aboutsummaryrefslogtreecommitdiff
path: root/R
AgeCommit message (Collapse)AuthorFilesLines
2019-10-31Comment out example code that fails in pkgdownJohannes Ranke1-2/+5
2019-10-31Add likelihood ratio test and other methods, fixesJohannes Ranke6-18/+191
The likelihood ratio test method is lrtest, in addition, methods for update and residuals were added.
2019-10-29Return single parameters correctly from confintJohannes Ranke1-11/+15
Static documentation rebuilt by pkgdown
2019-10-28Parallel computation for confidence intervalsJohannes Ranke1-18/+82
Only on Linux at the moment. Some more examples in the help page. Remove the distribution argument for the quadratic method
2019-10-28Improve formattingJohannes Ranke1-0/+1
2019-10-28Fix the cutoff for likelihood based intervalsJohannes Ranke1-4/+16
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
2019-10-26Fix checks and testsJohannes Ranke2-1/+4
Static documentation rebuilt by pkgdown
2019-10-26Address some check and test failuresJohannes Ranke2-1/+2
2019-10-26parms and confint methodsJohannes Ranke3-22/+190
The confint method can do profile likelihood based confidence intervals!
2019-10-25Use roxygen for functions and methodsJohannes Ranke33-2087/+3364
2019-10-22Go back to d_3 for errmod = "obs"Johannes Ranke1-1/+1
in the hope that this makes plotting cross-platform also for this error model
2019-10-21Improve some plotting routines, more testsJohannes Ranke2-26/+36
Static documentation rebuilt by pkgdown
2019-10-21Improve tests, remove geometric_meanJohannes Ranke1-4/+0
2019-10-21Refactor mkinfit, infrastructure workJohannes Ranke2-157/+178
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 Ranke1-9/+21
- Reconcile docs and code for max_twa_parent - Correct links to docs in twa vignette - Static documentation rebuilt by pkgdown
2019-09-02Some changes to improve plots on beamer slidesJohannes Ranke3-15/+22
2019-07-09Adaptations for gmkinJohannes Ranke1-1/+3
Address winbuilder check problems, update check log, update of static docs
2019-07-08Support summarizing older fitsJohannes Ranke1-8/+10
generated with mkin < 0.9.49.5
2019-07-05Static documentation rebuilt by pkgdownJohannes Ranke1-0/+1
2019-06-05Add error model algorithm to outputJohannes Ranke1-8/+19
2019-06-04Fix a bug introduced in the last commitJohannes Ranke1-2/+4
2019-06-04For the d_3 algorithm, report which was better, if anyJohannes Ranke1-2/+13
2019-06-04Additional algorithm "d_c", more tests, docsJohannes Ranke1-46/+71
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.
2019-06-04Algorithms direct, two-, three-, fourstep, IRLSJohannes Ranke1-9/+41
All of them are working now and allow for comparison Based on SFO, DFOP and HS fits to twelve test datasets, only the combination of direct and threestep is needed to find the lowest AIC
2019-06-03Status von Samstag morgen - untestedJohannes Ranke1-37/+63
2019-05-23Fix a bug that could lead to wrong chi2 error levelsJohannes Ranke1-0/+1
2019-05-20Only use colors for error model "obs"Johannes Ranke1-3/+3
2019-05-08Add functionality to plot the error modelJohannes Ranke4-15/+116
by plotting squared residuals against predicted values, and showing the variance function used in the fitted error model. Rebuild docs
2019-05-07Fix hessian calculationsJohannes Ranke1-7/+8
Static documentation rebuilt by pkgdown
2019-05-07After the OLS step, use OLS parameter estimatesJohannes Ranke1-24/+24
- Fix the respective error in the code - Static documentation rebuilt by pkgdown
2019-05-03Improve error model fittingJohannes Ranke2-15/+36
Now we have a three stage fitting process for nonconstant error models: - Unweighted least squares - Only optimize the error model - Optimize both Static documentation rebuilt by pkgdown
2019-05-02Better initials for error model parametersJohannes Ranke1-8/+21
- Also make it possible to specify initial values for error model parameters. - Run tests - Rebuild docs
2019-04-24Improve output and update testsJohannes Ranke1-5/+9
Remove skipped tests as I do not intend to reactivate them
2019-04-10Address failure on travisJohannes Ranke1-1/+1
Also reduce the digits in the representative half-live given by nafta()
2019-04-10Adapt tests, vignettes and examplesJohannes Ranke3-68/+90
- Write the NEWS - Static documentation rebuilt by pkgdown - Adapt mkinerrmin - Fix (hopefully all) remaining problems in mkinfit
2019-04-08Remove zero observations, adapt logLikJohannes Ranke2-24/+11
Zero observations at time zero made fitting the two-component error model fail. A concentration of exactly zero does not make sense anyways, as we generally have a limit of detection
2019-04-05Report negative log-likelihood during fitsJohannes Ranke1-4/+10
If not quiet = TRUE
2019-04-04Direct error model fitting worksJohannes Ranke1-366/+133
- No IRLS required - Removed optimization algorithms other than Port - Removed the dependency on FME - Fitting the error model 'obs' is much faster for the FOCUS_2006_D dataset and the FOMC_SFO model (1 second versus 3.4 seconds) - Vignettes build slower. Compiled models needs 3 minutes instead of 1.5 - For other vignettes, the trend is less clear. Some fits are faster, even for error_model = "const". FOCUS_Z is faster (34.9 s versus 44.1 s) - Standard errors and confidence intervals are slightly smaller - Removed code for plotting during the fit, as I hardly ever used it - Merged the two cost functions (using transformed and untransformed parameters) into one log-likelihood function
2019-03-04signif for DTx when printing nafta resultsJohannes Ranke1-1/+1
In order to be able to test cross-platform
2019-03-04Review tests and examples based on winbuilder resultsJohannes Ranke1-3/+3
Static documentation rebuilt by pkgdown
2019-02-27Comment out unused codeJohannes Ranke2-27/+27
2019-02-27Increase test coverageJohannes Ranke1-8/+17
2019-02-26NAFTA SOP Attachment vignetteJohannes Ranke2-3/+7
Also: - Change rounding in print.nafta - Add dots argument to nafta() - Use cores=1 in examples - Restrict N in IORE model to values > 0
2019-02-26Add another NAFTA dataset + testJohannes Ranke1-1/+2
2019-02-25Static documentation rebuilt by current pkgdownJohannes Ranke1-3/+7
2019-02-22Implement the NAFTA evaluation schemeJohannes Ranke1-0/+105
2019-02-22Further adaptations for the logistic modelJohannes Ranke3-4/+9
- Make mmkin compatible - Return DT50 values corresponding to k0 and kmax - Turn incompatible parameter names in parms.ini from an error to a warning, in order to make it possible to use this argument in calls to mmkin
2019-02-21Add the logistic modelJohannes Ranke6-17/+43
2019-01-31Restore NAMESPACEJohannes Ranke1-16/+1
which was accidentally overwritten by pkgdown -> roxygen
2019-01-31Export to CAKE study fileJohannes Ranke1-0/+80

Contact - Imprint