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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.
2020-05-12Rerun tests and checks, CRAN commentsJohannes Ranke1-5/+5
2020-05-11Release to CRANv0.9.50.1Johannes Ranke1-3/+3
2020-05-11Add analytical solution for DFOP-SFOJohannes Ranke1-8/+8
This is about twice as fast as deSolve compiled in the case of FOCUS D
2020-05-11Analytical solutions for all SFO variantsJohannes Ranke1-27/+16
2020-05-11Don't run visual tests on r-devel for nowJohannes Ranke1-14/+25
https://github.com/r-lib/vdiffr/issues/86
2020-05-11Avoid merge() and data.frame() in cost functionJohannes Ranke1-10/+10
also for deSolve and eigenvalue based solutions. This noticeably increases performance for these methods, see test.log and benchmark vignette.
2020-05-10Default to analytical for coupled models if availableJohannes Ranke1-10/+10
This revealed that transforming rates is necessary for fitting the analytical solution of the SFO-SFO model to the FOCUS D dataset. Benchmarks show that fitting coupled models with deSolve got a bit slower through the latest changes
2020-05-09Avoid the call to merge for analytical solutionsJohannes Ranke1-16/+17
This increases performance up to a factor of five!
2020-05-08We do not need the n.outtimes argument for mkinfitJohannes Ranke1-9/+9
As we set the tolerance for ode() appropriately
2020-05-08Avoid duplicate merge in tc error model fitJohannes Ranke1-11/+11
This increases the performance in the complete test suite by about 20 secs from 120 to around 100 secs. I tried improving merge speed by using data.table on another branch, but this did not give a noticeable performance gain.
2020-05-08Slight performance gain by reducing default n.outtimesJohannes Ranke1-14/+14
2020-05-08Roxygenize, adapt testsJohannes Ranke1-7/+7
2020-05-07Another overhaul of analytical solutionsJohannes Ranke1-11/+11
Still in preparation for analytical solutions of coupled models
2020-05-06Change implementation of analytical solutionsJohannes Ranke1-15/+15
Preparing for symbolic solutions for more than one compound
2020-04-22Support SFORB with formation fractionsJohannes Ranke1-9/+9
2020-04-20Increase test tolerance for residualsJohannes Ranke1-4/+4
This was done to address the test failure on r-devel-linux-x86_64-debian-gcc on CRAN
2020-04-18Avoid assignment to .GlobalEnv for CRANJohannes Ranke1-9/+7
2020-04-17Fix summarizing old objectsJohannes Ranke1-7/+9

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