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2022-11-16We get about 25% performance gainJohannes Ranke3-16/+19
with the custom lsoda call, avoiding repeated getNativeSymbolInfo calls. It's just that we should not be calling foreign functions from different packages, because the may change without notice. Using getNativeSymbolInfo for "call_lsoda" avoids the CRAN note, and a similar call could probably be used for "unlock_solver", avoiding the NOTE in checks for cran, but we should not do this in a CRAN package.
2022-11-14Automatic starting parameters for saem.mmkinJohannes Ranke1-1/+15
For the case of mkin transformations. This gives faster convergence, and appears to avoid problems with numeric ODE solutions
2022-11-08Show DFOP g equivalent of SFORB in summary, testJohannes Ranke1-2/+3
2022-11-08Simplify SFORB also in the endpoint functionJohannes Ranke1-9/+8
2022-11-08Simplify SFORB analytical solution, whitespaceJohannes Ranke2-4/+4
I do not know why the formulae for b1 and b2 on page 64 of FOCUS kinetics (2014) were not simplified. Clearly, the term k12 * k21 - (k12 + k1output) * k21) can be simplified to - k1output * k21 The test for equivalence of DFOP and SFORB fits verifies that the change is OK. I also removed trailing whitespaces, substituted tab characters by two whitespaces and removed indenting of text in paragraphs describing parameters in roxygen comments to unify formatting.
2022-11-04Attempt at automatic setting of random effectsJohannes Ranke1-3/+15
Based on parameters in the separate fits that fail the t-test.
2022-11-04Make it easy to override maxsteps for lsodaJohannes Ranke1-15/+18
The hope was to be more successful in saemix fits, but I did not notice an improvement (e.g. for a failing likelihood calculation with importance sampling, where the error message suggested to increase maxsteps).
2022-11-04Never fail with errors in saem.mmkinJohannes Ranke1-4/+0
I think it is always preferable to be able to investigate the saemix object returned.
2022-11-03Update docsJohannes Ranke1-1/+2
2022-11-01Add tex_listing()Johannes Ranke1-0/+20
2022-11-01Add read_spreadsheetJohannes Ranke1-0/+55
2022-11-01Fix plotting saem fits with covariatesJohannes Ranke2-0/+11
2022-11-01Fix illparms testsJohannes Ranke1-1/+1
2022-11-01Improved printing for illparms()Johannes Ranke1-2/+5
For the case of single fits and no ill-defined parameters found
2022-10-31Fix R CMD checkJohannes Ranke3-3/+14
2022-10-29Update multistart docsJohannes Ranke1-2/+2
2022-10-28Rename parhist to parplot and make it genericJohannes Ranke3-11/+14
That parhist name was not the brightest idea, as it does not show histograms.
2022-10-28Export status method for mhmkin, move to status.RJohannes Ranke1-0/+6
2022-10-28Rename 'convergence' method to 'status'Johannes Ranke3-40/+39
The reason is that it is misleading in the case of saem.mmkin objects, because convergence is not really checked there.
2022-10-26Update multistart example code and vignetteJohannes Ranke1-9/+2
2022-10-26Remove kernel density estimate from llhistJohannes Ranke1-3/+2
2022-10-25Complete documentation and fix a bugJohannes Ranke3-4/+19
The bug was introduced by the changes in summary.saem.mmkin.R and surfaced in the tests when using saemix transformations.
2022-10-21Add a simple anova method for model comparisonJohannes Ranke4-1/+57
Update docs
2022-10-14Select best fit from multistart, use in parhistJohannes Ranke2-4/+32
- Add 'best' and 'which.best' generics with methods for multistart objects - Per default, scale the parameters in parhist plots using the fit with the highest log likelihood.
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.
2022-09-29Add set_nd_nq previously in pfmJohannes Ranke1-0/+103
pfm depends on mkin anyways, so reexporting set_nd_nq and set_nd_nq_focus in pfm should provide reasonable continuity.
2022-09-28Fix handling of multistart fits with failuresJohannes Ranke2-4/+7
2022-09-19Make the multistart method work on WindowsJohannes Ranke1-7/+19
2022-09-19Improve parhist and llhistJohannes Ranke1-7/+3
In particular, adapt the display of parameter boxplots for saem fits using mkin transformations to the way used for saem fits using saemix transformations, i.e. always show parameters on the natural scale, and normalised them by dividing by the median from the multiple runs.
2022-09-16Improve multistart documentation, bugfixJohannes Ranke3-14/+94
- Split out llhist and parhist documentation - Add example code for multistart - Create a multistart vignette, because the example code fails when run by pkgdown - Fix multistart for the case of mkin transformations in the saem fit
2022-09-16Improve docs and update pkgdownJohannes Ranke2-15/+16
2022-09-16Diagnostic plots for multistart methodJohannes Ranke3-4/+25
2022-09-13More work on multistartJohannes Ranke3-2/+14
2022-08-14Basic multistart method for saem.mmkin objectsJohannes Ranke3-9/+55
2022-08-10Update docsJohannes Ranke1-1/+6
2022-08-10Batch processing for hierarchical fitsJohannes Ranke3-7/+112
- '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
2022-07-26Import parallel instead of depending on itJohannes Ranke1-2/+2
This cleans up the startup message. Loading parallel is not that important, users wanting to use it will know what to do. Also, add codemeta.json to .Rbuildignore
2022-07-21Summary method for mmkin objectsJohannes Ranke4-1/+122
Also, add a method for gathering convergence information and a method for gathering information on ill-defined parameters
2022-05-18Remove outdated comment in FOCUS L vignette, update docsJohannes Ranke2-12/+12
This also adds the first benchmark results obtained on my laptop system
2022-04-13More control of y axes in plot.mkinfit, updatesJohannes Ranke1-1/+2
Documentation and test results were updated, the latter with regard to the previous work on plot.mixed.mmkin.
2022-04-09Improvements to mean_degparms() and plot.mixed.mmkin()Johannes Ranke3-4/+22
- New argument 'default_log_parms' for mean_degparms() - 'plot.mixed.mmkin': Pass the frame argument also to residual plots, take the 'default_log_parms' argument for 'mean_degparms' used for constructing approximate population curves, plot population curve last to avoid that it is covered by data
2022-03-19Improvements to CAKE_export()Johannes Ranke1-2/+2
2022-03-16Use saemix in help page, typo in vignetteJohannes Ranke1-35/+36
2022-03-14Reduce check time for CRAN, releasev1.1.0Johannes Ranke3-5/+6
2022-03-07Remove nlmixr interface for release of mkin 1.1.0Johannes Ranke6-426/+3
I am postponing my attempts to get the nlmixr interface to CRAN, given some problems with nlmixr using R-devel under Windows, see https://github.com/nlmixrdevelopment/nlmixr/issues/596 and https://github.com/r-hub/rhub/issues/512, which is fixed by the removal of nlmixr from the testsuite. For the tests to be more platform independent, the biphasic mixed effects models test dataset was defined in a way that fitting should be more robust (less ill-defined).
2022-03-03Update link to 2,4-D dataJohannes Ranke1-1/+1
2022-03-02Make tests more platform independent, update docsJohannes Ranke1-2/+1
2022-03-02Fix nlmixr fits with parallel metabolitesJohannes Ranke1-0/+24
2022-03-02Add a test for tffm0()Johannes Ranke1-8/+12
2022-03-01Add some more testsJohannes Ranke1-0/+1

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