Age | Commit message (Collapse) | Author | Files | Lines | |
---|---|---|---|---|---|
2023-01-09 | Prebuilt PDF vignettes, summary_listing | Johannes Ranke | 1 | -12/+22 | |
2022-12-19 | Rename template folder, create format | Johannes Ranke | 1 | -5/+16 | |
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. | |||||
2022-12-15 | List random effects correlations in output if any | Johannes Ranke | 1 | -10/+10 | |
Update docs | |||||
2022-12-12 | Run tests with new CPU and RAM | Johannes Ranke | 1 | -26/+26 | |
2022-12-07 | Check slopes in saemix covariate models | Johannes Ranke | 1 | -25/+16 | |
2022-12-06 | Some parplot improvements | Johannes Ranke | 1 | -16/+25 | |
llquant argument, improved legend text, tests | |||||
2022-12-02 | Update test log with current R-devel | Johannes Ranke | 1 | -42/+23 | |
One printout and four plots are different using current R-devel. These are currently skipped on CRAN. These test were run with the development version of saemix (my branch installable_dev_version). If saemix from CRAN is used, there are some more differences due to different error model parameters | |||||
2022-12-02 | Avoid error message at testthat termination | Johannes Ranke | 1 | -24/+23 | |
https://github.com/r-lib/processx/issues/236 | |||||
2022-12-01 | Possibility to manually specify no_random_effects in mhmkin | Johannes Ranke | 2 | -28/+28 | |
2022-11-29 | Complete starting values in summary for saem.mmkin fits | Johannes Ranke | 2 | -18/+18 | |
Also update tests to the changes in mhmkin (see NEWS) | |||||
2022-11-19 | Confirm which test fail on R-develv1.2.1 | Johannes Ranke | 2 | -36/+110 | |
2022-11-18 | Move two saem fits from setup script to skipped tests | Johannes Ranke | 1 | -22/+22 | |
Save winbuilder/CRAN check time... | |||||
2022-11-18 | Use cluster with two cores to reduce windows check time | Johannes Ranke | 1 | -18/+19 | |
2022-11-18 | Make mixed model test data permanent to ensure reproducibility | Johannes Ranke | 2 | -16/+16 | |
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. | |||||
2022-11-18 | Round parameters with signif() before printing | Johannes Ranke | 2 | -11/+11 | |
This will hopefully make the test pass on all relevant platforms. | |||||
2022-11-18 | Pass error.init to saemix_model, show in parplot | Johannes Ranke | 2 | -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. | |||||
2022-11-18 | Improve logLik.mkinfit to attach nobs attribute | Johannes Ranke | 1 | -29/+32 | |
The lack of that attribute lead to a failure to calculate the BIC in test_AIC.R on R-devel from yesterday. | |||||
2022-11-16 | Reduce testing on CRAN serversv1.2.0 | Johannes Ranke | 1 | -1/+0 | |
2022-11-16 | Update DESCRIPTION and NEWS, check and test | Johannes Ranke | 2 | -20/+20 | |
2022-11-16 | Address platform dependence that surfaced on winbuilder | Johannes Ranke | 1 | -23/+23 | |
2022-11-15 | Import saemix for easier profiling, update online docs | Johannes Ranke | 1 | -8/+8 | |
2022-11-14 | Automatic starting parameters for saem.mmkin | Johannes Ranke | 2 | -18/+18 | |
For the case of mkin transformations. This gives faster convergence, and appears to avoid problems with numeric ODE solutions | |||||
2022-11-08 | Show DFOP g equivalent of SFORB in summary, test | Johannes Ranke | 1 | -13/+13 | |
2022-11-08 | Simplify SFORB also in the endpoint function | Johannes Ranke | 1 | -13/+13 | |
2022-11-08 | Simplify SFORB analytical solution, whitespace | Johannes Ranke | 1 | -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. | |||||
2022-11-04 | Attempt at automatic setting of random effects | Johannes Ranke | 2 | -21/+21 | |
Based on parameters in the separate fits that fail the t-test. | |||||
2022-11-04 | Never fail with errors in saem.mmkin | Johannes Ranke | 1 | -8/+2 | |
I think it is always preferable to be able to investigate the saemix object returned. | |||||
2022-11-01 | Add read_spreadsheet | Johannes Ranke | 1 | -1/+1 | |
2022-11-01 | Fix plotting saem fits with covariates | Johannes Ranke | 2 | -10/+10 | |
2022-11-01 | Fix illparms tests | Johannes Ranke | 1 | -45/+12 | |
2022-11-01 | Improved printing for illparms() | Johannes Ranke | 2 | -17/+50 | |
For the case of single fits and no ill-defined parameters found | |||||
2022-10-31 | Fix R CMD check | Johannes Ranke | 2 | -11/+11 | |
2022-10-29 | Another attempt to make the test robust | Johannes Ranke | 2 | -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. | |||||
2022-10-28 | Rename parhist to parplot and make it generic | Johannes Ranke | 1 | -21/+21 | |
That parhist name was not the brightest idea, as it does not show histograms. | |||||
2022-10-28 | Export status method for mhmkin, move to status.R | Johannes Ranke | 1 | -20/+20 | |
2022-10-28 | Update test to renamed method | Johannes Ranke | 1 | -13/+13 | |
2022-10-26 | Really test anova output, test covariates | Johannes Ranke | 1 | -11/+11 | |
2022-10-26 | Reduced sfo model for multistart.saem.mkin tests | Johannes Ranke | 1 | -13/+13 | |
2022-10-26 | Remove kernel density estimate from llhist | Johannes Ranke | 1 | -15/+15 | |
2022-10-26 | Try to make multistart (more) reproducible | Johannes Ranke | 1 | -9/+9 | |
2022-10-26 | Tests pass locally | Johannes Ranke | 1 | -21/+19 | |
2022-10-26 | Make multistart work with testthat scopes | Johannes Ranke | 1 | -12/+20 | |
Also skip long-running test with saem using the analytical from mkin | |||||
2022-10-25 | Change DFOP mixed model data in tests, updates | Johannes Ranke | 1 | -12/+12 | |
2022-10-25 | Complete documentation and fix a bug | Johannes Ranke | 2 | -13/+19 | |
The bug was introduced by the changes in summary.saem.mmkin.R and surfaced in the tests when using saemix transformations. | |||||
2022-10-17 | SFORB in saem, update for mhmkin and multistart | Johannes Ranke | 1 | -8/+8 | |
2022-10-14 | Select best fit from multistart, use in parhist | Johannes Ranke | 1 | -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. | |||||
2022-10-05 | Simplify the removal of random effects | Johannes Ranke | 1 | -10/+10 | |
This is achieved by introducing the argument 'no_random_effect' to the saem function. | |||||
2022-09-30 | Test the package with saemix development version | Johannes Ranke | 1 | -43/+12 | |
2022-09-29 | Add set_nd_nq previously in pfm | Johannes Ranke | 1 | -14/+46 | |
pfm depends on mkin anyways, so reexporting set_nd_nq and set_nd_nq_focus in pfm should provide reasonable continuity. | |||||
2022-09-28 | Fix handling of multistart fits with failures | Johannes Ranke | 1 | -14/+2 | |