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2023-04-06Fix a bug with moved DLLs and current deSolveJohannes Ranke1-4/+3
In mkinmod, dll_info was not included in the returned model object in the case that the DLL was moved to a user defined directory. This is now fixed.
2023-04-02Deal with covariates in summary for saem.mmkin objectsJohannes Ranke1-1/+10
2023-03-23Support covariates in endpoints()Johannes Ranke2-8/+29
2023-03-22Merge branch 'main' into covariate_parms_and_endpointsJohannes Ranke1-1/+1
2023-03-22Fix typo in mkinerrminJohannes Ranke1-1/+1
Thanks to Sebastian Meyer for spotting it.
2023-03-22Fix plotting saemix without covariates, polishJohannes Ranke1-4/+11
Better linetypes and labels
2023-03-20Support covariates in parms and plot.saem.mmkinJohannes Ranke3-53/+113
2023-03-15Start parms and endpoints for covariatesJohannes Ranke2-3/+13
2023-02-26Improve documentation of the formatJohannes Ranke1-2/+19
2023-02-23Basic check if covariate data are usableJohannes Ranke1-4/+11
2023-02-17Update online docs, fix bug that surfacedJohannes Ranke1-5/+6
2023-02-17Finish adapting to upcoming deSolveJohannes Ranke4-24/+19
2023-02-17Merge remote-tracking branch 'origin/main' into faster_lsodaJohannes Ranke1-4/+3
2023-02-13Update mmkin docs, parallel is not loaded any moreJohannes Ranke1-4/+3
2023-02-13WIP adapting to new deSolve with faster lsodaJohannes Ranke2-83/+20
2023-02-13Merge branch 'main' into custom_lsoda_callJohannes Ranke15-78/+277
2023-01-09Prebuilt PDF vignettes, summary_listingJohannes Ranke3-33/+60
2023-01-05Don't preschedule multistart runsJohannes Ranke1-2/+5
Sometimes a lot of them fail, so we were wasting time
2023-01-04Update documentation of 'use_of_ff' argumentJohannes Ranke1-1/+1
2023-01-03Improved skeleton for hierarchical fitsJohannes Ranke1-0/+1
Now with working pathway fits using SFORB-SFO2 (only two parallel metabolites instead of three) as the data for compound Ia was not sufficient for a reliable fit.
2023-01-02Fix no_random_effect with character vectorJohannes Ranke1-1/+1
2023-01-02Echo R code per default in markdown templateJohannes Ranke1-1/+1
2022-12-19Rename template folder, create formatJohannes Ranke2-1/+40
Instead of rmarkdown::pdf_document, mkin::hierarchical_kinetics is used as a document format in the template. In this way, the template file can be freed from some R code and yaml options that the average user does not have to be aware of.
2022-12-15List random effects correlations in output if anyJohannes Ranke2-4/+20
Update docs
2022-12-07Fix parplot for the case of failed multistart runsJohannes Ranke2-2/+2
2022-12-07Check slopes in saemix covariate modelsJohannes Ranke1-1/+13
2022-12-06Some parplot improvementsJohannes Ranke1-4/+12
llquant argument, improved legend text, tests
2022-12-02Avoid redundant warnings in summariesJohannes Ranke1-2/+3
2022-12-01Possibility to manually specify no_random_effects in mhmkinJohannes Ranke1-20/+71
2022-11-29Complete starting values in summary for saem.mmkin fitsJohannes Ranke1-1/+10
Also update tests to the changes in mhmkin (see NEWS)
2022-11-25mhmkin: Easy specification of ill-defined parmsJohannes Ranke1-18/+20
The argument 'no_random_effect' now accepts an illparms.mhmkin object
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
2022-11-16We get about 25% performance gainJohannes Ranke5-33/+131
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.
2022-11-15Import 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

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