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2022-11-16We get about 25% performance gainJohannes Ranke1-1/+2
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 Ranke8-1341/+1343
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 Ranke1-6/+9
2022-11-04Attempt at automatic setting of random effectsJohannes Ranke3-2/+25
Based on parameters in the separate fits that fail the t-test.
2022-11-01Fix plotting saem fits with covariatesJohannes Ranke1-1/+1
2022-11-01Fix illparms testsJohannes Ranke2-4/+4
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

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