Changelog

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mkin 1.2.6

‘inst/rmarkdown/templates/hierarchical_kinetics/skeleton/skeleton.Rmd’: Fix an erroneous call to the ‘endpoints()’ function

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mkin 1.2.5 (2023-08-09)

‘vignettes/mesotrione_parent_2023.rnw’: Prebuilt vignette showing how covariate modelling can be done for all relevant parent degradation models.
‘inst/testdata/mesotrione_soil_efsa_2016}.xlsx’: Another example spreadsheets for use with ‘read_spreadsheet()’, featuring pH dependent degradation
R/illparms.R: Fix the detection of ill-defined slope or error model parameters for the case that the estimate is negative

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mkin 1.2.4 (2023-05-19)

R/endpoints.R: Fix the calculation of endpoints for user specified covariate values

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mkin 1.2.3.1 (unreleased)

Small fixes to get the online docs right (example code in R/hierarchical_kinetics, cluster setup in cyantraniliprole and dmta pathway vignettes, graphics and model comparison in multistart vignette), rebuild online docs

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mkin 1.2.3 (2023-04-17)

‘R/{endpoints,parms,plot.mixed.mmkin,summary.saem.mmkin}.R’: Calculate parameters and endpoints and plot population curves for specific covariate values, or specific percentiles of covariate values used in saem fits.
Depend on current deSolve version with the possibility to avoid resolving symbols in a shared library (compiled models) over and over, thanks to Thomas Petzoldt.
‘inst/rmarkdown/templates/hierarchical_kinetics/skeleton/skeleton.Rmd’: Start a new cluster after creating a model stored in the user specified location, because otherwise symbols are not found by the worker processes.
‘R/mkinerrmin.R’: Fix typo in subset (use of = instead of ==), thanks to Sebastian Meyer for spotting this during his work on R 4.3.0.

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mkin 1.2.2 (unreleased)

‘inst/rmarkdown/templates/hierarchical_kinetics’: R markdown template to facilitate the application of hierarchical kinetic models.
‘inst/testdata/{cyantraniliprole_soil_efsa_2014,lambda-cyhalothrin_soil_efsa_2014}.xlsx’: Example spreadsheets for use with ‘read_spreadsheet()’.
‘R/mhmkin.R’: Allow an ‘illparms.mhmkin’ object or a list with suitable dimensions as value of the argument ‘no_random_effects’, making it possible to exclude random effects that were ill-defined in simpler variants of the set of degradation models. Remove the possibility to exclude random effects based on separate fits, as it did not work well.
‘R/intervals.R’: Include correlations of random effects in the model in case there are any.

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mkin 1.2.1 (2022-11-19)

‘{data,R}/ds_mixed.rda’: Include the test data in the package instead of generating it in ‘tests/testthat/setup_script.R’. Refactor the generating code to make it consistent and update tests.
‘tests/testthat/setup_script.R’: Excluded another ill-defined random effect for the DFOP fit with ‘saem’, in an attempt to avoid a platform dependence that surfaced on Fedora systems on the CRAN check farm
‘tests/testthat/test_mixed.R’: Round parameters found by saemix to two significant digits before printing, to also help to avoid platform dependence of tests
‘R/loglik.mkinfit.R’: Add ‘nobs’ attribute to the resulting ‘logLik’ object, in order to make test_AIC.R succeed on current R-devel

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mkin 1.2.0 (2022-11-17)

‘R/saem.R’: ‘logLik’, ‘update’ and ‘anova’ methods for ‘saem.mmkin’ objects.
‘R/saem.R’: Automatic estimation of start parameters for random effects for the case of mkin transformations, nicely improving convergence and reducing problems with iterative ODE solutions.
‘R/status.R’: New generic to show status information for fit array objects with methods for ‘mmkin’, ‘mhmkin’ and ‘multistart’ objects.
‘R/tex_listings.R’: Conveniently include summaries of fit objects in R markdown documents that are compiled to LaTeX.

