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2022-10-29Another attempt to make the test robustJohannes Ranke4-20/+44
As the last update failed on travis. Now we should be more robust, as rounding to one digit works better when parameters are log-transformed (mkin transformations) in the output.
2022-10-29Make test independent of saemix error model parameter patchJohannes Ranke2-4/+3
As mentioned in d44c17da6d62568b
2022-10-29Next version will be 1.2.0, complete NEWSJohannes Ranke2-8/+8
2022-10-29Merge branch 'update_online_docs_v1.1.1'Johannes Ranke1-56/+62
2022-10-29Rebuild vignette with rbenchmark installedJohannes Ranke1-56/+62
2022-10-29Update multistart docsJohannes Ranke21-31/+382
2022-10-28Rename parhist to parplot and make it genericJohannes Ranke16-51/+63
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 Ranke5-59/+70
2022-10-28Update test to renamed methodJohannes Ranke2-14/+14
2022-10-28Rename 'convergence' method to 'status'Johannes Ranke9-75/+71
The reason is that it is misleading in the case of saem.mmkin objects, because convergence is not really checked there.
2022-10-26Really test anova output, test covariatesJohannes Ranke5-52/+38
2022-10-26We don't use KernSmooth any moreJohannes Ranke1-2/+1
2022-10-26Update multistart example code and vignetteJohannes Ranke16-63/+137
2022-10-26Don't test parhist and llhist on travis, docsJohannes Ranke18-73/+741
2022-10-26Reduced sfo model for multistart.saem.mkin testsJohannes Ranke6-45/+147
2022-10-26Remove kernel density estimate from llhistJohannes Ranke7-47/+112
2022-10-26Skip llhist and parhist tests as platform dependentJohannes Ranke1-0/+1
2022-10-26Try to make multistart (more) reproducibleJohannes Ranke4-152/+148
2022-10-26Tests pass locallyJohannes Ranke1-21/+19
2022-10-26Make multistart work with testthat scopesJohannes Ranke7-18/+301
Also skip long-running test with saem using the analytical from mkin
2022-10-25Test multistart methodJohannes Ranke2-0/+19
2022-10-25Round also for nlme print method...Johannes Ranke2-7/+8
2022-10-25Increase rounding in test for travisJohannes Ranke2-2/+2
As the "const" error model parameters is stored on log scale in nlme
2022-10-25Explanatory commentJohannes Ranke1-0/+1
2022-10-25Avoid another platform dependenceJohannes Ranke2-2/+7
Caused by the fact that printing error model parameters in nlme summaries do not honor the digits argument.
2022-10-25Change DFOP mixed model data in tests, updatesJohannes Ranke9-1282/+1298
2022-10-25Address platform dependencies that surfaced on travisJohannes Ranke2-5/+10
2022-10-25Another attempt to restore coverage on codecovJohannes Ranke1-2/+3
2022-10-25Install covr on travis to restore codecov coverageJohannes Ranke1-1/+1
2022-10-25Complete documentation and fix a bugJohannes Ranke11-29/+69
The bug was introduced by the changes in summary.saem.mmkin.R and surfaced in the tests when using saemix transformations.
2022-10-25Revert accidental changeJohannes Ranke1-21/+27
2022-10-21Explain chisq tests in anovaJohannes Ranke1-1/+2
Now that I understand how anova.lmer from which I ported the code produces mostly meaningful likelihood ratio tests in the table.
2022-10-21Adapt summary.saem.mmkin to covariate modelsJohannes Ranke1-7/+6
Dissipation times are calculated for covariate values of zero currently, which will usually not be very useful.
2022-10-21Add a simple anova method for model comparisonJohannes Ranke7-5/+175
Update docs
2022-10-21Make update.saem.mmkin work with objects from multistartJohannes Ranke1-6/+10
In particular, objects selected using best.multistart can now be updated, as the starting parameters are inserted into the call, without reference to 'start_parms' which will not be available outside the multistart method.
2022-10-20First working version setting up covariate modelsJohannes Ranke1-4/+53
2022-10-18Don't fail if one of the Hessians can't be computedJohannes Ranke1-1/+8
2022-10-17Fix selecting by log likelihood in parhistJohannes Ranke1-8/+21
2022-10-17SFORB in saem, update for mhmkin and multistartJohannes Ranke6-9/+94
2022-10-14update method for mhmkin objects, clarify commentJohannes Ranke2-2/+25
2022-10-14Select best fit from multistart, use in parhistJohannes Ranke6-31/+117
- 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.
2022-10-13Cope with failed FIM inversionsJohannes Ranke3-10/+29
2022-10-05Simplify the removal of random effectsJohannes Ranke5-29/+94
This is achieved by introducing the argument 'no_random_effect' to the saem function.
2022-10-04Add set_nd_nq to pkgdown topicsJohannes Ranke1-0/+1
2022-09-30Test the package with saemix development versionJohannes Ranke1-43/+12
2022-09-30Install development version of saemix on travisJohannes Ranke1-0/+1
I need this version for the parhist.multistart method, otherwise results for the two-component error model parameters can switch between positive and negative values.
2022-09-30r2u is now the default for r-ciJohannes Ranke1-1/+1
2022-09-29Add set_nd_nq previously in pfmJohannes Ranke7-18/+405
pfm depends on mkin anyways, so reexporting set_nd_nq and set_nd_nq_focus in pfm should provide reasonable continuity.
2022-09-29More adaptations to deal with failed saem fitsJohannes Ranke1-2/+8
2022-09-29Adapt to new format of failed saem.mmkin fitsJohannes Ranke2-8/+13

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