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2023-04-01Update tests on 5950xJohannes Ranke4-121/+121
Update platform dependent test plots
2023-03-22Fix typo in mkinerrminJohannes Ranke4-121/+121
Thanks to Sebastian Meyer for spotting it.
2023-02-13Merge branch 'main' into custom_lsoda_callJohannes Ranke25-401/+344
2022-12-06Some parplot improvementsJohannes Ranke3-90/+85
llquant argument, improved legend text, tests
2022-12-01Possibility to manually specify no_random_effects in mhmkinJohannes Ranke4-39/+43
2022-11-29Complete starting values in summary for saem.mmkin fitsJohannes Ranke5-25/+24
Also update tests to the changes in mhmkin (see NEWS)
2022-11-19Confirm which test fail on R-develv1.2.1Johannes Ranke1-1/+2
2022-11-18Move two saem fits from setup script to skipped testsJohannes Ranke5-12/+18
Save winbuilder/CRAN check time...
2022-11-18Use cluster with two cores to reduce windows check timeJohannes Ranke2-8/+16
2022-11-18Make mixed model test data permanent to ensure reproducibilityJohannes Ranke17-245/+160
To ensure that tests on different platforms work on the same data, the mixed modelling test data previosly generated in tests/testthat/setup_script.R were generated once using the script in inst/dataset/generation/ds_mixed.R, and are now distributed with the package.
2022-11-18Round parameters with signif() before printingJohannes Ranke2-5/+10
This will hopefully make the test pass on all relevant platforms.
2022-11-18Pass error.init to saemix_model, show in parplotJohannes Ranke3-4/+8
Due to an oversight, error.init was not really passed to saemix_model in saem.mmkin. The new initial values were reverted to c(1, 1), in order to avoid changing the test results. Initial values for error model parameters are now shown in parplot.multistart.
2022-11-18Avoid ill-determined fit, it is platform dependentJohannes Ranke2-12/+11
The previous test lead to an error on the Fedora test systems (gcc and clang) on CRAN: ... Results have changed from known value recorded in 'print_dfop_saemix_1.txt'. old[13:24] vs new[13:24] "" "Fitted parameters:" " estimate lower upper" - "parent_0 100.09 98.94 101.25" + "parent_0 100.17 99.01 101.33" - "log_k1 -2.68 -2.91 -2.45" + "log_k1 -2.66 -2.89 -2.43" "log_k2 -4.12 -4.24 -4.00" - "g_qlogis -0.41 -0.63 -0.20" + "g_qlogis -0.43 -0.65 -0.21" - "a.1 0.91 0.67 1.15" + "a.1 0.91 0.67 1.16" "b.1 0.05 0.04 0.06" - "SD.log_k1 0.36 0.21 0.50" + "SD.log_k1 0.35 0.21 0.50" and 2 more ...
2022-11-18Typo that did not affect test resultsJohannes Ranke1-1/+1
2022-11-16Reduce testing on CRAN serversv1.2.0Johannes Ranke3-5/+7
2022-11-16Address platform dependence that surfaced on winbuilderJohannes Ranke1-1/+6
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

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