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mkin 1.1.1 (2022-07-12)

’R/{mkinmod,mkinpredict}.R: Store DLL information in mkinmod objects and use that information in mkinpredict to avoid a performance regression brought by a bugfix in R 4.2.x. Thanks to Tomas Kalibera for his analysis of the problem on the r-package-devel list and his suggestion on how to fix it.
‘vignettes/FOCUS_L.rmd’: Remove an outdated note referring to a failure to calculate the covariance matrix for DFOP with the L2 dataset. Since 0.9.45.5 the covariance matrix is available
‘vignettes/web_only/benchmarks.rmd’: Add the first benchmark data using my laptop system, therefore add the CPU when showing the benchmark results.
‘plot.mkinfit’: Respect argument ‘maxabs’ for residual plots, and make it possible to give ylim as a list, for row layouts

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mkin 1.1.0 (2022-03-14)

Mixed-effects models

Reintroduce the interface to saemix version 3.0 (now on CRAN), in particular the generic function ‘saem’ with a generator ‘saem.mmkin’, currently using ‘saemix_model’ and ‘saemix_data’, summary and plot methods

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mkin 1.0.5 (2021-09-15)

‘dimethenamid_2018’: Correct the data for the Borstel soil. The five observations from Staudenmaier (2013) that were previously stored as “Borstel 2” are actually just a subset of the 16 observations in “Borstel 1” which is now simply “Borstel”

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mkin 1.0.4 (2021-04-20)

All plotting functions setting graphical parameters: Use on.exit() for resetting graphical parameters
‘plot.mkinfit’: Use xlab and xlim for the residual plot if show_residuals is TRUE
‘mmkin’: Use cores = 1 per default on Windows to make it easier for first time users

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mkin 1.0.3 (2021-02-15)

Review and update README, the ‘Introduction to mkin’ vignette and some of the help pages

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mkin 1.0.2 (Unreleased)

‘mkinfit’: Keep model names stored in ‘mkinmod’ objects, avoiding their loss in ‘gmkin’

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mkin 1.0.1 (2021-02-10)

‘confint.mmkin’, ‘nlme.mmkin’, ‘transform_odeparms’: Fix example code in dontrun sections that failed with current defaults
‘logLik.mkinfit’: Improve example code to avoid warnings and show convenient syntax
‘mkinresplot’: Re-add Katrin Lindenberger as coauthor who was accidentally removed long ago
Increase test tolerance for some parameter comparisons that also proved to be platform dependent

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mkin 1.0.0 (2021-02-03)

General

‘mkinmod’ models gain arguments ‘name’ and ‘dll_dir’ which, in conjunction with a current version of the ‘inline’ package, make it possible to still use the DLL used for fast ODE solutions with ‘deSolve’ after saving and restoring the ‘mkinmod’ object.

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mkin 0.9.50.3 (2020-10-08)

‘parms’: Add a method for mmkin objects
‘mmkin’ and ‘confint(method = ’profile’): Use all cores detected by parallel::detectCores() per default
‘confint(method = ’profile’): Choose accuracy based on ‘rel_tol’ argument, relative to the bounds obtained by the quadratic approximation
‘endpoints’: Back-calculate DT50 value from DT90 also for the biphasic models DFOP, HS and SFORB

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mkin 0.9.50.2 (2020-05-12)

Increase tolerance for a platform specific test results on the Solaris test machine on CRAN
Updates and corrections (using the spelling package) to the documentation

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mkin 0.9.50.1 (2020-05-11)

Support SFORB with formation fractions
‘mkinmod’: Make ‘use_of_ff’ = “max” the default
Improve performance by a) avoiding expensive calls in the cost function like merge() and data.frame(), and b) by implementing analytical solutions for SFO-SFO and DFOP-SFO

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mkin 0.9.49.11 (2020-04-20)

Increase a test tolerance to make it pass on all CRAN check machines

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mkin 0.9.49.10 (2020-04-18)

‘nlme.mmkin’: An nlme method for mmkin row objects and an associated S3 class with print, plot, anova and endpoint methods
‘mean_degparms, nlme_data, nlme_function’: Three new functions to facilitate building nlme models from mmkin row objects
‘endpoints’: Don’t return the SFORB list component if it’s empty. This reduces distraction and complies with the documentation
‘summary.mkinfit’: Add AIC, BIC and log likelihood to the summary

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mkin 0.9.49.9 (2020-03-31)

‘mkinmod’: Use pkgbuild::has_compiler instead of Sys.which(‘gcc’), as the latter will often fail even if Rtools are installed
‘mkinds’: Use roxygen for documenting fields and methods of this R6 class

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mkin 0.9.49.8 (2020-01-09)

‘aw’: Generic function for calculating Akaike weights, methods for mkinfit objects and mmkin columns
‘loftest’: Add a lack-of-fit test
‘plot_res’, ‘plot_sep’ and ‘mkinerrplot’: Add the possibility to show standardized residuals and make it the default for fits with error models other than ‘const’
‘confint.mkinfit’: Make the quadratic approximation the default, as the likelihood profiling takes a lot of time, especially if the fit has more than three parameters

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mkin 0.9.49.7 (2019-11-01)

Fix a bug introduced in 0.9.49.6 that occurred if the direct optimisation yielded a higher likelihood than the three-step optimisation in the d_3 algorithm, which caused the fitted parameters of the three-step optimisation to be returned instead of the parameters of the direct optimisation
Add a ‘nobs’ method for mkinfit objects, enabling the default ‘BIC’ method from the stats package. Also, add a ‘BIC’ method for mmkin column objects.

