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2021-09-15Correction of the dimethenamid datasetJohannes Ranke1-2/+2
The data given in previous mkin versions for "Borstel 2" (Staudenmaier 2013) are in fact a subset of the "Borstel 1" data, with the "Borstel 2" data simply being further analysed for isomer composition by Staudenmaier (2013). While correcting this, the URL of the RAR published by EFSA was updated, as the EFSA Register of Questions was replaced by the Open EFSA portal. This also affects the recent publication in "Environments" [1], where these two datasets were pooled. However, the influence on the final results can be expected to be minimal. Out of the 16 observations for the Borstel soil, five were erroneously duplicated which just changes the weight of the different sampling points and modifies the variance. The conclusions of the publication are qualitative and are not considered to be affected. [1] https://doi.org/10.3390/environments8080071
2021-04-21Version 1.0.4 published yesterdayv1.0.4Johannes Ranke1-2/+3
2021-03-31Bug fix in plot.mkinfitJohannes Ranke1-1/+1
In residual plots, use xlab and xlim if appropriate
2021-02-24Reset graphical parameters with on.exit()Johannes Ranke4-5/+5
plot.mixed.mmkin did not reset graphical parameters at all. The other plotting functions did not use on.exit, so this change should make the use of the plotting functions safer.
2021-02-15Improve README, introductory vignette and some other docsv1.0.3Johannes Ranke1-0/+5
Also bump version to 1.0.3.
2021-02-13Update for gmkin 0.6.12v1.0.2Johannes Ranke1-2/+9
mkinfit: Keep model names stored in mkinmod objects, avoiding their loss in gmkin
2021-02-04Documentation improvements, mainly fixing example codeJohannes Ranke7-33/+40
The errors in the example code were in the \dontrun sections, so they were not caught by CRAN checks. In addition, the static help files generated with pkgdown were cached, so I noticed the errors only after completely regenerating the documentation for version 1.0.0.
2021-02-03Prepare for v1.0.0v1.0.0Johannes Ranke4-806/+5
- Improve authorship and copyright information - Prepare pkgdown config - Remove dependence on saemix as we need the development version which is not ready for CRAN - Temporarily remove saemix interface to check code coverage of the rest
2021-01-25Some more plotting improvementsJohannes Ranke2-6/+6
2021-01-25Change default ylab in plot.mkinfit, explicit ylab for plot.mmkinJohannes Ranke2-3/+5
See NEWS.md. Closes #12
2021-01-22We do not need to suppress saemix plots any moreJohannes Ranke1-12/+1
This makes fitting with saem within parallel::mclapply much faster and, surprisingly, much less hungry for RAM.
2021-01-11Rebuild docsJohannes Ranke1-1/+1
2021-01-06Make saemix and corresponding tests optionalJohannes Ranke1-0/+2
Address release critical check and test issues
2020-12-21plot.mixed: Possibility to overlay predictionsJohannes Ranke1-6/+31
2020-12-19Possibility to override automatic starting parameters for saemJohannes Ranke1-4/+10
2020-12-19Dimethenamid data, normalisation optionsJohannes Ranke3-8/+40
2020-12-16And add the second candidate modelJohannes Ranke1-0/+4
2020-12-16Print the model not the data for D24Johannes Ranke1-1/+1
2020-12-16Add printout of d24 model and update docsJohannes Ranke1-0/+1
2020-12-15Remove leftoversJohannes Ranke1-3/+2
2020-12-10nlme with varConstProp is releasedJohannes Ranke1-0/+3
Also fix incompatibility with saem fits from earlier mkin versions
2020-12-09Make saem using mkinpredict work againJohannes Ranke2-47/+54
I threw out mclapply as it did not play well with the linear algebra routines used in the saemix code. Most of the change is actually indentation in the code creating the model function. But there is an important fix in mkinpredict which I had broken.
2020-12-09Add more tests and fix HS in saemJohannes Ranke1-2/+2
2020-12-09More testsJohannes Ranke2-5/+5
2020-12-09Test print method for mixed.mmkinJohannes Ranke1-2/+2
2020-12-09Some more testsJohannes Ranke1-2/+2
2020-12-08mixed.mmkin and test coverageJohannes Ranke5-57/+188
2020-12-07Possibility to use saemix transformations in some casesJohannes Ranke1-45/+127
Namely for SFO, DFOP, SFO-SFO and DFOP-SFO
2020-12-07Attempt to be more failsafe in saemix runsJohannes Ranke1-2/+8
2020-12-03Small doc improvementJohannes Ranke1-2/+2
2020-12-02Possibility to specify random effects structuresJohannes Ranke1-17/+13
The default is pdDiag again, as we often have a small number of datasets in degradation kinetics.
2020-11-30Complete rebuild of static docs of dev versionJohannes Ranke1-2/+4
2020-11-30Log-Cholesky parameterisation as default in nlme.mmkinJohannes Ranke3-20/+29
2020-11-27Improved way to have persistent DLLs for mkinmodJohannes Ranke3-36/+37
Depends on inline >= 0.16.2 (including the bug fixes from eddelbuettel/inline#18), which provides 'moveDLL' to store the DLL for a compiled function in a safe place in case the argument 'dll_dir' is specified in the call to 'mkinmod'. Huge thanks to Dirk @eddelbuettel for his review and support for the work on the inline package.
2020-11-24Support storing mkinmod compiled code as CFunc objectsJohannes Ranke3-34/+53
With automatic reloading in mkinfit and mkinpredict in case the DLL is not loaded and the original DLL path has been cleaned up. Depends on jranke/inline@974bdea04fcedfafaab231e6f359c88270b56cb9 See inline#13
2020-11-20export create_deg_funcJohannes Ranke1-0/+1
2020-11-19Depend on parallel, doc improvementsJohannes Ranke3-25/+24
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.
2020-11-13More work on f_time_norm_focusJohannes Ranke1-0/+2
2020-11-13Fixes for f_time_norm_focus, still very fragile...Johannes Ranke2-12/+41
2020-11-13Annotation of the fixJohannes Ranke1-1/+1
2020-11-13Fixed plotting of non-analytical solutions in saemJohannes Ranke3-22/+26
2020-11-12Model names in lrtest.mmkin, fix for print.mmkinJohannes Ranke2-2/+5
Fix the display of warnings and errors in print.mmkin, the matrix was erroneously transposed.
2020-11-12Use preprocessed data for 2,4-D, update docsJohannes Ranke1-6/+8
2020-11-12mkindsg class to hold groups of datasetsJohannes Ranke12-16/+233
- 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()
2020-11-11Fix docs and passing of dot arguments for saemJohannes Ranke1-6/+2
2020-11-11Rename saemix file, option to suppress saemix messagesJohannes Ranke1-4/+10
2020-11-11Check on r-devel, address NOTEJohannes Ranke1-1/+2
2020-11-11Add print and plot calls to the saem example codeJohannes Ranke1-3/+5
2020-11-10Digits for summary methods, print.saem.mmkinJohannes Ranke4-18/+49
2020-11-09I do not have a parms.nlme.mmkin methodJohannes Ranke1-2/+1

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