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2021-02-13Merge branch 'master' into saemixJohannes Ranke1-1/+5
Run make testcheck to regenerate logs with merge conflicts
2021-02-13Update for gmkin 0.6.12v1.0.2Johannes Ranke1-0/+4
mkinfit: Keep model names stored in mkinmod objects, avoiding their loss in gmkin
2021-02-06Reintroduce interface to saemixJohannes Ranke1-0/+10
Also after the upgrade from buster to bullseye of my local system, some test results for saemix have changed.
2021-02-06Increase test tolerance for parameter comparisonsv1.0.1Johannes Ranke1-0/+2
Platform dependence also revealed after upgrade to bullseye
2021-02-06Address issue revealed by additional tests on CRANJohannes Ranke1-0/+2
Remove tests relying on non-convergence of the FOMC fit to the FOCUS A dataset, as this is platform dependent. After the upgrade, the fit converges on this system as well, although neither ATLAS is used, nor R was configured disabling long doubles (these were the conditions under which the tests failed on CRAN).
2021-02-04Documentation improvements, mainly fixing example codeJohannes Ranke1-0/+8
The errors in the example code were in the \dontrun sections, so they were not caught by CRAN checks. In addition, the static help files generated with pkgdown were cached, so I noticed the errors only after completely regenerating the documentation for version 1.0.0.
2021-02-03Prepare for v1.0.0v1.0.0Johannes Ranke1-12/+3
- Improve authorship and copyright information - Prepare pkgdown config - Remove dependence on saemix as we need the development version which is not ready for CRAN - Temporarily remove saemix interface to check code coverage of the rest
2021-01-25Some more plotting improvementsJohannes Ranke1-2/+2
2021-01-25Change default ylab in plot.mkinfit, explicit ylab for plot.mmkinJohannes Ranke1-0/+5
See NEWS.md. Closes #12
2021-01-06Make saemix and corresponding tests optionalJohannes Ranke1-9/+17
Address release critical check and test issues
2020-12-08mixed.mmkin and test coverageJohannes Ranke1-0/+2
2020-12-07Updates after inline 0.3.17 has been releasedJohannes Ranke1-1/+1
2020-11-27Closes #11Johannes Ranke1-0/+2
2020-11-12mkindsg class to hold groups of datasetsJohannes Ranke1-0/+8
- D24_2014 dataset on aerobic soil degradation of 2,4-D from the EU assessment as mkindsg object with metadata - f_time_norm_focus() to do time-step normalisation using the FOCUS method - focus_soil_moisture data with default moisture contents at pF1, pF 2 and pF 2.5 for USDA soil types from FOCUS GW guidance - Dataset generation scripts in inst/dataset_generation - Depend on R >= 2.15.1 in order to facilitate the use of utils::globalVariables()
2020-11-09saemix.mmkin and nlme.mmkin inherit from mixed.mmkinJohannes Ranke1-1/+3
With a plot method. The class mixed.mmkin is currently only a virtual class created to unify the plotting method.
2020-11-08Improve saem method, add summaryJohannes Ranke1-0/+2
Also make the endpoints function work for saem objects.
2020-11-06Fast analytical solutions for saemix, update.mmkinJohannes Ranke1-0/+4
Also, use logit transformation for g and for solitary formation fractions, addressing #10.
2020-10-27Add summary method for nlme.mmkin objectsJohannes Ranke1-3/+1
Improve and update docs
2020-10-24Plot method for nlme.mmkin objectsJohannes Ranke1-0/+2
Update docs
2020-10-24Printing method for mmkin objectsJohannes Ranke1-0/+2
2020-10-15Reintroduce saemix helper functionsJohannes Ranke1-1/+5
2020-10-08Fix issues for releaseJohannes Ranke1-1/+1
2020-10-08Avoid dep on dev version of saemix for releaseJohannes Ranke1-3/+1
2020-09-01Back-calculated DT50 values for biphasic modelsJohannes Ranke1-0/+2
2020-07-17mkinfit: Ignore unused components of state.iniJohannes Ranke1-0/+2
2020-07-15Improve handling of (partially) failing fitsJohannes Ranke1-0/+4
2020-05-29Warn if standardized residuals are unlikely normalJohannes Ranke1-0/+2
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 Ranke1-0/+2
2020-05-26Use all cores per default, confint toleranceJohannes Ranke1-0/+4
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.
2020-05-25First working version of saemix helper functionsJohannes Ranke1-0/+2
saemix_data depends on a development version of saemix, see pull request saemixdevelopment/saemixextension#2
2020-05-14Add a parms method for mmkin objectsJohannes Ranke1-0/+4
2020-05-12Improve documentation, now using a spell checkerJohannes Ranke1-4/+10
2020-05-11Add analytical solution for DFOP-SFOJohannes Ranke1-0/+2
This is about twice as fast as deSolve compiled in the case of FOCUS D
2020-05-07Another overhaul of analytical solutionsJohannes Ranke1-0/+2
Still in preparation for analytical solutions of coupled models
2020-04-22Support SFORB with formation fractionsJohannes Ranke1-1/+5
2020-04-20Prepare release to address failed CRAN checkJohannes Ranke1-0/+2
2020-04-20Increase test tolerance for residualsJohannes Ranke1-0/+2
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 Ranke1-1/+1
2020-04-17News entry, static documentation rebuilt by pkgdownJohannes Ranke1-0/+2
2020-04-15Adapt endpoint() to also work for nlme.mmkin objectsJohannes Ranke1-1/+1
2020-04-15A plot method for nlme.mmkin fitsJohannes Ranke1-0/+2
2020-04-04Add three functions to facilitate the use of nlmeJohannes Ranke1-0/+2
2020-04-03Compiled models article, reduce distractionsJohannes Ranke1-1/+9
- 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()
2020-03-31Update NEWS, static documentation rebuilt by pkgdownv0.9.49.9Johannes Ranke1-1/+3
2020-03-30Static documentation rebuilt by pkgdownJohannes Ranke1-1/+5
2020-01-08Typos in NEWS, update static docsJohannes Ranke1-1/+1
2019-11-13Calculate Akaike weightsJohannes Ranke1-0/+2
2019-11-09Add a lack-of-fit testJohannes Ranke1-0/+2
- 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
2019-11-04Scaled residual plotsJohannes Ranke1-0/+2
2019-11-04Include fixed parameters in model names in lrtestJohannes Ranke1-1/+3

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