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mkin 0.9.49.6 (2019-10-31)

Implement a likelihood ratio test as a method for ‘lrtest’ from the lmtest package
Add an ‘update’ method for mkinfit objects which remembers fitted parameters if appropriate
Add a ‘residuals’ method for mkinfit objects that supports scaling based on the error model
Support summarizing ‘mkinfit’ objects generated with versions < 0.9.49.5

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mkin 0.9.49.5 (2019-07-04)

Several algorithms for minimization of the negative log-likelihood for non-constant error models (two-component and variance by variable). In the case the error model is constant variance, least squares is used as this is more stable. The default algorithm ‘d_3’ tries direct minimization and a three-step procedure, and returns the model with the highest likelihood.
The argument ‘reweight.method’ to mkinfit and mmkin is now obsolete, use ‘error_model’ and ‘error_model_algorithm’ instead
Add a test that checks if we get the best known AIC for parent only fits to 12 test datasets. Add these test datasets for this purpose.
Add example datasets obtained from risk assessment reports published by the European Food Safety Agency.

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mkin 0.9.48.1 (2019-03-04)

Add the function ‘logLik.mkinfit’ which makes it possible to calculate an AIC for mkinfit objects
Add the function ‘AIC.mmkin’ to make it easy to compare columns of mmkin objects
‘add_err’: Respect the argument giving the number of replicates in the synthetic dataset
‘nafta’: Add evaluations according to the NAFTA guidance

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mkin 0.9.47.5 (2018-09-14)

Make the two-component error model stop in cases where it is inadequate to avoid nls crashes on windows
Move two vignettes to a location where they will not be built on CRAN (to avoid more NOTES from long execution times)
Exclude more example code from testing on CRAN to avoid NOTES from long execution times

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mkin 0.9.47.3

‘mkinfit’: Improve fitting the error model for reweight.method = ‘tc’. Add ‘manual’ to possible arguments for ‘weight’
Test that FOCUS_2006_C can be evaluated with DFOP and reweight.method = ‘tc’

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mkin 0.9.47.2 (2018-07-19)

‘sigma_twocomp’: Rename ‘sigma_rl’ to ‘sigma_twocomp’ as the Rocke and Lorenzato model assumes lognormal distribution for large y. Correct references to the Rocke and Lorenzato model accordingly.
‘mkinfit’: Use 1.1 as starting value for N parameter of IORE models to obtain convergence in more difficult cases. Show parameter names when ‘trace_parms’ is ‘TRUE’.

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mkin 0.9.47.1 (2018-02-06)

Skip some tests on CRAN and winbuilder to avoid timeouts
‘test_data_from_UBA_2014’: Added this list of datasets containing experimental data used in the expertise from 2014
‘mkinfit’: Added the iterative reweighting method ‘tc’ using the two-component error model from Rocke and Lorenzato. NA values in the data are not returned any more.
‘summary.mkinfit’: Show versions of mkin and R used for fitting (not the ones used for the summary) if the fit was generated with mkin >= 0.9.47.1

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mkin 0.9.46.3 (2017-11-16)

README.md, vignettes/mkin.Rmd: URLs were updated
synthetic_data_for_UBA: Add the code used to generate the data in the interest of reproducibility

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mkin 0.9.46.2 (2017-10-10)

Converted the vignette FOCUS_Z from tex/pdf to markdown/html
DESCRIPTION: Add ORCID

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mkin 0.9.46.1 (2017-09-14)

plot.mkinfit: Fix scaling of residual plots for the case of separate plots for each observed variable
plot.mkinfit: Use all data points of the fitted curve for y axis scaling for the case of separate plots for each observed variable
Documentation updates

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mkin 0.9.46 (2017-07-24)

Remove test_FOMC_ill-defined.R as it is too platform dependent

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mkin 0.9.45.2 (2017-07-24)

Rename twa to max_twa_parent to avoid conflict with twa from my pfm package
Update URLs in documentation
Limit test code to one core to pass on windows
Switch from microbenchmark to rbenchmark as the former is not supported on all platforms

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mkin 0.9.45.1 (2016-12-20)

New features

A twa function, calculating maximum time weighted average concentrations for the parent (SFO, FOMC and DFOP).

