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2022-11-01Improved printing for illparms()Johannes Ranke2-1/+3
For the case of single fits and no ill-defined parameters found
2022-10-29Another attempt to make the test robustJohannes Ranke2-1/+25
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
2022-10-28Rename parhist to parplot and make it genericJohannes Ranke5-5/+6
That parhist name was not the brightest idea, as it does not show histograms.
2022-10-28Update test to renamed methodJohannes Ranke1-1/+1
2022-10-26Really test anova output, test covariatesJohannes Ranke2-5/+22
2022-10-26Don't test parhist and llhist on travis, docsJohannes Ranke1-7/+17
2022-10-26Reduced sfo model for multistart.saem.mkin testsJohannes Ranke5-32/+134
2022-10-26Remove kernel density estimate from llhistJohannes Ranke3-17/+86
2022-10-26Skip llhist and parhist tests as platform dependentJohannes Ranke1-0/+1
2022-10-26Try to make multistart (more) reproducibleJohannes Ranke3-143/+139
2022-10-26Make multistart work with testthat scopesJohannes Ranke5-3/+261
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 Ranke8-1270/+1286
2022-10-25Address platform dependencies that surfaced on travisJohannes Ranke2-5/+10
2022-10-25Complete documentation and fix a bugJohannes Ranke2-10/+21
The bug was introduced by the changes in summary.saem.mmkin.R and surfaced in the tests when using saemix transformations.
2022-10-17SFORB in saem, update for mhmkin and multistartJohannes Ranke1-0/+15
2022-10-05Simplify the removal of random effectsJohannes Ranke1-14/+38
This is achieved by introducing the argument 'no_random_effect' to the saem function.
2022-09-29Add set_nd_nq previously in pfmJohannes Ranke3-4/+90
pfm depends on mkin anyways, so reexporting set_nd_nq and set_nd_nq_focus in pfm should provide reasonable continuity.
2022-09-16Rerun test with saemix 3.1 from CRANJohannes Ranke2-4/+4
Apparently, the change I introduced into saemix saemixdevelopment/saemixextension#34 to fix error model parameters to positive values slightly influences the results. So this is now with the CRAN version to keep test results in sync with Travis
2022-09-16Diagnostic plots for multistart methodJohannes Ranke2-4/+4
2022-08-10Naming of random effects for reduced parameter modelsJohannes Ranke2-0/+69
2022-08-10Increase test coverage, require saemix version 3.1Johannes Ranke6-5/+34
2022-08-10Batch processing for hierarchical fitsJohannes Ranke5-2/+33
- '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
2022-08-08Error on unsupported saemix transformationsJohannes Ranke1-1/+3
Also, support FOMC with saemix transformations
2022-08-08Fix fitting HS with saemix transformationsJohannes Ranke1-7/+8
2022-07-21Remove platform sensitive convergence testsJohannes Ranke2-11/+11
2022-07-21Summary method for mmkin objectsJohannes Ranke6-5038/+1195
Also, add a method for gathering convergence information and a method for gathering information on ill-defined parameters
2022-07-12Tests before releasev1.1.1Johannes Ranke3-1/+3870
2022-07-12Avoid spawning multiple cores in tests on CRANJohannes Ranke1-2/+2
2022-07-08Store DLL info in mkinmod objects for performanceJohannes Ranke2-1169/+1169
Thanks to Tomas Kalibera for his analysis of the problem on the r-package-devel mailing list and for the suggestion on how to fix it. See the current benchmark vignette for the new data on mkin 1.1.1 with R 4.2.1, with unprecedented performance.
2022-04-13More control of y axes in plot.mkinfit, updatesJohannes Ranke4-7/+7
Documentation and test results were updated, the latter with regard to the previous work on plot.mixed.mmkin.
2022-03-19Test saemix without special analytical solutionsJohannes Ranke1-0/+12
Also increase the performance a bit (from about 210 s to about 140 s in the case of DFOP with four chains and 300, 100 iterations).
2022-03-19Improvements to CAKE_export()Johannes Ranke3-9/+18
2022-03-14Reduce check time for CRAN, releasev1.1.0Johannes Ranke4-19/+17
2022-03-08Avoid using multiple processes on CRAN check machinesJohannes Ranke1-3/+3
2022-03-07Remove nlmixr interface for release of mkin 1.1.0Johannes Ranke8-2421/+2231
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).
2022-03-03Reintroduce the skipped test, with a workaroundJohannes Ranke1-8/+15
2022-03-03Skip a test that assigns to the global environmentJohannes Ranke1-0/+1
2022-03-03More work to try to pass tests on R-devel winbuilderJohannes Ranke5-30/+24
2022-03-02Skip some tests on CRAN to reduce loadJohannes Ranke1-0/+2
In the hope that winbuilder will cope better then
2022-03-02Make tests more platform independent, update docsJohannes Ranke14-1393/+1343
2022-03-02Fix nlmixr fits with parallel metabolitesJohannes Ranke1-3/+14
2022-03-02Add a test for tffm0()Johannes Ranke1-0/+10
2022-03-01Avoid using cat() for default output, testsJohannes Ranke2-4/+13
2022-03-01Add some more testsJohannes Ranke7-35/+137

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