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2020-11-19Depend on parallel, doc improvementsJohannes Ranke1-3/+3
By depending on parallel instead of importing it, functions to set up and stop a cluster are always available when mkin is loaded. The use of multicore processing in mmkin on Windows is now documented in the help file, which brings mkin closer to a version 1.0 #9.
2020-11-12mkindsg class to hold groups of datasetsJohannes Ranke1-1/+2
- D24_2014 dataset on aerobic soil degradation of 2,4-D from the EU assessment as mkindsg object with metadata - f_time_norm_focus() to do time-step normalisation using the FOCUS method - focus_soil_moisture data with default moisture contents at pF1, pF 2 and pF 2.5 for USDA soil types from FOCUS GW guidance - Dataset generation scripts in inst/dataset_generation - Depend on R >= 2.15.1 in order to facilitate the use of utils::globalVariables()
2020-10-22Improve interface to experimental version of nlmeJohannes Ranke1-1/+1
The experimental nlme version in my drat repository contains the variance function structure varConstProp which makes it possible to use the two-component error model in generalized nonlinear models using nlme::gnls() and in mixed effects models using nlme::nlme().
2020-10-15Reintroduce saemix helper functionsJohannes Ranke1-3/+3
2020-10-08Fix another URL, add devcheck targetv0.9.50.3Johannes Ranke1-1/+1
2020-10-08Fix issues for releaseJohannes Ranke1-2/+2
2020-10-08Avoid dep on dev version of saemix for releaseJohannes Ranke1-2/+2
2020-09-10Regenerate docs with current roxygenJohannes Ranke1-1/+1
2020-07-20Require upcoming nlme version, remove anova.nlme.mmkinJohannes Ranke1-1/+1
The method is no longer necessary, now that Bug 17761 is fixed upstream https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17761
2020-07-15Bump date to trigger Travis build after clearing cacheJohannes Ranke1-1/+1
2020-05-25Tell travis where to find the required saemix versionJohannes Ranke1-2/+2
2020-05-25First working version of saemix helper functionsJohannes Ranke1-1/+1
saemix_data depends on a development version of saemix, see pull request saemixdevelopment/saemixextension#2
2020-05-14Update version number, better example formattingJohannes Ranke1-2/+2
2020-05-12Improve documentation, now using a spell checkerJohannes Ranke1-2/+3
2020-05-12Documentation improvements, rebuild static docsJohannes Ranke1-0/+1
2020-05-11Add analytical solution for DFOP-SFOJohannes Ranke1-2/+2
This is about twice as fast as deSolve compiled in the case of FOCUS D
2020-05-07Another overhaul of analytical solutionsJohannes Ranke1-2/+2
Still in preparation for analytical solutions of coupled models
2020-05-06Change implementation of analytical solutionsJohannes Ranke1-1/+1
Preparing for symbolic solutions for more than one compound
2020-04-20Prepare release to address failed CRAN checkJohannes Ranke1-2/+2
2020-04-18Fix NOTE, prepare for releasev0.9.49.10Johannes Ranke1-2/+2
2020-04-14Keep order of datasets in nlme_data, add a plotJohannes Ranke1-1/+1
2020-04-10Trigger rebuild after deleting caches on travisJohannes Ranke1-1/+1
According to the hint of @jimhester received in the Travis Forum - thanks!
2020-04-07Add some tests for the nlme convenience functionsJohannes Ranke1-2/+2
2020-04-03Merge branch 'master' into mxkinJohannes Ranke1-2/+2
Merge DESCRIPTION manually to combine dependencies and rerun check to update check.log
2020-03-31Static documentation rebuilt by pkgdownJohannes Ranke1-2/+2
2020-03-30Static documentation rebuilt by pkgdownJohannes Ranke1-1/+1
2020-03-30Don't check for gcc on the path in mkinmodJohannes Ranke1-1/+1
Roxygen update -> formatting changes in Rd files
2020-03-30Add new dependenciesJohannes Ranke1-1/+1
2020-03-30First nlme fits for models with a metaboliteJohannes Ranke1-1/+1
2020-01-09Remove unused FME package from DESCRIPTION textJohannes Ranke1-7/+6
2020-01-08Todays date in DESCRIPTION, update check logv0.9.49.8Johannes Ranke1-1/+1
2019-11-01Make the 'quadratic' the default for 'confint'Johannes Ranke1-1/+1
Also the documentation was improved here and there
2019-11-01Fix bug in yesterdays release, add methods for BICJohannes Ranke1-2/+2
2019-10-31Increase tolerance of a test for winbuilderv0.9.49.6Johannes Ranke1-1/+1
- Update DESCRIPTION for release
2019-10-31Add likelihood ratio test and other methods, fixesJohannes Ranke1-1/+2
The likelihood ratio test method is lrtest, in addition, methods for update and residuals were added.
2019-10-28Fix the cutoff for likelihood based intervalsJohannes Ranke1-1/+1
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 Ranke1-2/+1
Static documentation rebuilt by pkgdown
2019-10-21Refactor mkinfit, infrastructure workJohannes Ranke1-1/+1
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.
2019-09-02Some changes to improve plots on beamer slidesJohannes Ranke1-1/+1
2019-07-05Static documentation rebuilt by pkgdownJohannes Ranke1-2/+2
2019-07-04Address failures of CRAN checks, improve NEWSv0.9.49.5Johannes Ranke1-1/+1
Static documentation rebuilt by pkgdown
2019-07-03Update DESCRIPTION, improve NEWSJohannes Ranke1-1/+1
Static documentation rebuilt by pkgdown
2019-06-04Additional algorithm "d_c", more tests, docsJohannes Ranke1-2/+2
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/+1
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 Ranke1-3/+4
- Write the NEWS - Static documentation rebuilt by pkgdown - Adapt mkinerrmin - Fix (hopefully all) remaining problems in mkinfit
2019-04-04Direct error model fitting worksJohannes Ranke1-4/+4
- 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
2019-03-19Set URL to documentation pageJohannes Ranke1-1/+1
2019-03-04Review tests and examples based on winbuilder resultsJohannes Ranke1-2/+1
Static documentation rebuilt by pkgdown
2019-02-27Fix CAKE export test to actually workJohannes Ranke1-1/+1
Also test the model specification via the link argument

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