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2022-11-14Automatic starting parameters for saem.mmkinJohannes Ranke1-1/+28
For the case of mkin transformations. This gives faster convergence, and appears to avoid problems with numeric ODE solutions
2022-11-08Same SFORB simplification for saem.mmkin fitsJohannes Ranke1-2/+2
2022-11-08Show DFOP g equivalent of SFORB in summary, testJohannes Ranke2-8/+11
2022-11-08Simplify SFORB also in the endpoint functionJohannes Ranke1-11/+10
2022-11-08Simplify SFORB analytical solution, whitespaceJohannes Ranke1-64/+64
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 Ranke1-4/+24
Based on parameters in the separate fits that fail the t-test.
2022-11-04Make it easy to override maxsteps for lsodaJohannes Ranke1-23/+26
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 Ranke1-6/+0
I think it is always preferable to be able to investigate the saemix object returned.
2022-11-01Add tex_listing()Johannes Ranke1-0/+32
2022-11-01Add read_spreadsheetJohannes Ranke1-0/+113
2022-11-01Fix plotting saem fits with covariatesJohannes Ranke2-47/+72
2022-11-01Fix a bug, couldn't set class attribute on NULLJohannes Ranke1-1/+1
2022-11-01Fix illparms testsJohannes Ranke1-1/+1
2022-11-01Improved printing for illparms()Johannes Ranke1-4/+20
For the case of single fits and no ill-defined parameters found
2022-10-31Fix R CMD checkJohannes Ranke1-3/+5
2022-10-31Possibility to override the error model in update.saemJohannes Ranke2-11/+14
2022-10-31Add anova.mhmkin methodJohannes Ranke1-0/+16
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
2022-10-29Update multistart docsJohannes Ranke1-2/+2
2022-10-28Rename parhist to parplot and make it genericJohannes Ranke4-8/+15
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 Ranke2-39/+43
2022-10-28Rename 'convergence' method to 'status'Johannes Ranke5-27/+25
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 Ranke1-0/+5
2022-10-26Update multistart example code and vignetteJohannes Ranke1-9/+3
2022-10-26Remove kernel density estimate from llhistJohannes Ranke1-11/+9
2022-10-26Make multistart work with testthat scopesJohannes Ranke1-3/+20
Also skip long-running test with saem using the analytical from mkin
2022-10-25Complete documentation and fix a bugJohannes Ranke3-2/+6
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 Ranke2-4/+116
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 Ranke3-1/+69
2022-10-14update method for mhmkin objects, clarify commentJohannes Ranke2-2/+25
2022-10-14Select best fit from multistart, use in parhistJohannes Ranke2-14/+68
- 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 Ranke1-4/+33
This is achieved by introducing the argument 'no_random_effect' to the saem function.
2022-09-29Add set_nd_nq previously in pfmJohannes Ranke1-0/+164
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
2022-09-28Fix handling of multistart fits with failuresJohannes Ranke6-60/+147
2022-09-26Make BIC.mhmkin work with failed fitsJohannes Ranke1-1/+4

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