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2022-11-14Automatic starting parameters for saem.mmkinJohannes Ranke14-1362/+1407
For the case of mkin transformations. This gives faster convergence, and appears to avoid problems with numeric ODE solutions
2022-11-14Comment on an errorJohannes Ranke1-1/+1
I will not correct the error in order to keep the benchmarks consistent
2022-11-11Simplify travis configJohannes Ranke1-10/+1
2022-11-08Same SFORB simplification for saem.mmkin fitsJohannes Ranke1-2/+2
2022-11-08Show DFOP g equivalent of SFORB in summary, testJohannes Ranke5-29/+36
2022-11-08Simplify SFORB also in the endpoint functionJohannes Ranke3-33/+31
2022-11-08Simplify SFORB analytical solution, whitespaceJohannes Ranke4-88/+88
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.
2022-11-07Make print and summary for saem.mmkin more robustJohannes Ranke2-8/+18
If the likelihood computed by importance sampling, these methods failed. Now they report "Not available" or NA, respectively.
2022-11-04Further improvement of robustness of anova methodJohannes Ranke1-9/+9
2022-11-04Fix anova.saem.mmkin for unavailable likelihoodsJohannes Ranke1-4/+10
2022-11-04Attempt at automatic setting of random effectsJohannes Ranke7-30/+85
Based on parameters in the separate fits that fail the t-test.
2022-11-04Make it easy to override maxsteps for lsodaJohannes Ranke2-38/+44
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).
2022-11-04Make illparms.mhmkin and anova.saem.mmkin more robustJohannes Ranke3-12/+14
2022-11-04Never fail with errors in saem.mmkinJohannes Ranke3-18/+2
I think it is always preferable to be able to investigate the saemix object returned.
2022-11-03Update for cgit...Johannes Ranke1-1/+1
2022-11-03Update docsJohannes Ranke8-2/+337
2022-11-01Add tex_listing()Johannes Ranke5-1/+58
2022-11-01Add read_spreadsheetJohannes Ranke5-2/+171
2022-11-01Update online docsJohannes Ranke30-176/+275
2022-11-01Fix plotting saem fits with covariatesJohannes Ranke7-58/+94
2022-11-01Fix a bug, couldn't set class attribute on NULLJohannes Ranke1-1/+1
2022-11-01Fix illparms testsJohannes Ranke5-51/+18
2022-11-01Improved printing for illparms()Johannes Ranke7-24/+80
For the case of single fits and no ill-defined parameters found
2022-10-31Fix R CMD checkJohannes Ranke7-17/+32
2022-10-31Possibility to override the error model in update.saemJohannes Ranke2-11/+14
2022-10-31Add anova.mhmkin methodJohannes Ranke2-0/+18
2022-10-30Correct documentation of sorting in anova.saem.mmkin()Johannes Ranke1-3/+4
2022-10-30saem summary in case of non-invertible FIM partsJohannes Ranke1-7/+13
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

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