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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 Ranke1-14/+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
2019-04-10Adapt tests, vignettes and examplesJohannes Ranke1-65/+87
- Write the NEWS - Static documentation rebuilt by pkgdown - Adapt mkinerrmin - Fix (hopefully all) remaining problems in mkinfit
2019-04-08Remove zero observations, adapt logLikJohannes Ranke1-0/+7
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
2019-02-27Comment out unused codeJohannes Ranke1-21/+21
2019-02-27Increase test coverageJohannes Ranke1-8/+17
2019-02-26NAFTA SOP Attachment vignetteJohannes Ranke1-0/+4
Also: - Change rounding in print.nafta - Add dots argument to nafta() - Use cores=1 in examples - Restrict N in IORE model to values > 0
2019-02-22Further adaptations for the logistic modelJohannes Ranke1-2/+2
- 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 Ranke1-3/+6
2018-11-23Add logLik method to enable AIC() on mkinfit modelsJohannes Ranke1-1/+1
Further relax two tests to pass build on Travis
2018-09-21Improve fitting the two-component error modelJohannes Ranke1-47/+83
with respect to accuracy and robustness.
2018-09-20Use the median absolute deviance for fittingJohannes Ranke1-5/+16
as the absolute value is a biased estimator for the standard deviation
2018-09-15Remove correlation test as gmkin on windows still crashesJohannes Ranke1-18/+10
Clean up the code a bit
2018-09-14Update NEWSJohannes Ranke1-2/+4
Static documentation rebuilt by pkgdown
2018-09-14Avoid nls crashes by checking for a correlation firstJohannes Ranke1-0/+7
2018-09-13Enable new error model in gmkinJohannes Ranke1-7/+20
Also improve the irls fitting of the error model and add a test for FOCUS_2006_C where the second component of the error model is zero
2018-07-18Correct references to the Rocke and Lorenzato modelJohannes Ranke1-3/+3
Rename 'sigma_rl' to 'sigma_twocomp' as the Rocke and Lorenzato model assumes lognormal distribution for large y. Rebuild static documentation.
2018-07-04Improve IORE fitting, use 1.1 as N starting valueJohannes Ranke1-1/+4
2018-02-02mkinfit: Work around a bug in the current FME versionJohannes Ranke1-6/+15
that prevented the convergence message to be returned in the case of non-convergence.
2018-02-02Show R and mkin version used for fitting in the summaryJohannes Ranke1-2/+15
For fits generated with previous version, the version numbers used for fitting were not stored in the fit object. Therefore, the versions used for fitting can only be shown for fits generated with mkin containing this commit.
2018-01-30Reweighting with two-component error modelJohannes Ranke1-20/+89
Static documentation except articles rebuilt by pkgdown
2017-09-06Fix comment that was copied without checkingJohannes Ranke1-1/+1
2016-11-17Show diffs in correct mathematical form in summaryJohannes Ranke1-1/+2
2016-11-17Remove trailing whitespace, clean headersJohannes Ranke1-45/+45
Also ignore test.R in the top level directory, as it is not meant to be public
2016-06-27Improve listing of weights in output, update NEWSJohannes Ranke1-1/+7
2016-06-17Change the title of the package, small bugfixJohannes Ranke1-1/+1
2016-04-21Avoid unnecessary stop in edge case, improve warningsJohannes Ranke1-6/+14
mkinfit: Do not error out in cases where the fit converges, but the Jacobian for the untransformed model cost can not be estimated. Give a warning instead and return NA for the t-test results. summary.mkinfit: Give a warning message when the covariance matrix can not be obtained. A test has been added to containing such an edge case to check that the warnings are correctly issued and the fit does not terminate.
2016-03-23Added 'from_max_mean' to 'mkinfit'.Johannes Ranke1-1/+14
- Now it is easier to do decline kinetics from the maximum occurrence - Static documentation rebuilt by staticdocs::build_site() - Fixed an URL in the README, thanks to the win-builder check with R-devel
2015-11-06Improve formatting of summaryJohannes Ranke1-4/+4
2015-10-21Avoid an error printing old mkinfit summariesJohannes Ranke1-5/+10
2015-06-30Start to import or qualify functions from stats, utils et al.Johannes Ranke1-2/+2
2015-06-21Do the t-test for untransformed parametersv0.9-36Johannes Ranke1-18/+71
2015-06-20Low-level generation of compiled modelsJohannes Ranke1-3/+3
As it is unclear if and when ccSolve will be published on CRAN, the generation, compilation and use of the C version of the system of differential equations was developed for mkin, inspired and guided by the code from the ccSolve package. Many thanks again to Karline Soetaert for all of her work on this and other R packages. Now all model types, including the Hockey-Stick model for the parent compund and the IORE model for parent and/or metabolites can be compiled.
2015-04-16Update copyright header, improve documentation of solution_typeJohannes Ranke1-12/+17
2015-04-16Check compiled mkinmod versions in examples and testsJohannes Ranke1-0/+3
Tests all pass (Linux)
2015-02-20Add termination message to mkinfit, prepare releaseJohannes Ranke1-1/+9
2015-02-20Fix printing the summary if iterations are not availableJohannes Ranke1-1/+4
This was broken for using method.modFit = "SANN"
2014-11-12IORE working for parent and metabolites, introduce mkinsubJohannes Ranke1-2/+7
2014-11-12Merge branch 'master' into ioreJohannes Ranke1-48/+127
2014-11-12Fix a typo in the list of possible argumentsJohannes Ranke1-1/+1
Thanks to Michael Brauer for the hint
2014-10-22Always include 0 on y axis when plotting during the fitJohannes Ranke1-1/+1
2014-10-15Switch to using the Port algorithm per defaultJohannes Ranke1-1/+1
2014-10-14Further formatting improvement for differential equationsJohannes Ranke1-1/+1
2014-10-06Avoid a warning produced by initial fits in gmkinJohannes Ranke1-7/+9
2014-08-20Fix mkinfit for a special situationJohannes Ranke1-7/+7
See NEWS.md: When the parent was not the (only) variable with the highest value out of all variables in the observed data, it could happen that the initial value (state.ini) was not initialised.

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