still in preparation for analytical solutions of coupled models
2020-05-07Static documentation rebuilt by pkgdownJohannes Ranke1-97/+74
2020-04-20Prepare release to address failed CRAN checkJohannes Ranke1-4/+13
2020-04-17News entry, static documentation rebuilt by pkgdownJohannes Ranke1-0/+1
2020-04-15Adapt endpoint() to also work for nlme.mmkin objectsJohannes Ranke1-1/+1
2020-04-15A plot method for nlme.mmkin fitsJohannes Ranke1-0/+1
2020-04-10Improve nlme function docsJohannes Ranke1-1/+1
2020-04-04Static documentation rebuilt by pkgdownJohannes Ranke1-0/+1
2020-04-03Compiled models article, reduce distractionsJohannes Ranke1-3/+14
- 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
2020-03-30Static documentation rebuilt by pkgdownJohannes Ranke1-3/+12
2020-01-09Remove unused FME package from DESCRIPTION textJohannes Ranke1-1/+1
2020-01-08Typos in NEWS, update static docsJohannes Ranke1-1/+1
2019-11-13Calculate Akaike weightsJohannes Ranke1-0/+1
2019-11-09Add a lack-of-fit testJohannes Ranke1-0/+1
- 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
2019-11-04Static documentation rebuilt by pkgdownJohannes Ranke1-0/+1
2019-11-04Include fixed parameters in model names in lrtestJohannes Ranke1-2/+3
2019-11-01Make the 'quadratic' the default for 'confint'Johannes Ranke1-1/+10
Also the documentation was improved here and there
2019-11-01Fix bug in yesterdays release, add methods for BICJohannes Ranke1-4/+14
2019-10-31Add likelihood ratio test and other methods, fixesJohannes Ranke1-0/+4
The likelihood ratio test method is lrtest, in addition, methods for update and residuals were added.
2019-10-26Fix checks and testsJohannes Ranke1-0/+1
Static documentation rebuilt by pkgdown
2019-10-25Static documentation rebuilt by pkgdownJohannes Ranke1-1/+0
2019-10-21Static documentation rebuilt by pkgdownJohannes Ranke1-1/+4
2019-10-21Refactor mkinfit, infrastructure workJohannes Ranke1-1/+4
mkinfit objects now include an ll() function to calculate the log-likelihood. Part of the code was refactored, hopefully making it easier to read and maintain. IRLS is currently the default algorithm for the error model "obs", for no particular reason. This may be subject to change when I get around to investigate. Slow tests are now in a separate subdirectory and will probably only be run by my own Makefile target. Formatting of test logs is improved. Roundtripping error model parameters works with a precision of 10% when we use lots of replicates in the synthetic data (see slow tests). This is not new in this commit, but as I think it is reasonable this closes #7.
2019-09-18Correct and rebuild docsJohannes Ranke1-8/+19
- Reconcile docs and code for max_twa_parent - Correct links to docs in twa vignette - Static documentation rebuilt by pkgdown
2019-07-09Adaptations for gmkinJohannes Ranke1-3/+4
Address winbuilder check problems, update check log, update of static docs
2019-07-05Static documentation rebuilt by pkgdownJohannes Ranke1-2/+12
2019-07-04Address failures of CRAN checks, improve NEWSv0.9.49.5Johannes Ranke1-4/+5
Static documentation rebuilt by pkgdown
2019-07-03Update DESCRIPTION, improve NEWSJohannes Ranke1-10/+10
Static documentation rebuilt by pkgdown
2019-06-04Additional algorithm "d_c", more tests, docsJohannes Ranke1-7/+9
The new algorithm tries direct optimization of the likelihood, as well as a three step procedure. In this way, we consistently get the model with the highest likelihood for SFO, DFOP and HS for all 12 new test datasets.
2019-05-08Add functionality to plot the error modelJohannes Ranke1-3/+4
by plotting squared residuals against predicted values, and showing the variance function used in the fitted error model. Rebuild docs
2019-05-07After the OLS step, use OLS parameter estimatesJohannes Ranke1-3/+3
- Fix the respective error in the code - Static documentation rebuilt by pkgdown
2019-04-10Adapt tests, vignettes and examplesJohannes Ranke1-2/+18
- Write the NEWS - Static documentation rebuilt by pkgdown - Adapt mkinerrmin - Fix (hopefully all) remaining problems in mkinfit
2019-03-04Review tests and examples based on winbuilder resultsJohannes Ranke1-3/+3
Static documentation rebuilt by pkgdown
2019-02-26Static documentation rebuilt by pkgdownJohannes Ranke1-0/+3
2019-02-25Static documentation rebuilt by current pkgdownJohannes Ranke1-1/+1

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