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2020-07-15Improve handling of (partially) failing fitsJohannes Ranke2-22/+29
2020-07-15Use try() within mmkinJohannes Ranke1-1/+1
This keeps mmkin from stopping if one of the fits fails. Instead, a try-error is assigned to the respective position in the mmkin object.
2020-06-15Fix a bug, update for current vdiffrJohannes Ranke2-83/+1
Vignette FOCUS_L failed as I had introduced a bug in the handling of warnings. Current vdiffr only runs visual tests if R < 4.1.0, skipping r-devel for now, see https://github.com/r-lib/vdiffr/commit/630a29d013361fd63fea242f531e2db6aef37919
2020-05-29Improve handling of warnings, reorganize testsJohannes Ranke3-14/+111
2020-05-29Warn if standardized residuals are unlikely normalJohannes Ranke2-46/+59
This revealed a bug in the data returned in mkinfit$data in the case of the d_3 algorithm, which also affected the residual plot - the data from the direct fitting was not returned even if this was the better method.
2020-05-28use_of_ff = "max" for shorthand models like "SFO"Johannes Ranke1-1/+1
2020-05-27Improve mkinmod docsJohannes Ranke1-26/+39
2020-05-26Use all cores per default, confint toleranceJohannes Ranke5-50/+78
Also, use more intelligent starting values for the variance of the random effects for saemix. While this does not appear to speed up the convergence, it shows where this variance is greatly reduced by using mixed-effects models as opposed to the separate independent fits.
2020-05-25Tell travis where to find the required saemix versionJohannes Ranke1-6/+5
2020-05-25First working version of saemix helper functionsJohannes Ranke1-0/+118
saemix_data depends on a development version of saemix, see pull request saemixdevelopment/saemixextension#2
2020-05-18Add commentJohannes Ranke1-1/+2
2020-05-15Improve docsJohannes Ranke1-16/+14
2020-05-15Use markdown links in mkinfit documentationJohannes Ranke1-24/+24
2020-05-14Update version number, better example formattingJohannes Ranke1-13/+15
2020-05-14Add a parms method for mmkin objectsJohannes Ranke1-2/+32
2020-05-14Test markdown link, article update due to .rmd extensionJohannes Ranke1-1/+1
2020-05-12Another documentation updateJohannes Ranke1-9/+8
2020-05-12Update vignettes and docsJohannes Ranke1-1/+0
2020-05-12Improve documentation, now using a spell checkerJohannes Ranke6-6/+6
2020-05-12Documentation improvements, rebuild static docsJohannes Ranke2-4/+13
2020-05-11Add analytical solution for DFOP-SFOJohannes Ranke1-1/+23
This is about twice as fast as deSolve compiled in the case of FOCUS D
2020-05-11Analytical solutions for all SFO variantsJohannes Ranke2-15/+48
2020-05-11Reduce precision of traced parameters, formattingJohannes Ranke1-2/+2
2020-05-11Avoid merge() and data.frame() in cost functionJohannes Ranke5-28/+32
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 Ranke2-3/+4
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 Ranke6-72/+83
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 Ranke1-10/+3
As we set the tolerance for ode() appropriately
2020-05-08Avoid duplicate merge in tc error model fitJohannes Ranke1-10/+7
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 Ranke1-2/+2
2020-05-08Analytical SFO_SFO about as fast as deSolve compiledJohannes Ranke2-19/+52
2020-05-07Another overhaul of analytical solutionsJohannes Ranke7-116/+74
Still in preparation for analytical solutions of coupled models
2020-05-07Merge parent solutions to one fileJohannes Ranke2-2/+9
- 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 Ranke7-186/+231
2020-05-06Change implementation of analytical solutionsJohannes Ranke3-94/+104
Preparing for symbolic solutions for more than one compound
2020-05-06Formatting, README update, color palette of R 4.xJohannes Ranke1-32/+32
2020-05-06Remove redundant commentsJohannes Ranke1-7/+0
2020-04-22Support SFORB with formation fractionsJohannes Ranke2-33/+22
2020-04-22Remove GPL header from test filesJohannes Ranke1-3/+3
2020-04-18Fix NOTE, prepare for releasev0.9.49.10Johannes Ranke1-1/+1
2020-04-18Avoid assignment to .GlobalEnv for CRANJohannes Ranke2-15/+32
2020-04-17Fix summarizing old objectsJohannes Ranke1-6/+12
2020-04-17Add AIC, BIC and log likelihood to summary.mkinfitJohannes Ranke1-0/+7
2020-04-16mean_degparms: Fix rownames in random effectsJohannes Ranke1-1/+1
2020-04-15Adapt endpoint() to also work for nlme.mmkin objectsJohannes Ranke2-8/+36
2020-04-15Include random effects in starting parametersJohannes Ranke3-79/+131
- 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 Ranke2-4/+108
2020-04-14Add a nlme method for mmkin row objectsJohannes Ranke2-10/+92

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