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mkin 0.9.45 (2016-12-08)

Minor changes

plot.mkinfit and plot.mmkin: If the plotting device is tikz, LaTeX markup is being used for the chi2 error in the graphs.

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mkin 0.9.44 (2016-06-29)

Bug fixes

The test test_FOMC_ill-defined failed on several architectures, so the test is now skipped

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mkin 0.9.43 (2016-06-28)

Major changes

The title was changed to Kinetic evaluations of chemical degradation data

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mkin 0.9.42 (2016-03-25)

Major changes

Add the argument from_max_mean to mkinfit, for fitting only the decline from the maximum observed value for models with a single observed variable

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mkin 0.9-41 (2015-11-09)

Minor changes

Add an R6 class mkinds representing datasets with a printing method

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mkin 0.9-40 (2015-07-21)

Bug fixes

@@ -480,7 +445,7 @@

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mkin 0.9-39 (2015-06-26)

Major changes

New function mmkin(): This function takes a character vector of model shorthand names, or alternatively a list of mkinmod models, as well as a list of dataset as main arguments. It returns a matrix of mkinfit objects, with a row for each model and a column for each dataset. A subsetting method with single brackets is available. Fitting the models in parallel using the parallel package is supported.

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mkin 0.9-38 (2015-06-24)

Minor changes

vignettes/compiled_models.html: Show the performance improvement factor actually obtained when building the vignette, as well as mkin version, some system info and the CPU model used for building the vignette.

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mkin 0.9-36 (2015-06-21)

Major changes

summary.mkinfit(): A one-sided t-test for significant difference of untransformed parameters from zero is now always shown, based on the assumption of normal distribution for estimators of all untransformed parameters. Use with caution, as this assumption is unrealistic e.g. for rate constants in these nonlinear kinetic models.

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mkin 0.9-35 (2015-05-15)

Major changes

Switch from RUnit to testthat for testing

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mkin 0.9-34 (2014-11-22)

New features

Add the convenience function mkinsub() for creating the lists used in mkinmod()

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mkin 0.9-33 (2014-10-22)

New features

The initial value (state.ini) for the observed variable with the highest observed residue is set to 100 in case it has no time zero observation and state.ini = "auto"

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mkin 0.9-32 (2014-07-24)

New features

The number of degrees of freedom is difficult to define in the case of ilr transformation of formation fractions. Now for each source compartment the number of ilr parameters (=number of optimised parameters) is divided by the number of pathways to metabolites (=number of affected data series) which leads to fractional degrees of freedom in some cases.

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mkin 0.9-31 (2014-07-14)

Bug fixes

The internal renaming of optimised parameters in Version 0.9-30 led to errors in the determination of the degrees of freedom for the chi2 error level calulations in mkinerrmin() used by the summary function.

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mkin 0.9-30 (2014-07-11)

New features

It is now possible to use formation fractions in combination with turning off the sink in mkinmod().

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mkin 0.9-29 (2014-06-27)

R/mkinresplot.R: Make it possible to specify xlim
R/geometric_mean.R, man/geometric_mean.Rd: Add geometric mean function
R/endpoints.R, man/endpoints.Rd: Calculate additional (pseudo)-DT50 values for FOMC, DFOP, HS and SFORB. Avoid calculation of formation fractions from rate constants when they are directly fitted

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mkin 0.9-28 (2014-05-20)

Do not backtransform confidence intervals for formation fractions if more than one compound is formed, as such parameters only define the pathways as a set
Add historical remarks and some background to the main package vignette
Correct ‘isotropic’ into ‘isometric’ for the ilr transformation

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mkin 0.9-27 (2014-05-10)

Fork the GUI into a separate package gmkin
DESCRIPTION, NAMESPACE, TODO: Adapt and add copyright information
Remove files belonging to the GUI
Add gmkin workspace datasets FOCUS_2006_gmkin and FOCUS_2006_Z_gmkin

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mkin 0.9-24 (2013-11-06)

Bugfix re-enabling the fixing of any combination of initial values for state variables
Default values for kinetic rate constants are not all 0.1 any more but are “salted” with a small increment to avoid numeric artefacts with the eigenvalue based solutions
Backtransform fixed ODE parameters for the summary

