Age | Commit message (Collapse) | Author | Files | Lines | |
---|---|---|---|---|---|
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 | |
2022-09-16 | Improve multistart documentation, bugfix | Johannes Ranke | 1 | -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 | |||||
2022-09-16 | Rerun test with saemix 3.1 from CRAN | Johannes Ranke | 1 | -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 | |||||
2022-09-16 | Diagnostic plots for multistart method | Johannes Ranke | 1 | -14/+14 | |
2022-08-10 | Batch processing for hierarchical fits | Johannes Ranke | 1 | -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 | |||||
2022-08-08 | Error on unsupported saemix transformations | Johannes Ranke | 1 | -9/+9 | |
Also, support FOMC with saemix transformations | |||||
2022-08-08 | Fix fitting HS with saemix transformations | Johannes Ranke | 1 | -12/+10 | |
2022-07-22 | Move logs into own directory to clean root | Johannes Ranke | 6 | -0/+276 | |