aboutsummaryrefslogtreecommitdiff
AgeCommit message (Collapse)AuthorFilesLines
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in an attempt to circumvent outdated apt repositories for r-api-35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
2020-04-17News entry, static documentation rebuilt by pkgdownJohannes Ranke2-0/+3
2020-04-17Add AIC, BIC and log likelihood to summary.mkinfitJohannes Ranke4-0/+22
2020-04-16Test the new endpoint function on nlme.mmkinJohannes Ranke1-0/+3
2020-04-16Increase test coverageJohannes Ranke3-12/+37
2020-04-16mean_degparms: Fix rownames in random effectsJohannes Ranke1-1/+1
2020-04-15Adapt endpoint() to also work for nlme.mmkin objectsJohannes Ranke8-22/+101
2020-04-15Include random effects in starting parametersJohannes Ranke25-236/+420
- mean_degparms() now optionally returns starting values for fixed and random effects, which makes it possible to obtain acceptable fits also in more difficult cases (with more parameters) - Fix the anova method, as it is currently not enough to inherit from lme: https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17761 - Show fit information, and per default also errmin information in plot.nlme.mmkin() - Examples for nlme.mmkin: Decrease tolerance and increase the number of iterations in the PNLS step in order to be able to fit FOMC-SFO and DFOP-SFO
2020-04-15Show fit information even if show_errmin = FALSEJohannes Ranke1-4/+5
2020-04-15A plot method for nlme.mmkin fitsJohannes Ranke16-118/+800
2020-04-14Add a nlme method for mmkin row objectsJohannes Ranke6-23/+270
2020-04-14Keep order of datasets in nlme_data, add a plotJohannes Ranke5-6/+51
2020-04-10Address build config validation hintsJohannes Ranke1-2/+4
2020-04-10Improve nlme function docsJohannes Ranke15-75/+162
2020-04-10Trigger rebuild after deleting caches on travisJohannes Ranke1-1/+1
According to the hint of @jimhester received in the Travis Forum - thanks!
2020-04-09Add another visual test for coverageJohannes Ranke3-17/+151
2020-04-09Travis: Reduce another test toleranceJohannes Ranke1-1/+2
2020-04-09Tests on Travis: Residuals tolerance and skip another plotJohannes Ranke2-4/+4
2020-04-09Improve test coverage and fix nlme testJohannes Ranke7-21/+370
No idea why I had to do more assignments all of a sudden in test_nlme.R

Contact - Imprint