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2022-10-05Simplify the removal of random effectsJohannes Ranke1-0/+12
This is achieved by introducing the argument 'no_random_effect' to the saem function.
2022-09-16Diagnostic plots for multistart methodJohannes Ranke1-1/+1
2022-09-13More work on multistartJohannes Ranke1-0/+6
2022-08-10Batch processing for hierarchical fitsJohannes Ranke1-3/+6
- 'R/mhmkin.R': New method for performing multiple hierarchical mkin fits in one function call, optionally in parallel. - 'R/saem.R': 'logLik' and 'update' methods for 'saem.mmkin' objects. - 'R/illparms.R': Add methods for 'saem.mmkin' and 'mhmkin' objects. tests: Use 2 cores on travis, should work according to docs
2022-03-01Add some more testsJohannes Ranke1-0/+1
2021-07-23Merge branch 'master' into nlmixrJohannes Ranke1-1/+1
After the merge, run make test and accept the new snapshot for the mixed model fit for an nlme object
2021-03-19test_log_parms for plot.mixed.mmkin, roxygen runJohannes Ranke1-3/+7
2021-03-09Some improvements for borderline casesJohannes Ranke1-2/+17
- fit_with_errors for saem() - test_log_parms for mean_degparms() and saem()
2021-02-06Reintroduce interface to saemixJohannes Ranke1-0/+155
Also after the upgrade from buster to bullseye of my local system, some test results for saemix have changed.
2021-02-03Prepare for v1.0.0v1.0.0Johannes Ranke1-155/+0
- 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
2021-01-22We 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 Ranke1-4/+4
2021-01-06Make saemix and corresponding tests optionalJohannes Ranke1-4/+4
Address release critical check and test issues
2020-12-21plot.mixed: Possibility to overlay predictionsJohannes Ranke1-0/+5
2020-12-16Add printout of d24 model and update docsJohannes Ranke1-2/+0
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 Ranke1-4/+22
2020-11-13More work on f_time_norm_focusJohannes Ranke1-3/+4
2020-11-11Update static docsJohannes Ranke1-5/+9
2020-11-11Add print and plot calls to the saem example codeJohannes Ranke1-2/+5
2020-11-10Digits for summary methods, print.saem.mmkinJohannes Ranke1-0/+7
2020-11-09saemix.mmkin and nlme.mmkin inherit from mixed.mmkinJohannes Ranke1-2/+3
With a plot method. The class mixed.mmkin is currently only a virtual class created to unify the plotting method.
2020-11-09Some work on example code, pkgdown updateJohannes Ranke1-2/+7
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 Ranke1-4/+8
Also make the endpoints function work for saem objects.
2020-11-07Create saem generic for fitting saemix modelsJohannes Ranke1-0/+100
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.

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