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2021-11-17Update required saemix version, update testsJohannes Ranke1-30/+30
2021-09-16Adapt and improve the dimethenamid vignetteJohannes Ranke1-3/+3
Adapt to the corrected data and unify control parameters for saemix and nlmixr with saem. Update docs
2021-09-16Merge branch 'master' into nlmixrJohannes Ranke1-27/+13
2021-09-15Fix Open EFSA URL, changelog for 1.0.5v1.0.5Johannes Ranke1-4/+4
The EFSA URL failed on winbuilder because some cookie sets a different domain, so I am now using \href{} with the full link as link text instead of \url{}
2021-09-15Update test result to corrected data, version bumpJohannes Ranke1-8/+8
2021-07-23Merge branch 'master' into nlmixrJohannes Ranke1-20/+22
After the merge, run make test and accept the new snapshot for the mixed model fit for an nlme object
2021-07-23Rerun tests, use current vdiffr on travisJohannes Ranke1-33/+9
2021-06-17Let backtransform_odeparms handle nlmixr formation fractionsJohannes Ranke1-21/+24
Also adapt summary.nlmixr.mmkin to correctly handle the way formation fractions are translated to nlmixr
2021-04-21Merge branch 'master' into saemixJohannes Ranke1-20/+29
2021-04-21Version 1.0.4 published yesterdayv1.0.4Johannes Ranke1-18/+25
2021-03-31Bug fix in plot.mkinfitJohannes Ranke1-8/+25
In residual plots, use xlab and xlim if appropriate
2021-03-09Some improvements for borderline casesJohannes Ranke1-18/+18
- fit_with_errors for saem() - test_log_parms for mean_degparms() and saem()
2021-02-15Fully rebuild docs, rerun tests and checkJohannes Ranke1-14/+14
2021-02-15Merge branch 'master' into saemixJohannes Ranke1-1/+1
2021-02-15Improve README, introductory vignette and some other docsv1.0.3Johannes Ranke1-2/+2
Also bump version to 1.0.3.
2021-02-13Merge branch 'master' into saemixJohannes Ranke1-10/+10
Run make testcheck to regenerate logs with merge conflicts
2021-02-13Update for gmkin 0.6.12v1.0.2Johannes Ranke1-8/+8
mkinfit: Keep model names stored in mkinmod objects, avoiding their loss in gmkin
2021-02-06Reintroduce interface to saemixJohannes Ranke1-10/+17
Also after the upgrade from buster to bullseye of my local system, some test results for saemix have changed.
2021-02-06Increase test tolerance for parameter comparisonsv1.0.1Johannes Ranke1-10/+10
Platform dependence also revealed after upgrade to bullseye
2021-02-04Documentation improvements, mainly fixing example codeJohannes Ranke1-2/+2
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 Ranke1-33/+20
- 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
2021-01-06Make saemix and corresponding tests optionalJohannes Ranke1-23/+29
Address release critical check and test issues
2020-12-19Dimethenamid data, normalisation optionsJohannes Ranke1-8/+8
2020-12-10Add a test for saemix with deSolveJohannes Ranke1-9/+16
But skip the test as it takes too long to always run
2020-12-09Make saem using mkinpredict work againJohannes Ranke1-7/+7
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.
2020-12-09Some test fixesJohannes Ranke1-38/+7
2020-12-09Add more tests and fix HS in saemJohannes Ranke1-9/+40
2020-12-09Fix a test I accidentally brokeJohannes Ranke1-17/+12
2020-12-09Any yet more testsJohannes Ranke1-14/+19
2020-12-09Fix tests and rerunJohannes Ranke1-28/+10
2020-12-08mixed.mmkin and test coverageJohannes Ranke1-17/+23
2020-12-02Possibility to specify random effects structuresJohannes Ranke1-13/+9
The default is pdDiag again, as we often have a small number of datasets in degradation kinetics.
2020-11-30Log-Cholesky parameterisation as default in nlme.mmkinJohannes Ranke1-9/+13
2020-11-27Improved way to have persistent DLLs for mkinmodJohannes Ranke1-6/+6
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 Ranke1-8/+8
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
2020-11-19Update tests, improve CAKE_export testJohannes Ranke1-20/+21
2020-11-08Improve saem method, add summaryJohannes Ranke1-3/+3
Also make the endpoints function work for saem objects.
2020-11-07Create saem generic for fitting saemix modelsJohannes Ranke1-14/+7
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.
2020-11-06Fast analytical solutions for saemix, update.mmkinJohannes Ranke1-9/+16
Also, use logit transformation for g and for solitary formation fractions, addressing #10.
2020-11-04Revert to use starting values for random effects in nlme.mmkinJohannes Ranke1-5/+5
2020-10-27Add summary method for nlme.mmkin objectsJohannes Ranke1-10/+10
Improve and update docs
2020-10-08Fix issues for releaseJohannes Ranke1-10/+10
2020-07-17mkinfit: Ignore unused components of state.iniJohannes Ranke1-4/+5
2020-07-15Improve handling of (partially) failing fitsJohannes Ranke1-5/+5
2020-06-15Test plots on r-devel onlyJohannes Ranke1-14/+25
following the arguments of Xavier Robin https://github.com/r-lib/vdiffr/issues/86#issuecomment-636447231
2020-06-15Fix a bug, update for current vdiffrJohannes Ranke1-11/+11
Vignette FOCUS_L failed as I had introduced a bug in the handling of warnings. Current vdiffr only runs visual tests if R < 4.1.0, skipping r-devel for now, see https://github.com/r-lib/vdiffr/commit/630a29d013361fd63fea242f531e2db6aef37919
2020-05-29Improve handling of warnings, reorganize testsJohannes Ranke1-19/+12
2020-05-29Warn if standardized residuals are unlikely normalJohannes Ranke1-11/+18
This revealed a bug in the data returned in mkinfit$data in the case of the d_3 algorithm, which also affected the residual plot - the data from the direct fitting was not returned even if this was the better method.
2020-05-28use_of_ff = "max" for shorthand models like "SFO"Johannes Ranke1-7/+7
2020-05-26Use all cores per default, confint toleranceJohannes Ranke1-10/+10
Also, use more intelligent starting values for the variance of the random effects for saemix. While this does not appear to speed up the convergence, it shows where this variance is greatly reduced by using mixed-effects models as opposed to the separate independent fits.

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