Age | Commit message (Collapse) | Author | Files | Lines | |
---|---|---|---|---|---|
2022-12-02 | Avoid redundant warnings in summaries | Johannes Ranke | 2 | -3/+4 | |
2022-12-02 | Avoid error message at testthat termination | Johannes Ranke | 2 | -26/+29 | |
https://github.com/r-lib/processx/issues/236 | |||||
2022-12-02 | Update online docs | Johannes Ranke | 7 | -14/+95 | |
2022-12-01 | Possibility to manually specify no_random_effects in mhmkin | Johannes Ranke | 9 | -94/+187 | |
2022-11-29 | Complete starting values in summary for saem.mmkin fits | Johannes Ranke | 9 | -45/+55 | |
Also update tests to the changes in mhmkin (see NEWS) | |||||
2022-11-25 | mhmkin: Easy specification of ill-defined parms | Johannes Ranke | 3 | -28/+28 | |
The argument 'no_random_effect' now accepts an illparms.mhmkin object | |||||
2022-11-24 | Start online docs of the development version | Johannes Ranke | 181 | -8344/+7033 | |
2022-11-22 | Update and improve README | Johannes Ranke | 2 | -31/+34 | |
2022-11-22 | Start new development version | Johannes Ranke | 5 | -19/+18 | |
2022-11-19 | Confirm which test fail on R-develv1.2.1 | Johannes Ranke | 3 | -37/+112 | |
2022-11-18 | Move two saem fits from setup script to skipped tests | Johannes Ranke | 6 | -34/+40 | |
Save winbuilder/CRAN check time... | |||||
2022-11-18 | Use cluster with two cores to reduce windows check time | Johannes Ranke | 6 | -28/+40 | |
2022-11-18 | Update docs | Johannes Ranke | 14 | -18/+279 | |
2022-11-18 | Make mixed model test data permanent to ensure reproducibility | Johannes Ranke | 24 | -262/+324 | |
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 | 5 | -17/+24 | |
This will hopefully make the test pass on all relevant platforms. | |||||
2022-11-18 | Prepare follow-up release to fix CRAN checks | Johannes Ranke | 1 | -2/+2 | |
2022-11-18 | Remove candidate patches that were accidentally committed | Johannes Ranke | 2 | -1703/+0 | |
2022-11-18 | Update NEWS | Johannes Ranke | 1 | -0/+10 | |
2022-11-18 | Pass error.init to saemix_model, show in parplot | Johannes Ranke | 9 | -29/+51 | |
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 | Avoid ill-determined fit, it is platform dependent | Johannes Ranke | 2 | -12/+11 | |
The previous test lead to an error on the Fedora test systems (gcc and clang) on CRAN: ... Results have changed from known value recorded in 'print_dfop_saemix_1.txt'. old[13:24] vs new[13:24] "" "Fitted parameters:" " estimate lower upper" - "parent_0 100.09 98.94 101.25" + "parent_0 100.17 99.01 101.33" - "log_k1 -2.68 -2.91 -2.45" + "log_k1 -2.66 -2.89 -2.43" "log_k2 -4.12 -4.24 -4.00" - "g_qlogis -0.41 -0.63 -0.20" + "g_qlogis -0.43 -0.65 -0.21" - "a.1 0.91 0.67 1.15" + "a.1 0.91 0.67 1.16" "b.1 0.05 0.04 0.06" - "SD.log_k1 0.36 0.21 0.50" + "SD.log_k1 0.35 0.21 0.50" and 2 more ... | |||||
2022-11-18 | Improve logLik.mkinfit to attach nobs attribute | Johannes Ranke | 2 | -29/+33 | |
The lack of that attribute lead to a failure to calculate the BIC in test_AIC.R on R-devel from yesterday. | |||||
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 | |