From d185c26e4909efbae9dc4210ed9eac4b2600910e Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Sun, 11 Mar 2018 22:12:51 +0100 Subject: Static docs rebuilt again, with current pkgdown --- .gitignore | 1 - GNUmakefile | 5 +- docs/NEWS.html | 610 +++++++++++++++++++++++++ docs/README.html | 200 ++++++++ docs/articles/FOCUS_D.html | 13 +- docs/articles/FOCUS_L.R | 86 ---- docs/articles/FOCUS_L.html | 49 +- docs/articles/FOCUS_Z.html | 7 +- docs/articles/compiled_models.html | 19 +- docs/articles/index.html | 2 + docs/articles/mkin.html | 7 +- docs/articles/twa.html | 7 +- docs/authors.html | 12 +- docs/index.html | 15 +- docs/news/index.html | 2 + docs/pkgdown.css | 15 + docs/pkgdown.yml | 20 + docs/reference/DFOP.solution.html | 6 + docs/reference/Extract.mmkin.html | 17 +- docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html | 9 + docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html | 9 + docs/reference/FOCUS_2006_HS_ref_A_to_F.html | 9 + docs/reference/FOCUS_2006_SFO_ref_A_to_F.html | 9 + docs/reference/FOCUS_2006_datasets.html | 5 + docs/reference/FOMC.solution.html | 9 + docs/reference/HS.solution.html | 6 + docs/reference/IORE.solution.html | 6 + docs/reference/SFO.solution.html | 5 + docs/reference/SFORB.solution.html | 9 + docs/reference/add_err.html | 7 + docs/reference/endpoints.html | 8 + docs/reference/geometric_mean.html | 5 + docs/reference/ilr.html | 5 + docs/reference/index.html | 2 + docs/reference/max_twa_parent.html | 9 + docs/reference/mccall81_245T.html | 13 +- docs/reference/mkin_long_to_wide.html | 7 + docs/reference/mkin_wide_to_long.html | 6 + docs/reference/mkinds.html | 5 + docs/reference/mkinerrmin.html | 6 + docs/reference/mkinfit.html | 23 +- docs/reference/mkinmod.html | 10 + docs/reference/mkinparplot.html | 6 + docs/reference/mkinplot.html | 5 + docs/reference/mkinpredict.html | 13 +- docs/reference/mkinresplot.html | 8 + docs/reference/mkinsub.html | 6 + docs/reference/mmkin.html | 6 + docs/reference/plot.mkinfit.html | 10 + docs/reference/plot.mmkin.html | 9 + docs/reference/print.mkinds.html | 5 + docs/reference/print.mkinmod.html | 5 + docs/reference/schaefer07_complex_case.html | 7 + docs/reference/sigma_rl.html | 7 + docs/reference/summary.mkinfit.html | 14 +- docs/reference/synthetic_data_for_UBA.html | 17 + docs/reference/test_data_from_UBA_2014.html | 6 + docs/reference/transform_odeparms.html | 19 +- 58 files changed, 1256 insertions(+), 162 deletions(-) create mode 100644 docs/NEWS.html create mode 100644 docs/README.html delete mode 100644 docs/articles/FOCUS_L.R create mode 100644 docs/pkgdown.yml diff --git a/.gitignore b/.gitignore index 0e341812..75005f00 100644 --- a/.gitignore +++ b/.gitignore @@ -1,5 +1,4 @@ docs/articles/*_cache/ -docs/articles/*.R install.log mkin*.tar.gz mkin.tar diff --git a/GNUmakefile b/GNUmakefile index 4955a3e2..d56eee90 100644 --- a/GNUmakefile +++ b/GNUmakefile @@ -59,6 +59,7 @@ quickcheck: build-no-vignettes clean: $(RM) -r vignettes/*_cache $(RM) -r vignettes/*_files + $(RM) -r vignettes/*.R $(RM) Rplots.pdf test: quickinstall @@ -73,9 +74,7 @@ vignettes/%.html: vignettes/mkin_vignettes.css vignettes/references.bib vignette vignettes: vignettes/mkin.html vignettes/FOCUS_D.html vignettes/FOCUS_L.html vignettes/FOCUS_Z.html vignettes/compiled_models.html pd: - "$(RBIN)/Rscript" -e "pkgdown::build_news()" - "$(RBIN)/Rscript" -e "pkgdown::build_reference(run_dont_run = TRUE)" - "$(RBIN)/Rscript" -e "pkgdown::build_home()" + "$(RBIN)/Rscript" -e "pkgdown::build_site()" git add -A git commit -m 'Static documentation except articles rebuilt by pkgdown' -e diff --git a/docs/NEWS.html b/docs/NEWS.html new file mode 100644 index 00000000..8ea2aff9 --- /dev/null +++ b/docs/NEWS.html @@ -0,0 +1,610 @@ + + + + + + + + +/home/jranke/git/mkin/NEWS.md • mkin + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+
+ + + +
+ +
+
+
+

/home/jranke/git/mkin/NEWS.md

+
+ + +
+

+mkin 0.9.47.1 (2017-02-06)

+
    +

  • Skip some test 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.

