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2022-11-18Round parameters with signif() before printingJohannes Ranke2-11/+11
This will hopefully make the test pass on all relevant platforms.
2022-11-18Pass error.init to saemix_model, show in parplotJohannes Ranke2-19/+20
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 Ranke1-29/+32
The lack of that attribute lead to a failure to calculate the BIC in test_AIC.R on R-devel from yesterday.
2022-11-16Reduce testing on CRAN serversv1.2.0Johannes Ranke1-1/+0
2022-11-16Update DESCRIPTION and NEWS, check and testJohannes Ranke2-20/+20
2022-11-16Address platform dependence that surfaced on winbuilderJohannes Ranke1-23/+23
2022-11-15Import saemix for easier profiling, update online docsJohannes Ranke1-8/+8
2022-11-14Automatic starting parameters for saem.mmkinJohannes Ranke2-18/+18
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 Ranke1-13/+13
2022-11-08Simplify SFORB also in the endpoint functionJohannes Ranke1-13/+13
2022-11-08Simplify SFORB analytical solution, whitespaceJohannes Ranke1-20/+20
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.
2022-11-04Attempt at automatic setting of random effectsJohannes Ranke2-21/+21
Based on parameters in the separate fits that fail the t-test.
2022-11-04Never fail with errors in saem.mmkinJohannes Ranke1-8/+2
I think it is always preferable to be able to investigate the saemix object returned.
2022-11-01Add read_spreadsheetJohannes Ranke1-1/+1
2022-11-01Fix plotting saem fits with covariatesJohannes Ranke2-10/+10
2022-11-01Fix illparms testsJohannes Ranke1-45/+12
2022-11-01Improved printing for illparms()Johannes Ranke2-17/+50
For the case of single fits and no ill-defined parameters found
2022-10-31Fix R CMD checkJohannes Ranke2-11/+11
2022-10-29Another attempt to make the test robustJohannes Ranke2-19/+19
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.
2022-10-28Rename parhist to parplot and make it genericJohannes Ranke1-21/+21
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 Ranke1-20/+20
2022-10-28Update test to renamed methodJohannes Ranke1-13/+13
2022-10-26Really test anova output, test covariatesJohannes Ranke1-11/+11
2022-10-26Reduced sfo model for multistart.saem.mkin testsJohannes Ranke1-13/+13
2022-10-26Remove kernel density estimate from llhistJohannes Ranke1-15/+15
2022-10-26Try to make multistart (more) reproducibleJohannes Ranke1-9/+9
2022-10-26Tests pass locallyJohannes Ranke1-21/+19
2022-10-26Make multistart work with testthat scopesJohannes Ranke1-12/+20
Also skip long-running test with saem using the analytical from mkin
2022-10-25Change DFOP mixed model data in tests, updatesJohannes Ranke1-12/+12
2022-10-25Complete documentation and fix a bugJohannes Ranke2-13/+19
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 Ranke1-8/+8
2022-10-14Select best fit from multistart, use in parhistJohannes Ranke1-13/+13
- 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.
2022-10-05Simplify the removal of random effectsJohannes Ranke1-10/+10
This is achieved by introducing the argument 'no_random_effect' to the saem function.
2022-09-30Test the package with saemix development versionJohannes Ranke1-43/+12
2022-09-29Add set_nd_nq previously in pfmJohannes Ranke1-14/+46
pfm depends on mkin anyways, so reexporting set_nd_nq and set_nd_nq_focus in pfm should provide reasonable continuity.
2022-09-28Fix handling of multistart fits with failuresJohannes Ranke1-14/+2
2022-09-16Improve multistart documentation, bugfixJohannes Ranke1-2/+14
- Split out llhist and parhist documentation - Add example code for multistart - Create a multistart vignette, because the example code fails when run by pkgdown - Fix multistart for the case of mkin transformations in the saem fit
2022-09-16Rerun test with saemix 3.1 from CRANJohannes Ranke1-10/+10
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 Ranke1-14/+14
2022-08-10Batch processing for hierarchical fitsJohannes Ranke1-10/+11
- '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
2022-08-08Error on unsupported saemix transformationsJohannes Ranke1-9/+9
Also, support FOMC with saemix transformations
2022-08-08Fix fitting HS with saemix transformationsJohannes Ranke1-12/+10
2022-07-22Move logs into own directory to clean rootJohannes Ranke6-0/+276

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