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2020-05-18Add commentJohannes Ranke1-1/+2
2020-05-15Improve docsJohannes Ranke2-23/+15
2020-05-15Use markdown links in mkinfit documentationJohannes Ranke4-95/+97
2020-05-14Update version number, better example formattingJohannes Ranke11-38/+35
2020-05-14Add a parms method for mmkin objectsJohannes Ranke7-8/+143
2020-05-14Test markdown link, article update due to .rmd extensionJohannes Ranke15-79/+98
2020-05-13Further formatting improvement of benchmark vignetteJohannes Ranke13-672/+631
Also, use .rmd extension instead of .Rmd for vignettes.
2020-05-12Another documentation updateJohannes Ranke4-43/+39
2020-05-12Update pkgdownJohannes Ranke3-31/+166
2020-05-12Improve formatting of benchmark vignetteJohannes Ranke3-39/+182
2020-05-12Add a link to the benchmark vignette to the docsJohannes Ranke8-1/+21
2020-05-12Update vignettes and docsJohannes Ranke100-1662/+1767
2020-05-12Update .Rbuildignorev0.9.50.2Johannes Ranke2-2/+1
2020-05-12Rerun tests and checks, CRAN commentsJohannes Ranke6-15/+13
2020-05-12Improve documentation, now using a spell checkerJohannes Ranke36-148/+370
2020-05-12Address solaris platform dependence revealed on CRANJohannes Ranke1-1/+2
2020-05-12Documentation improvements, rebuild static docsJohannes Ranke86-1102/+1165
2020-05-11Release to CRANv0.9.50.1Johannes Ranke4-4/+8
2020-05-11Merge branch 'master' of kolab.jrwb.de:mkinJohannes Ranke0-0/+0
2020-05-11Add analytical solution for DFOP-SFOJohannes Ranke17-30/+88
This is about twice as fast as deSolve compiled in the case of FOCUS D
2020-05-11Add analytical solution for DFOP-SFOJohannes Ranke6-11/+65
This is about twice as fast as deSolve compiled with FOCUS D
2020-05-11Analytical solutions for all SFO variantsJohannes Ranke8-73/+128
2020-05-11Don't run visual tests on r-devel for nowJohannes Ranke4-16/+29
https://github.com/r-lib/vdiffr/issues/86
2020-05-11Reduce precision of traced parameters, formattingJohannes Ranke2-123/+123
2020-05-11Avoid merge() and data.frame() in cost functionJohannes Ranke36-715/+799
also for deSolve and eigenvalue based solutions. This noticeably increases performance for these methods, see test.log and benchmark vignette.
2020-05-10Default to analytical for coupled models if availableJohannes Ranke8-157/+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
2020-05-09Avoid the call to merge for analytical solutionsJohannes Ranke14-112/+135
This increases performance up to a factor of five!
2020-05-09Make mkinpredict consistently return a dataframeJohannes Ranke1-16/+16
2020-05-08Profiling suggests the merge in mkinfit is the bottleneckJohannes Ranke1-0/+3
2020-05-08We do not need the n.outtimes argument for mkinfitJohannes Ranke2-19/+12
As we set the tolerance for ode() appropriately
2020-05-08Avoid duplicate merge in tc error model fitJohannes Ranke2-21/+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.
2020-05-08Slight performance gain by reducing default n.outtimesJohannes Ranke3-18/+18
2020-05-08Roxygenize, adapt testsJohannes Ranke9-114/+128
2020-05-08Analytical SFO_SFO about as fast as deSolve compiledJohannes Ranke2-19/+52
2020-05-07Don't use binary version of covrJohannes Ranke1-2/+0
in an attempt to circumvent outdated apt repositories for r-api-35
2020-05-07Another overhaul of analytical solutionsJohannes Ranke45-390/+626
Still in preparation for analytical solutions of coupled models
2020-05-07Merge parent solutions to one fileJohannes Ranke10-9/+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
2020-05-07Static documentation rebuilt by pkgdownJohannes Ranke40-1032/+1531
2020-05-06Change implementation of analytical solutionsJohannes Ranke12-226/+248
Preparing for symbolic solutions for more than one compound
2020-05-06Formatting, README update, color palette of R 4.xJohannes Ranke7-347/+347
2020-05-06Remove redundant commentsJohannes Ranke1-7/+0
2020-04-22Support SFORB with formation fractionsJohannes Ranke9-51/+59
2020-04-22Remove GPL header from test filesJohannes Ranke19-329/+3
2020-04-20Updated build and check logsv0.9.49.11Johannes Ranke2-2/+2
2020-04-20Prepare release to address failed CRAN checkJohannes Ranke10-37/+42
2020-04-20Increase test tolerance for residualsJohannes Ranke4-7/+9
This was done to address the test failure on r-devel-linux-x86_64-debian-gcc on CRAN
2020-04-18Fix NOTE, prepare for releasev0.9.49.10Johannes Ranke5-27/+8
2020-04-18Avoid assignment to .GlobalEnv for CRANJohannes Ranke16-56/+271
2020-04-17Advertise nlme related functionalityJohannes Ranke2-0/+4
2020-04-17Fix summarizing old objectsJohannes Ranke3-14/+22

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