Age | Commit message (Collapse) | Author | Files | Lines | |
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2020-04-20 | Prepare release to address failed CRAN check | Johannes Ranke | 3 | -27/+21 | |
2020-04-18 | Avoid assignment to .GlobalEnv for CRAN | Johannes Ranke | 3 | -6/+188 | |
2020-04-15 | Adapt endpoint() to also work for nlme.mmkin objects | Johannes Ranke | 2 | -10/+48 | |
2020-04-15 | Include random effects in starting parameters | Johannes Ranke | 17 | -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 | |||||
2020-04-15 | A plot method for nlme.mmkin fits | Johannes Ranke | 5 | -16/+592 | |
2020-04-14 | Keep order of datasets in nlme_data, add a plot | Johannes Ranke | 2 | -2/+34 | |
2020-04-10 | Improve nlme function docs | Johannes Ranke | 7 | -26/+114 | |
2020-04-04 | Static documentation rebuilt by pkgdown | Johannes Ranke | 3 | -5/+211 | |
2020-04-03 | Compiled models article, reduce distractions | Johannes Ranke | 2 | -4/+8 | |
- 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() | |||||
2020-03-31 | Use inline documentation for R6 class mkinds | Johannes Ranke | 2 | -26/+44 | |
2020-03-30 | Static documentation rebuilt by pkgdown | Johannes Ranke | 22 | -214/+353 | |
2020-01-09 | Remove unused FME package from DESCRIPTION text | Johannes Ranke | 2 | -2/+2 | |
2019-12-16 | Argument ymax for plot.mmkin | Johannes Ranke | 1 | -2/+6 | |
2019-12-09 | Consistently use "two-component error model" | Johannes Ranke | 2 | -5/+5 | |
instead of "two component error model" | |||||
2019-11-13 | Improve formatting using markdown | Johannes Ranke | 1 | -6/+6 | |
2019-11-13 | Calculate Akaike weights | Johannes Ranke | 2 | -0/+220 | |
2019-11-13 | Likelihood ratio test for mmkin columns with two fits | Johannes Ranke | 2 | -3/+7 | |
2019-11-09 | Add a lack-of-fit test | Johannes Ranke | 7 | -0/+349 | |
- 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 | |||||
2019-11-05 | Fix standardized residual plots in 'plot_res' | Johannes Ranke | 2 | -4/+5 | |
2019-11-04 | Static documentation rebuilt by pkgdown | Johannes Ranke | 8 | -16/+31 | |
2019-11-04 | Include fixed parameters in model names in lrtest | Johannes Ranke | 2 | -16/+34 | |
2019-11-01 | Another documentation fix | Johannes Ranke | 1 | -5/+4 | |
2019-11-01 | Make the 'quadratic' the default for 'confint' | Johannes Ranke | 8 | -397/+104 | |
Also the documentation was improved here and there | |||||
2019-11-01 | Fix bug in yesterdays release, add methods for BIC | Johannes Ranke | 31 | -627/+141 | |
2019-10-31 | Comment out example code that fails in pkgdown | Johannes Ranke | 1 | -1/+6 | |
2019-10-31 | Add likelihood ratio test and other methods, fixes | Johannes Ranke | 8 | -49/+1223 | |
The likelihood ratio test method is lrtest, in addition, methods for update and residuals were added. | |||||
2019-10-29 | Return single parameters correctly from confint | Johannes Ranke | 1 | -11/+22 | |
Static documentation rebuilt by pkgdown | |||||
2019-10-28 | Parallel computation for confidence intervals | Johannes Ranke | 1 | -10/+113 | |
Only on Linux at the moment. Some more examples in the help page. Remove the distribution argument for the quadratic method | |||||
2019-10-28 | Improve formatting | Johannes Ranke | 1 | -2/+2 | |
2019-10-28 | Fix the cutoff for likelihood based intervals | Johannes Ranke | 1 | -9/+22 | |
The cutoff now matches what is given by Venzon and Moolgavkar (1988). Also, confidence intervals closely match intervals obtained with stats4::confint in the test case where an stats4::mle object is created from the likelihood function in one test case. Static documentation rebuilt by pkgdown | |||||
2019-10-26 | Fix checks and tests | Johannes Ranke | 3 | -6/+470 | |
Static documentation rebuilt by pkgdown | |||||
2019-10-25 | Static documentation rebuilt by pkgdown | Johannes Ranke | 44 | -1272/+1273 | |
2019-10-21 | Quote percent signs in Rhelp files | Johannes Ranke | 2 | -16/+14 | |
Static documentation rebuilt by pkgdown | |||||
2019-10-21 | Static documentation rebuilt by pkgdown | Johannes Ranke | 3 | -28/+22 | |
2019-10-21 | Improve some plotting routines, more tests | Johannes Ranke | 8 | -21/+44 | |
Static documentation rebuilt by pkgdown | |||||
2019-10-21 | Static documentation rebuilt by pkgdown | Johannes Ranke | 1 | -6/+0 | |
2019-10-21 | Improve tests, remove geometric_mean | Johannes Ranke | 1 | -194/+0 | |
2019-10-21 | Refactor mkinfit, infrastructure work | Johannes Ranke | 1 | -89/+83 | |
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. | |||||
2019-09-19 | Revert a change in the original add_err function | Johannes Ranke | 1 | -4/+4 | |
that I made in the first attempt to work around the issue with the %in% operator in the example code Static documentation rebuilt by pkgdown | |||||
2019-09-19 | Static documentation rebuilt by pkgdown | Johannes Ranke | 8 | -24/+486 | |
Use lazy = TRUE in the pd target for generating pkgdown documentation | |||||
2019-09-18 | Static documentation rebuilt by pkgdown | Johannes Ranke | 5 | -23/+23 | |
to check if the link to the pfm package is correctly generated by pkgdown after preparing the pfm package docs accordingly | |||||
2019-09-18 | Add url: tag to _pkgdown.yml | Johannes Ranke | 5 | -23/+23 | |
Static documentation rebuilt by pkgdown | |||||
2019-09-18 | Further corrections of the twa vignette | Johannes Ranke | 5 | -22/+22 | |
Static documentation rebuilt by pkgdown | |||||
2019-09-18 | Correct and rebuild docs | Johannes Ranke | 52 | -640/+1088 | |
- Reconcile docs and code for max_twa_parent - Correct links to docs in twa vignette - Static documentation rebuilt by pkgdown | |||||
2019-07-09 | Adaptations for gmkin | Johannes Ranke | 7 | -38/+37 | |
Address winbuilder check problems, update check log, update of static docs | |||||
2019-07-05 | Static documentation rebuilt by pkgdown | Johannes Ranke | 52 | -84/+91 | |
2019-07-04 | Address failures of CRAN checks, improve NEWSv0.9.49.5 | Johannes Ranke | 5 | -21/+21 | |
Static documentation rebuilt by pkgdown | |||||
2019-07-03 | Update DESCRIPTION, improve NEWS | Johannes Ranke | 6 | -23/+23 | |
Static documentation rebuilt by pkgdown | |||||
2019-06-05 | Add error model algorithm to output | Johannes Ranke | 7 | -39/+108 | |
2019-06-04 | Additional algorithm "d_c", more tests, docs | Johannes Ranke | 89 | -201/+474 | |
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. |