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mkin 0.9-22 (2013-10-26)

Get rid of the optimisation step in mkinerrmin - this was unnecessary. Thanks to KinGUII for the inspiration - actually this is equation 6-2 in FOCUS kinetics p. 91 that I had overlooked originally
Fix plot.mkinfit as it passed graphical arguments like main to the solver
Do not use plot=TRUE in mkinfit() example
Do not use 0 values at time zero for chi2 error level calculations. This is the way it is done in KinGUII and it makes sense. It does impact the chi2 error levels in the output. Generally they seem to be lower for metabolites now, presumably because the mean of the observed values is higher

For a detailed list of changes to the mkin source please consult the commit history on http://github.com/jranke/mkin

Example evaluations with (generalised) nonlinear least squares

Example evaluations with hierarchical models (nonlinear mixed-effects models)

Performance

Miscellaneous

Changelog

mkin 1.2.6

mkin 1.2.6

mkin 1.2.5 (2023-08-09)

mkin 1.2.5 (2023-08-09)

mkin 1.2.4 (2023-05-19)

mkin 1.2.4 (2023-05-19)

mkin 1.2.3.1 (unreleased)

mkin 1.2.3.1 (unreleased)

mkin 1.2.3 (2023-04-17)

mkin 1.2.3 (2023-04-17)

mkin 1.2.2 (unreleased)

mkin 1.2.2 (unreleased)

mkin 1.2.1 (2022-11-19)

mkin 1.2.1 (2022-11-19)

mkin 1.2.0 (2022-11-17)

mkin 1.2.0 (2022-11-17)

mkin 1.1.1 (2022-07-12)

mkin 1.1.1 (2022-07-12)

mkin 1.1.0 (2022-03-14)

mkin 1.1.0 (2022-03-14)

Mixed-effects models

mkin 1.0.5 (2021-09-15)

mkin 1.0.5 (2021-09-15)

mkin 1.0.4 (2021-04-20)

mkin 1.0.4 (2021-04-20)

mkin 1.0.3 (2021-02-15)

mkin 1.0.3 (2021-02-15)

mkin 1.0.2 (Unreleased)

mkin 1.0.2 (Unreleased)

mkin 1.0.1 (2021-02-10)

mkin 1.0.1 (2021-02-10)

mkin 1.0.0 (2021-02-03)

mkin 1.0.0 (2021-02-03)

General

mkin 0.9.50.3 (2020-10-08)

mkin 0.9.50.3 (2020-10-08)

mkin 0.9.50.2 (2020-05-12)

mkin 0.9.50.2 (2020-05-12)

mkin 0.9.50.1 (2020-05-11)

mkin 0.9.50.1 (2020-05-11)

mkin 0.9.49.11 (2020-04-20)

mkin 0.9.49.11 (2020-04-20)

mkin 0.9.49.10 (2020-04-18)

mkin 0.9.49.10 (2020-04-18)

mkin 0.9.49.9 (2020-03-31)

mkin 0.9.49.9 (2020-03-31)

mkin 0.9.49.8 (2020-01-09)

mkin 0.9.49.8 (2020-01-09)

mkin 0.9.49.7 (2019-11-01)

mkin 0.9.49.7 (2019-11-01)

mkin 0.9.49.6 (2019-10-31)

mkin 0.9.49.6 (2019-10-31)

mkin 0.9.49.5 (2019-07-04)

mkin 0.9.49.5 (2019-07-04)

mkin 0.9.48.1 (2019-03-04)

mkin 0.9.48.1 (2019-03-04)

mkin 0.9.47.5 (2018-09-14)

mkin 0.9.47.5 (2018-09-14)

mkin 0.9.47.3

mkin 0.9.47.3

mkin 0.9.47.2 (2018-07-19)

mkin 0.9.47.2 (2018-07-19)

mkin 0.9.47.1 (2018-02-06)

mkin 0.9.47.1 (2018-02-06)

mkin 0.9.46.3 (2017-11-16)

mkin 0.9.46.3 (2017-11-16)

mkin 0.9.46.2 (2017-10-10)

mkin 0.9.46.2 (2017-10-10)

mkin 0.9.46.1 (2017-09-14)

mkin 0.9.46.1 (2017-09-14)

mkin 0.9.46 (2017-07-24)

mkin 0.9.46 (2017-07-24)

mkin 0.9.45.2 (2017-07-24)

mkin 0.9.45.2 (2017-07-24)