Age | Commit message (Collapse) | Author | Files | Lines | |
---|---|---|---|---|---|
2021-03-19 | test_log_parms for plot.mixed.mmkin, roxygen run | Johannes Ranke | 2 | -2/+9 | |
2021-03-16 | Convenience option to set nbiter.saemix | Johannes Ranke | 1 | -1/+5 | |
2021-03-09 | Some improvements for borderline cases | Johannes Ranke | 3 | -9/+61 | |
- fit_with_errors for saem() - test_log_parms for mean_degparms() and saem() | |||||
2021-02-24 | Reset graphical parameters with on.exit() | Johannes Ranke | 4 | -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. | |||||
2021-02-24 | Reset graphical parameters with on.exit() | Johannes Ranke | 4 | -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. | |||||
2021-02-15 | Merge branch 'master' into saemix | Johannes Ranke | 1 | -0/+5 | |
2021-02-15 | Improve README, introductory vignette and some other docsv1.0.3 | Johannes Ranke | 1 | -0/+5 | |
Also bump version to 1.0.3. | |||||
2021-02-13 | Merge branch 'master' into saemix | Johannes Ranke | 1 | -2/+9 | |
Run make testcheck to regenerate logs with merge conflicts | |||||
2021-02-13 | Update for gmkin 0.6.12v1.0.2 | Johannes Ranke | 1 | -2/+9 | |
mkinfit: Keep model names stored in mkinmod objects, avoiding their loss in gmkin | |||||
2021-02-06 | Reintroduce interface to saemix | Johannes Ranke | 4 | -5/+806 | |
Also after the upgrade from buster to bullseye of my local system, some test results for saemix have changed. | |||||
2021-02-04 | Documentation improvements, mainly fixing example code | Johannes Ranke | 7 | -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. | |||||
2021-02-03 | Prepare for v1.0.0v1.0.0 | Johannes Ranke | 4 | -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 | |||||
2021-01-25 | Some more plotting improvements | Johannes Ranke | 2 | -6/+6 | |
2021-01-25 | Change default ylab in plot.mkinfit, explicit ylab for plot.mmkin | Johannes Ranke | 2 | -3/+5 | |
See NEWS.md. Closes #12 | |||||
2021-01-22 | We do not need to suppress saemix plots any more | Johannes Ranke | 1 | -12/+1 | |
This makes fitting with saem within parallel::mclapply much faster and, surprisingly, much less hungry for RAM. | |||||
2021-01-11 | Rebuild docs | Johannes Ranke | 1 | -1/+1 | |
2021-01-06 | Make saemix and corresponding tests optional | Johannes Ranke | 1 | -0/+2 | |
Address release critical check and test issues | |||||
2020-12-21 | plot.mixed: Possibility to overlay predictions | Johannes Ranke | 1 | -6/+31 | |
2020-12-19 | Possibility to override automatic starting parameters for saem | Johannes Ranke | 1 | -4/+10 | |
2020-12-19 | Dimethenamid data, normalisation options | Johannes Ranke | 3 | -8/+40 | |
2020-12-16 | And add the second candidate model | Johannes Ranke | 1 | -0/+4 | |
2020-12-16 | Print the model not the data for D24 | Johannes Ranke | 1 | -1/+1 | |
2020-12-16 | Add printout of d24 model and update docs | Johannes Ranke | 1 | -0/+1 | |
2020-12-15 | Remove leftovers | Johannes Ranke | 1 | -3/+2 | |
2020-12-10 | nlme with varConstProp is released | Johannes Ranke | 1 | -0/+3 | |
Also fix incompatibility with saem fits from earlier mkin versions | |||||
2020-12-09 | Make saem using mkinpredict work again | Johannes Ranke | 2 | -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. | |||||
2020-12-09 | Add more tests and fix HS in saem | Johannes Ranke | 1 | -2/+2 | |
2020-12-09 | More tests | Johannes Ranke | 2 | -5/+5 | |
2020-12-09 | Test print method for mixed.mmkin | Johannes Ranke | 1 | -2/+2 | |
2020-12-09 | Some more tests | Johannes Ranke | 1 | -2/+2 | |
2020-12-08 | mixed.mmkin and test coverage | Johannes Ranke | 5 | -57/+188 | |
2020-12-07 | Possibility to use saemix transformations in some cases | Johannes Ranke | 1 | -45/+127 | |
Namely for SFO, DFOP, SFO-SFO and DFOP-SFO | |||||
2020-12-07 | Attempt to be more failsafe in saemix runs | Johannes Ranke | 1 | -2/+8 | |
2020-12-03 | Small doc improvement | Johannes Ranke | 1 | -2/+2 | |
2020-12-02 | Possibility to specify random effects structures | Johannes Ranke | 1 | -17/+13 | |
The default is pdDiag again, as we often have a small number of datasets in degradation kinetics. | |||||
2020-11-30 | Complete rebuild of static docs of dev version | Johannes Ranke | 1 | -2/+4 | |
2020-11-30 | Log-Cholesky parameterisation as default in nlme.mmkin | Johannes Ranke | 3 | -20/+29 | |
2020-11-27 | Improved way to have persistent DLLs for mkinmod | Johannes Ranke | 3 | -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. | |||||
2020-11-24 | Support storing mkinmod compiled code as CFunc objects | Johannes Ranke | 3 | -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 | |||||
2020-11-20 | export create_deg_func | Johannes Ranke | 1 | -0/+1 | |
2020-11-19 | Depend on parallel, doc improvements | Johannes Ranke | 3 | -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. | |||||
2020-11-13 | More work on f_time_norm_focus | Johannes Ranke | 1 | -0/+2 | |
2020-11-13 | Fixes for f_time_norm_focus, still very fragile... | Johannes Ranke | 2 | -12/+41 | |
2020-11-13 | Annotation of the fix | Johannes Ranke | 1 | -1/+1 | |
2020-11-13 | Fixed plotting of non-analytical solutions in saem | Johannes Ranke | 3 | -22/+26 | |
2020-11-12 | Model names in lrtest.mmkin, fix for print.mmkin | Johannes Ranke | 2 | -2/+5 | |
Fix the display of warnings and errors in print.mmkin, the matrix was erroneously transposed. | |||||
2020-11-12 | Use preprocessed data for 2,4-D, update docs | Johannes Ranke | 1 | -6/+8 | |
2020-11-12 | mkindsg class to hold groups of datasets | Johannes Ranke | 12 | -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() | |||||
2020-11-11 | Fix docs and passing of dot arguments for saem | Johannes Ranke | 1 | -6/+2 | |
2020-11-11 | Rename saemix file, option to suppress saemix messages | Johannes Ranke | 1 | -4/+10 | |