Age | Commit message (Collapse) | Author | Files | Lines | |
---|---|---|---|---|---|
2020-05-25 | Tell travis where to really find the saemix version... | Johannes Ranke | 1 | -1/+1 | |
2020-05-25 | Tell travis where to find the required saemix version | Johannes Ranke | 5 | -14/+14 | |
2020-05-25 | First working version of saemix helper functions | Johannes Ranke | 20 | -26/+694 | |
saemix_data depends on a development version of saemix, see pull request saemixdevelopment/saemixextension#2 | |||||
2020-05-18 | Add comment | Johannes Ranke | 1 | -1/+2 | |
2020-05-15 | Improve docs | Johannes Ranke | 2 | -23/+15 | |
2020-05-15 | Use markdown links in mkinfit documentation | Johannes Ranke | 4 | -95/+97 | |
2020-05-14 | Update version number, better example formatting | Johannes Ranke | 11 | -38/+35 | |
2020-05-14 | Add a parms method for mmkin objects | Johannes Ranke | 7 | -8/+143 | |
2020-05-14 | Test markdown link, article update due to .rmd extension | Johannes Ranke | 15 | -79/+98 | |
2020-05-13 | Further formatting improvement of benchmark vignette | Johannes Ranke | 13 | -672/+631 | |
Also, use .rmd extension instead of .Rmd for vignettes. | |||||
2020-05-12 | Another documentation update | Johannes Ranke | 4 | -43/+39 | |
2020-05-12 | Update pkgdown | Johannes Ranke | 3 | -31/+166 | |
2020-05-12 | Improve formatting of benchmark vignette | Johannes Ranke | 3 | -39/+182 | |
2020-05-12 | Add a link to the benchmark vignette to the docs | Johannes Ranke | 8 | -1/+21 | |
2020-05-12 | Update vignettes and docs | Johannes Ranke | 100 | -1662/+1767 | |
2020-05-12 | Update .Rbuildignorev0.9.50.2 | Johannes Ranke | 2 | -2/+1 | |
2020-05-12 | Rerun tests and checks, CRAN comments | Johannes Ranke | 6 | -15/+13 | |
2020-05-12 | Improve documentation, now using a spell checker | Johannes Ranke | 36 | -148/+370 | |
2020-05-12 | Address solaris platform dependence revealed on CRAN | Johannes Ranke | 1 | -1/+2 | |
2020-05-12 | Documentation improvements, rebuild static docs | Johannes Ranke | 86 | -1102/+1165 | |
2020-05-11 | Release to CRANv0.9.50.1 | Johannes Ranke | 4 | -4/+8 | |
2020-05-11 | Merge branch 'master' of kolab.jrwb.de:mkin | Johannes Ranke | 0 | -0/+0 | |
2020-05-11 | Add analytical solution for DFOP-SFO | Johannes Ranke | 17 | -30/+88 | |
This is about twice as fast as deSolve compiled in the case of FOCUS D | |||||
2020-05-11 | Add analytical solution for DFOP-SFO | Johannes Ranke | 6 | -11/+65 | |
This is about twice as fast as deSolve compiled with FOCUS D | |||||
2020-05-11 | Analytical solutions for all SFO variants | Johannes Ranke | 8 | -73/+128 | |
2020-05-11 | Don't run visual tests on r-devel for now | Johannes Ranke | 4 | -16/+29 | |
https://github.com/r-lib/vdiffr/issues/86 | |||||
2020-05-11 | Reduce precision of traced parameters, formatting | Johannes Ranke | 2 | -123/+123 | |
2020-05-11 | Avoid merge() and data.frame() in cost function | Johannes Ranke | 36 | -715/+799 | |
also for deSolve and eigenvalue based solutions. This noticeably increases performance for these methods, see test.log and benchmark vignette. | |||||
2020-05-10 | Default to analytical for coupled models if available | Johannes Ranke | 8 | -157/+150 | |
This revealed that transforming rates is necessary for fitting the analytical solution of the SFO-SFO model to the FOCUS D dataset. Benchmarks show that fitting coupled models with deSolve got a bit slower through the latest changes | |||||
2020-05-09 | Avoid the call to merge for analytical solutions | Johannes Ranke | 14 | -112/+135 | |
This increases performance up to a factor of five! | |||||
2020-05-09 | Make mkinpredict consistently return a dataframe | Johannes Ranke | 1 | -16/+16 | |
2020-05-08 | Profiling suggests the merge in mkinfit is the bottleneck | Johannes Ranke | 1 | -0/+3 | |
2020-05-08 | We do not need the n.outtimes argument for mkinfit | Johannes Ranke | 2 | -19/+12 | |
As we set the tolerance for ode() appropriately | |||||
2020-05-08 | Avoid duplicate merge in tc error model fit | Johannes Ranke | 2 | -21/+18 | |
This increases the performance in the complete test suite by about 20 secs from 120 to around 100 secs. I tried improving merge speed by using data.table on another branch, but this did not give a noticeable performance gain. | |||||
2020-05-08 | Slight performance gain by reducing default n.outtimes | Johannes Ranke | 3 | -18/+18 | |
2020-05-08 | Roxygenize, adapt tests | Johannes Ranke | 9 | -114/+128 | |
2020-05-08 | Analytical SFO_SFO about as fast as deSolve compiled | Johannes Ranke | 2 | -19/+52 | |
2020-05-07 | Don't use binary version of covr | Johannes Ranke | 1 | -2/+0 | |
in an attempt to circumvent outdated apt repositories for r-api-35 | |||||
2020-05-07 | Another overhaul of analytical solutions | Johannes Ranke | 45 | -390/+626 | |
Still in preparation for analytical solutions of coupled models | |||||
2020-05-07 | Merge parent solutions to one file | Johannes Ranke | 10 | -9/+62 | |
- Combine R/*.solution.R into R/parent_solutions.R - Create a roxygen family of related functions - Reduce redundancy by using the inherit tag - Change the parent.0 argument to parent_0 to match the corresponding parameter name used in mkinfit | |||||
2020-05-07 | Static documentation rebuilt by pkgdown | Johannes Ranke | 40 | -1032/+1531 | |
2020-05-06 | Change implementation of analytical solutions | Johannes Ranke | 12 | -226/+248 | |
Preparing for symbolic solutions for more than one compound | |||||
2020-05-06 | Formatting, README update, color palette of R 4.x | Johannes Ranke | 7 | -347/+347 | |
2020-05-06 | Remove redundant comments | Johannes Ranke | 1 | -7/+0 | |
2020-04-22 | Support SFORB with formation fractions | Johannes Ranke | 9 | -51/+59 | |
2020-04-22 | Remove GPL header from test files | Johannes Ranke | 19 | -329/+3 | |
2020-04-20 | Updated build and check logsv0.9.49.11 | Johannes Ranke | 2 | -2/+2 | |
2020-04-20 | Prepare release to address failed CRAN check | Johannes Ranke | 10 | -37/+42 | |
2020-04-20 | Increase test tolerance for residuals | Johannes Ranke | 4 | -7/+9 | |
This was done to address the test failure on r-devel-linux-x86_64-debian-gcc on CRAN | |||||
2020-04-18 | Fix NOTE, prepare for releasev0.9.49.10 | Johannes Ranke | 5 | -27/+8 | |