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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
2020-04-14Keep order of datasets in nlme_data, add a plotJohannes Ranke1-2/+9
2020-04-10Improve nlme function docsJohannes Ranke1-34/+33
2020-04-07Improve documentation of mmkin objectsJohannes Ranke1-2/+3
2020-04-04Add three functions to facilitate the use of nlmeJohannes Ranke3-175/+219
2020-04-03Merge branch 'master' into mxkinJohannes Ranke4-95/+105
Merge DESCRIPTION manually to combine dependencies and rerun check to update check.log
2020-04-03Compiled models article, reduce distractionsJohannes Ranke2-10/+16
- Added a section with platform specific notes on getting compiled models to work to the compiled models article - Don't return empty SFORB parameter list from endpoints() if there is no SFORB model - Avoid warnings when using standardized = TRUE in plot.mmkin()
2020-03-31Use inline documentation for R6 class mkindsJohannes Ranke1-24/+29
2020-03-31Static documentation rebuilt by pkgdownJohannes Ranke1-2/+4
2020-03-30Don't check for gcc on the path in mkinmodJohannes Ranke1-60/+57
Roxygen update -> formatting changes in Rd files
2020-03-30Fixed example codeJohannes Ranke1-3/+2
2020-03-30First nlme fits for models with a metaboliteJohannes Ranke1-40/+78
2020-03-29First automatic generation of an nlme modelJohannes Ranke2-58/+133
2020-03-27Merge branch 'master' into mxkinJohannes Ranke7-29/+214
2020-03-18Clarify comment in example codeJohannes Ranke1-1/+1
2020-02-14Delete trailing whitespaceJohannes Ranke1-11/+11
2019-12-16Argument ymax for plot.mmkinJohannes Ranke1-10/+16
2019-12-09Consistently use "two-component error model"Johannes Ranke1-1/+1
instead of "two component error model"
2019-11-13Improve formatting using markdownJohannes Ranke1-9/+7
2019-11-13Calculate Akaike weightsJohannes Ranke1-0/+60
2019-11-13Likelihood ratio test for mmkin columns with two fitsJohannes Ranke1-3/+2
2019-11-12lrtest method for mmkin columns with two fitsJohannes Ranke1-0/+9
2019-11-09Add a lack-of-fit testJohannes Ranke2-5/+118
- Switch an example dataset in the test setup to a dataset with replicates, adapt tests - Skip the test for lrtest with an update specification as it does not only fail when pkgdown generates static help pages, but also in testthat
2019-11-06Attempt of an overall model for an mmkin rowJohannes Ranke1-0/+58
2019-11-05Fix standardized residual plots in 'plot_res'Johannes Ranke1-3/+5

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