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2021-06-09Rudimentary support for setting up nlmixr modelsJohannes Ranke7-29/+334
- All degradation models are specified as ODE models. This appears to be fast enough - Error models are being translated to nlmixr as close to the mkin error model as possible. When using the 'saem' backend, it appears not to be possible to use the same error model for more than one observed variable - No support yet for models with parallel formation of metabolites, where the ilr transformation is used in mkin per default - There is a bug in nlmixr which appears to be triggered if the data are not balanced, see nlmixrdevelopment/nlmixr#530 - There is a print and a plot method, the summary method is not finished
2021-04-21Merge branch 'master' into saemixJohannes Ranke1-2/+3
2021-04-21Version 1.0.4 published yesterdayv1.0.4Johannes Ranke1-2/+3
2021-03-19test_log_parms for plot.mixed.mmkin, roxygen runJohannes Ranke3-3/+19
2021-03-09Some improvements for borderline casesJohannes Ranke2-4/+26
- fit_with_errors for saem() - test_log_parms for mean_degparms() and saem()
2021-02-15Merge branch 'master' into saemixJohannes Ranke1-0/+4
2021-02-15Improve README, introductory vignette and some other docsv1.0.3Johannes Ranke1-0/+4
Also bump version to 1.0.3.
2021-02-06Reintroduce interface to saemixJohannes Ranke4-5/+269
Also after the upgrade from buster to bullseye of my local system, some test results for saemix have changed.
2021-02-04Documentation improvements, mainly fixing example codeJohannes Ranke7-50/+44
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 Ranke4-270/+6
- 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
2021-01-25Change default ylab in plot.mkinfit, explicit ylab for plot.mmkinJohannes Ranke2-1/+4
See NEWS.md. Closes #12
2021-01-22We do not need to suppress saemix plots any moreJohannes Ranke1-4/+0
This makes fitting with saem within parallel::mclapply much faster and, surprisingly, much less hungry for RAM.
2021-01-11Rebuild docsJohannes Ranke4-7/+7
2021-01-06Make saemix and corresponding tests optionalJohannes Ranke3-5/+7
Address release critical check and test issues
2020-12-21plot.mixed: Possibility to overlay predictionsJohannes Ranke2-1/+17
2020-12-19Dimethenamid data, normalisation optionsJohannes Ranke2-2/+39
2020-12-16And add the second candidate modelJohannes Ranke1-0/+4
2020-12-16and update docsJohannes Ranke1-1/+1
2020-12-16Add printout of d24 model and update docsJohannes Ranke2-2/+1
2020-12-09Make saem using mkinpredict work againJohannes Ranke1-13/+17
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.
2020-12-08mixed.mmkin and test coverageJohannes Ranke4-7/+94
2020-12-02Possibility to specify random effects structuresJohannes Ranke1-4/+5
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 Ranke4-20/+33
2020-11-27Improved way to have persistent DLLs for mkinmodJohannes Ranke1-6/+21
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 Ranke1-16/+15
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
2020-11-19Depend on parallel, doc improvementsJohannes Ranke4-85/+61
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 Ranke3-11/+20
2020-11-12Use preprocessed data for 2,4-D, update docsJohannes Ranke1-6/+8
2020-11-12mkindsg class to hold groups of datasetsJohannes Ranke7-23/+253
- 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()
2020-11-11Update static docsJohannes Ranke1-5/+9
2020-11-11Fix example code that was broken by use_of_ff = "max"Johannes Ranke1-6/+10
which is now the default
2020-11-11Skip vdiffr tests on travis as they are not robustJohannes Ranke1-1/+2
As can be seen in the miniscule change seen on R-devel in the reference plot updated with this commit
2020-11-11Add print and plot calls to the saem example codeJohannes Ranke1-2/+5
2020-11-10Digits for summary methods, print.saem.mmkinJohannes Ranke2-3/+11
2020-11-09saemix.mmkin and nlme.mmkin inherit from mixed.mmkinJohannes Ranke3-34/+12
With a plot method. The class mixed.mmkin is currently only a virtual class created to unify the plotting method.
2020-11-09Merge plot methods for nlme.mmkin and saem.mmkinJohannes Ranke3-103/+41
This avoids code duplication
2020-11-09Add plot method for saem.mmkin objectsJohannes Ranke2-6/+96
2020-11-09Doc improvementsJohannes Ranke1-0/+1
2020-11-09Some work on example code, pkgdown updateJohannes Ranke2-17/+31
2020-11-09Custom analytical solutions for saemixJohannes Ranke1-7/+16
Currently SFO-SFO and DFOP-SFO. Speed increase factor about 60
2020-11-08Improve saem method, add summaryJohannes Ranke3-8/+108
Also make the endpoints function work for saem objects.
2020-11-07Create saem generic for fitting saemix modelsJohannes Ranke2-57/+42
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.
2020-11-07Make deSolve predictions within saemix robustJohannes Ranke2-24/+29
Also, exclude the saemix function when loading saemix in the example code, to prevent overriding our generic
2020-11-06Make saemix an S3 generic in this packageJohannes Ranke1-14/+39
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.
2020-11-06Fast analytical solutions for saemix, update.mmkinJohannes Ranke4-53/+47
Also, use logit transformation for g and for solitary formation fractions, addressing #10.
2020-11-05Fix link and update docsJohannes Ranke1-2/+2
2020-11-04Update dynamic docsJohannes Ranke1-4/+7
2020-11-03Do not test residuals per default, improve nlme.mmkinJohannes Ranke1-0/+3
Do not give starting values for random effects in nlme.mmkin.
2020-10-27Add summary method for nlme.mmkin objectsJohannes Ranke4-10/+113
Improve and update docs

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