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2020-07-17mkinfit: Ignore unused components of state.iniJohannes Ranke1-0/+2
2020-07-15Improve handling of (partially) failing fitsJohannes Ranke1-0/+4
2020-05-29Warn if standardized residuals are unlikely normalJohannes Ranke1-0/+2
This revealed a bug in the data returned in mkinfit$data in the case of the d_3 algorithm, which also affected the residual plot - the data from the direct fitting was not returned even if this was the better method.
2020-05-28use_of_ff = "max" for shorthand models like "SFO"Johannes Ranke1-0/+2
2020-05-26Use all cores per default, confint toleranceJohannes Ranke1-0/+4
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 Ranke1-0/+2
saemix_data depends on a development version of saemix, see pull request saemixdevelopment/saemixextension#2
2020-05-14Add a parms method for mmkin objectsJohannes Ranke1-0/+4
2020-05-12Improve documentation, now using a spell checkerJohannes Ranke1-4/+10
2020-05-11Add analytical solution for DFOP-SFOJohannes Ranke1-0/+2
This is about twice as fast as deSolve compiled in the case of FOCUS D
2020-05-07Another overhaul of analytical solutionsJohannes Ranke1-0/+2
Still in preparation for analytical solutions of coupled models
2020-04-22Support SFORB with formation fractionsJohannes Ranke1-1/+5
2020-04-20Prepare release to address failed CRAN checkJohannes Ranke1-0/+2
2020-04-20Increase test tolerance for residualsJohannes Ranke1-0/+2
This was done to address the test failure on r-devel-linux-x86_64-debian-gcc on CRAN
2020-04-18Fix NOTE, prepare for releasev0.9.49.10Johannes Ranke1-1/+1
2020-04-17News entry, static documentation rebuilt by pkgdownJohannes Ranke1-0/+2
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/+2
2020-04-04Add three functions to facilitate the use of nlmeJohannes Ranke1-0/+2
2020-04-03Compiled models article, reduce distractionsJohannes Ranke1-1/+9
- 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/+3
2020-03-30Static documentation rebuilt by pkgdownJohannes Ranke1-1/+5
2020-01-08Typos in NEWS, update static docsJohannes Ranke1-1/+1
2019-11-13Calculate Akaike weightsJohannes Ranke1-0/+2
2019-11-09Add a lack-of-fit testJohannes Ranke1-0/+2
- 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
2019-11-04Scaled residual plotsJohannes Ranke1-0/+2
2019-11-04Include fixed parameters in model names in lrtestJohannes Ranke1-1/+3
2019-11-01Make the 'quadratic' the default for 'confint'Johannes Ranke1-0/+4
Also the documentation was improved here and there
2019-11-01Fix bug in yesterdays release, add methods for BICJohannes Ranke1-1/+7
2019-10-31Add likelihood ratio test and other methods, fixesJohannes Ranke1-0/+8
The likelihood ratio test method is lrtest, in addition, methods for update and residuals were added.
2019-10-26parms and confint methodsJohannes Ranke1-0/+2
The confint method can do profile likelihood based confidence intervals!
2019-10-22Go back to d_3 for errmod = "obs"Johannes Ranke1-2/+0
in the hope that this makes plotting cross-platform also for this error model
2019-10-21Refactor mkinfit, infrastructure workJohannes Ranke1-1/+7
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.
2019-09-18Add hockey stick formulas to maximum twa vignetteJohannes Ranke1-0/+2
2019-09-02Some changes to improve plots on beamer slidesJohannes Ranke1-1/+5
2019-07-08Support summarizing older fitsJohannes Ranke1-1/+3
generated with mkin < 0.9.49.5
2019-07-05Static documentation rebuilt by pkgdownJohannes Ranke1-0/+6
2019-07-04Address failures of CRAN checks, improve NEWSv0.9.49.5Johannes Ranke1-2/+4
Static documentation rebuilt by pkgdown
2019-07-03Update DESCRIPTION, improve NEWSJohannes Ranke1-8/+8
Static documentation rebuilt by pkgdown
2019-06-04Additional algorithm "d_c", more tests, docsJohannes Ranke1-3/+5
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.
2019-05-23Fix a bug that could lead to wrong chi2 error levelsJohannes Ranke1-1/+3
2019-05-08Add functionality to plot the error modelJohannes Ranke1-1/+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 Ranke1-1/+1
- Fix the respective error in the code - Static documentation rebuilt by pkgdown
2019-04-10Adapt tests, vignettes and examplesJohannes Ranke1-0/+17
- 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 Ranke1-1/+1
Static documentation rebuilt by pkgdown
2019-02-22Implement the NAFTA evaluation schemeJohannes Ranke1-1/+3
2019-02-21Add the logistic modelJohannes Ranke1-1/+3
2019-01-31Correct title for CAKE_exportJohannes Ranke1-1/+3
Add NEWS entry. Static documentation rebuilt by pkgdown
2018-11-26Add AIC method for mmkin column objectsJohannes Ranke1-1/+3
Static documentation rebuilt by pkgdown
2018-11-26Support logLik and AIC for manual weightsJohannes Ranke1-1/+3
Static documentation rebuilt by pkgdown
2018-09-21Improve fitting the two-component error modelJohannes Ranke1-1/+5
with respect to accuracy and robustness.

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