Age | Commit message (Collapse) | Author | Files | Lines | |
---|---|---|---|---|---|
2022-11-18 | Typo that did not affect test results | Johannes Ranke | 1 | -1/+1 | |
2022-11-17 | Complete update of online docs for v1.2.0 | Johannes Ranke | 166 | -4184/+9615 | |
2022-11-16 | Reduce testing on CRAN serversv1.2.0 | Johannes Ranke | 4 | -6/+7 | |
2022-11-16 | Update docs | Johannes Ranke | 4 | -8/+11 | |
2022-11-16 | Update DESCRIPTION and NEWS, check and test | Johannes Ranke | 4 | -27/+27 | |
2022-11-16 | Read in all data per default | Johannes Ranke | 1 | -1/+1 | |
2022-11-16 | Address platform dependence that surfaced on winbuilder | Johannes Ranke | 2 | -24/+29 | |
2022-11-16 | Update online docs | Johannes Ranke | 7 | -127/+183 | |
2022-11-16 | We get about 25% performance gain | Johannes Ranke | 19 | -94/+328 | |
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. | |||||
2022-11-15 | Import saemix for easier profiling, update online docs | Johannes Ranke | 16 | -180/+76 | |
2022-11-14 | Add saem benchmarks to index | Johannes Ranke | 7 | -7/+24 | |
2022-11-14 | Update online docs | Johannes Ranke | 36 | -1704/+1760 | |
2022-11-14 | Start benchmark vignette for saem fits | Johannes Ranke | 4 | -0/+2281 | |
2022-11-14 | Automatic starting parameters for saem.mmkin | Johannes Ranke | 14 | -1362/+1407 | |
For the case of mkin transformations. This gives faster convergence, and appears to avoid problems with numeric ODE solutions | |||||
2022-11-14 | Comment on an error | Johannes Ranke | 1 | -1/+1 | |
I will not correct the error in order to keep the benchmarks consistent | |||||
2022-11-11 | Simplify travis config | Johannes Ranke | 1 | -10/+1 | |
2022-11-08 | Same SFORB simplification for saem.mmkin fits | Johannes Ranke | 1 | -2/+2 | |
2022-11-08 | Show DFOP g equivalent of SFORB in summary, test | Johannes Ranke | 5 | -29/+36 | |
2022-11-08 | Simplify SFORB also in the endpoint function | Johannes Ranke | 3 | -33/+31 | |
2022-11-08 | Simplify SFORB analytical solution, whitespace | Johannes Ranke | 4 | -88/+88 | |
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. | |||||
2022-11-07 | Make print and summary for saem.mmkin more robust | Johannes Ranke | 2 | -8/+18 | |
If the likelihood computed by importance sampling, these methods failed. Now they report "Not available" or NA, respectively. | |||||
2022-11-04 | Further improvement of robustness of anova method | Johannes Ranke | 1 | -9/+9 | |
2022-11-04 | Fix anova.saem.mmkin for unavailable likelihoods | Johannes Ranke | 1 | -4/+10 | |
2022-11-04 | Attempt at automatic setting of random effects | Johannes Ranke | 7 | -30/+85 | |
Based on parameters in the separate fits that fail the t-test. | |||||
2022-11-04 | Make it easy to override maxsteps for lsoda | Johannes Ranke | 2 | -38/+44 | |
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). | |||||
2022-11-04 | Make illparms.mhmkin and anova.saem.mmkin more robust | Johannes Ranke | 3 | -12/+14 | |
2022-11-04 | Never fail with errors in saem.mmkin | Johannes Ranke | 3 | -18/+2 | |
I think it is always preferable to be able to investigate the saemix object returned. | |||||
2022-11-03 | Update for cgit... | Johannes Ranke | 1 | -1/+1 | |
2022-11-03 | Update docs | Johannes Ranke | 8 | -2/+337 | |
2022-11-01 | Add tex_listing() | Johannes Ranke | 5 | -1/+58 | |
2022-11-01 | Add read_spreadsheet | Johannes Ranke | 5 | -2/+171 | |
2022-11-01 | Update online docs | Johannes Ranke | 30 | -176/+275 | |
2022-11-01 | Fix plotting saem fits with covariates | Johannes Ranke | 7 | -58/+94 | |
2022-11-01 | Fix a bug, couldn't set class attribute on NULL | Johannes Ranke | 1 | -1/+1 | |
2022-11-01 | Fix illparms tests | Johannes Ranke | 5 | -51/+18 | |
2022-11-01 | Improved printing for illparms() | Johannes Ranke | 7 | -24/+80 | |
For the case of single fits and no ill-defined parameters found | |||||
2022-10-31 | Fix R CMD check | Johannes Ranke | 7 | -17/+32 | |
2022-10-31 | Possibility to override the error model in update.saem | Johannes Ranke | 2 | -11/+14 | |
2022-10-31 | Add anova.mhmkin method | Johannes Ranke | 2 | -0/+18 | |
2022-10-30 | Correct documentation of sorting in anova.saem.mmkin() | Johannes Ranke | 1 | -3/+4 | |
2022-10-30 | saem summary in case of non-invertible FIM parts | Johannes Ranke | 1 | -7/+13 | |
2022-10-29 | Another attempt to make the test robust | Johannes Ranke | 4 | -20/+44 | |
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. | |||||
2022-10-29 | Make test independent of saemix error model parameter patch | Johannes Ranke | 2 | -4/+3 | |
As mentioned in d44c17da6d62568b | |||||
2022-10-29 | Next version will be 1.2.0, complete NEWS | Johannes Ranke | 2 | -8/+8 | |
2022-10-29 | Merge branch 'update_online_docs_v1.1.1' | Johannes Ranke | 1 | -56/+62 | |
2022-10-29 | Rebuild vignette with rbenchmark installed | Johannes Ranke | 1 | -56/+62 | |
2022-10-29 | Update multistart docs | Johannes Ranke | 21 | -31/+382 | |
2022-10-28 | Rename parhist to parplot and make it generic | Johannes Ranke | 16 | -51/+63 | |
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 | 5 | -59/+70 | |
2022-10-28 | Update test to renamed method | Johannes Ranke | 2 | -14/+14 | |