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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
2020-11-09saemix.mmkin and nlme.mmkin inherit from mixed.mmkinJohannes Ranke3-113/+57
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 Ranke3-232/+95
This avoids code duplication
2020-11-09Add plot method for saem.mmkin objectsJohannes Ranke1-0/+218
2020-11-09object$mmkin_orig -> object$mmkinJohannes Ranke3-12/+10
2020-11-09Fix std in summary.nlme.mmkin(..., data = TRUE)Johannes Ranke1-1/+5
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 Ranke2-40/+108
Currently SFO-SFO and DFOP-SFO. Speed increase factor about 60
2020-11-08The call to saemix.predict fails with DFOP-SFOJohannes Ranke1-3/+3
2020-11-08Improve saem method, add summaryJohannes Ranke5-70/+341
Also make the endpoints function work for saem objects.
2020-11-07Create saem generic for fitting saemix modelsJohannes Ranke2-47/+48
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 Ranke2-15/+34
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 Ranke1-42/+72
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 Ranke5-111/+215
Also, use logit transformation for g and for solitary formation fractions, addressing #10.
2020-11-05Fix mean_degparms() if only one optimised parameterJohannes Ranke1-5/+7
2020-11-05Fix link and update docsJohannes Ranke1-2/+2
2020-11-04Revert to use starting values for random effects in nlme.mmkinJohannes Ranke1-1/+1

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