Age | Commit message (Collapse) | Author | Files | Lines | |
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2020-11-19 | Depend on parallel, doc improvements | Johannes Ranke | 144 | -1572/+3637 | |
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 | 4 | -11/+22 | |
2020-11-13 | Fixes for f_time_norm_focus, still very fragile... | Johannes Ranke | 4 | -18/+49 | |
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 | Update test output | Johannes Ranke | 1 | -1/+2 | |
2020-11-12 | Use preprocessed data for 2,4-D, update docs | Johannes Ranke | 5 | -40/+44 | |
2020-11-12 | mkindsg class to hold groups of datasets | Johannes Ranke | 27 | -41/+585 | |
- 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 | Update static docs | Johannes Ranke | 7 | -269/+306 | |
2020-11-11 | Fix example code that was broken by use_of_ff = "max" | Johannes Ranke | 1 | -6/+10 | |
which is now the default | |||||
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 | |
2020-11-11 | Skip vdiffr tests on travis as they are not robust | Johannes Ranke | 7 | -13/+17 | |
As can be seen in the miniscule change seen on R-devel in the reference plot updated with this commit | |||||
2020-11-11 | Check on r-devel, address NOTE | Johannes Ranke | 2 | -6/+17 | |
2020-11-11 | Add print and plot calls to the saem example code | Johannes Ranke | 14 | -65/+112 | |
2020-11-10 | Digits for summary methods, print.saem.mmkin | Johannes Ranke | 12 | -82/+137 | |
2020-11-09 | I do not have a parms.nlme.mmkin method | Johannes Ranke | 1 | -2/+1 | |
2020-11-09 | saemix.mmkin and nlme.mmkin inherit from mixed.mmkin | Johannes Ranke | 25 | -213/+450 | |
With a plot method. The class mixed.mmkin is currently only a virtual class created to unify the plotting method. | |||||
2020-11-09 | Merge plot methods for nlme.mmkin and saem.mmkin | Johannes Ranke | 19 | -359/+694 | |
This avoids code duplication | |||||
2020-11-09 | Add plot method for saem.mmkin objects | Johannes Ranke | 14 | -15/+637 | |
2020-11-09 | object$mmkin_orig -> object$mmkin | Johannes Ranke | 3 | -12/+10 | |
2020-11-09 | Fix std in summary.nlme.mmkin(..., data = TRUE) | Johannes Ranke | 1 | -1/+5 | |
2020-11-09 | Remove outdated doc page | Johannes Ranke | 1 | -1202/+0 | |
2020-11-09 | Doc improvements | Johannes Ranke | 4 | -6/+9 | |
2020-11-09 | Some work on example code, pkgdown update | Johannes Ranke | 14 | -212/+451 | |
2020-11-09 | Custom analytical solutions for saemix | Johannes Ranke | 6 | -70/+183 | |
Currently SFO-SFO and DFOP-SFO. Speed increase factor about 60 | |||||
2020-11-08 | The call to saemix.predict fails with DFOP-SFO | Johannes Ranke | 4 | -6/+6 | |
2020-11-08 | Update static docs | Johannes Ranke | 7 | -24/+482 | |
2020-11-08 | Improve saem method, add summary | Johannes Ranke | 13 | -82/+459 | |
Also make the endpoints function work for saem objects. | |||||
2020-11-07 | Update static docs for dev version | Johannes Ranke | 9 | -121/+450 | |
2020-11-07 | Create saem generic for fitting saemix models | Johannes Ranke | 10 | -123/+103 | |
The reasons for this decision were - Creating an saemix generic in the saemix package caused problems with roxygen, because functions like saemix.plot.xy were documented in their help files as S3 methods, although explicitly exported with @export - Creating an saemix generic in this package is possible, but would make it necessary to load samix with exclude = "saemix" in order to avoid overwriting the generic when loading saemix. - The return object of such an saemix generic in this package cannot be an S3 class with class attribute c("saemix.mmkin", "SaemixObject") similar to nlme.mmkin, as saemix returns an S4 class. - Extending the S4 class SaemixObject using simple inheritance to a class SaemixMmkinObject with additional slots did not work as expected. When the initialize method was left untouched, it prevented creation of an SaemixMmkinObject even if it was based on an initialised SaemixObject, as the initialize method seems to always be called by new(). This could potentially be circumvented by a coerce method. If an alternative initialize method was used, an SaemixMmkinObject could be created. However, the methods written for SaemixObjects only worked in some instances, either because they checked for the class, and not for class inheritance (like compare.saemix), or because the initialize method was called for some reason. Therefore, the idea of creating a derived S4 class was abandoned. - A side effect of this decision is that the introduction of the saem generic opens the possibility to use the same generic also for other backends like nlmixr with the SAEM algorithm. | |||||
2020-11-07 | Make deSolve predictions within saemix robust | Johannes Ranke | 4 | -39/+63 | |
Also, exclude the saemix function when loading saemix in the example code, to prevent overriding our generic | |||||
2020-11-06 | Make saemix an S3 generic in this package | Johannes Ranke | 3 | -59/+113 | |
This commit also defined saemix.mmkin for mmkin row objects. This works fine, but if we set the class of the returned object to c("saemix.mmkin", "saemix"), it is not an S4 class any more which make it impossible to use saemix functions on it. | |||||
2020-11-06 | Update benchmarks for dev version | Johannes Ranke | 5 | -69/+129 | |
2020-11-06 | Fast analytical solutions for saemix, update.mmkin | Johannes Ranke | 56 | -741/+1454 | |
Also, use logit transformation for g and for solitary formation fractions, addressing #10. | |||||
2020-11-05 | Fix mean_degparms() if only one optimised parameter | Johannes Ranke | 1 | -5/+7 | |
2020-11-05 | Fix link and update docs | Johannes Ranke | 10 | -97/+121 | |
2020-11-04 | Revert to use starting values for random effects in nlme.mmkin | Johannes Ranke | 7 | -20/+10 | |
2020-11-04 | Update dynamic docs | Johannes Ranke | 2 | -9/+13 | |
2020-11-04 | Deprecate cores > 1 in saemix_model | Johannes Ranke | 1 | -3/+5 | |
2020-11-03 | Do not test residuals per default, improve nlme.mmkin | Johannes Ranke | 3 | -7/+14 | |
Do not give starting values for random effects in nlme.mmkin. | |||||
2020-10-27 | Add summary method for nlme.mmkin objects | Johannes Ranke | 22 | -93/+949 | |
Improve and update docs | |||||
2020-10-26 | Small editorial change | Johannes Ranke | 1 | -1/+1 | |
2020-10-26 | Put the legend in its own area for plot.nlme.mmkin | Johannes Ranke | 21 | -115/+121 | |
2020-10-26 | Fix another bug in plot.nlme.mmkin | Johannes Ranke | 1 | -1/+2 | |
2020-10-26 | Fix a bug in plot.nlme.mmkin | Johannes Ranke | 1 | -1/+3 | |
2020-10-24 | Fix a bug for nlme with parent only, improve examples | Johannes Ranke | 13 | -150/+32 | |
2020-10-24 | Improve plot layout | Johannes Ranke | 6 | -61/+23 | |
2020-10-24 | Plot method for nlme.mmkin objects | Johannes Ranke | 20 | -189/+624 | |
Update docs |