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2022-11-18Make mixed model test data permanent to ensure reproducibilityJohannes Ranke1-0/+17
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.
2022-11-18Pass error.init to saemix_model, show in parplotJohannes Ranke2-5/+17
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.
2022-11-18Improve logLik.mkinfit to attach nobs attributeJohannes Ranke1-0/+1
The lack of that attribute lead to a failure to calculate the BIC in test_AIC.R on R-devel from yesterday.
2022-11-16Read in all data per defaultJohannes Ranke1-1/+1
2022-11-15Import saemix for easier profiling, update online docsJohannes Ranke1-1/+2
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.

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