    • +

  • ‘mkinfit’: Work around a bug in the current FME version that prevented the convergence message to be returned in the case of non-convergence.

    • +

  • ‘summary.mkinfit’: Improved output regarding weighting method. No predictions are returned for NA values in the model (see above).

    • +

  • ‘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

    • +
+
+
+

+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

    • +
+
+
+

+mkin 0.9.46.2 (2017-10-10)

+
    +

  • Converted the vignette FOCUS_Z from tex/pdf to markdown/html

    • +

  • DESCRIPTION: Add ORCID

    • +
+
+
+

+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

    • +
+
+
+

+mkin 0.9.46 (2017-07-24)

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

+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

    • +
+
+
+

+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).
    • +
+
+
+
+

+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.

    • +

  • Use pkgdown, the successor of staticdocs for generating static HTML documentation. Include example output and graphs also for dontrun sections.

    • +

  • plot.mkinfit: Plotting does not fail any more when the compiled model is not available, e.g. because it was removed from the temporary directory. In this case, the uncompiled model is now used for plotting

    • +
+
+
+
+

+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
    • +
+
+
+
+

+mkin 0.9.43 (2016-06-28)

+
+

+Major changes

+
    +

  • The title was changed to Kinetic evaluations of chemical degradation data

    • +

  • plot.mkinfit: Add the possibility to show fits (and residual plots if requested) separately for the observed variables

    • +

  • plot.mkinfit: Add the possibility to show the chi2 error levels in the plot, similar to the way they are shown in plot.mmkin

    • +

  • plot_sep: Add this function as a convenience wrapper for plotting observed variables of mkinfit objects separately, with chi2 error values and residual plots.

    • +

  • Vignettes: The main vignette mkin was converted to R markdown and updated. The other vignettes were also updated to show current improved functionality.

    • +

  • The function add_err was added to the package, making it easy to generate simulated data using an error model based on the normal distribution

    • +
+
+
+

+Minor changes

+
    +

  • Remove an outdated reference to the inline package in the compiled_models vignette

    • +

  • mkinfit: Do not error out in cases where the fit converges, but the Jacobian for the untransformed model cost can not be estimated. Give a warning instead and return NA for the t-test results.

    • +

  • summary.mkinfit: Give a warning message when the covariance matrix can not be obtained.

    • +

  • A test has been added to containing a corresponding edge case to check that the warnings are correctly issued and the fit does not terminate.

    • +

  • plot.mmkin: Round the chi2 error value to three significant digits, instead of two decimal digits.

    • +

  • mkinfit: Return the err values used on weighted fits as a column named err. Also include these inverse weights when the column value in the observed data is used, which is returned as observed in the data component of the mkinfit object.

    • +
+
+
+

+Bug fixes

+
    +

  • endpoints: When the name of a substance degrading to a metabolite (e.g. a parent compound) used in the model formulation ended in the letter f, some rate parameters could be listed as formation fractions with mixed up names. These would also appear in the summary.

    • +

  • mkinfit: Check for all observed variables when checking if the user tried to fix formation fractions when fitting them using ilr transformation.

    • +

  • plot.mmkin: Set the plot margins correctly, also in the case of a single fit to be plotted, so the main title is placed in a reasonable way.

    • +

  • plot.mkinfit: Correct default values for col_obs, pch_obs and lty_obs for the case that obs_vars is specified.

    • +
+
+
+
+

+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
    • +
+
+
+

+Minor changes

+
    +

  • Add plots to compiled_models vignette

    • +

  • Give an explanatory error message when mkinmod fails due to a missing definition of a target variable

    • +

  • print.mkinmod(): Improve formatting when printing mkinmod model definitions

    • +
+
+
+
+

+mkin 0.9-41 (2015-11-09)

+
+

+Minor changes

+
    +

  • Add an R6 class mkinds representing datasets with a printing method

    • +

  • Add a printing method for mkinmod objects

    • +

  • Make it possible to specify arbitrary strings as names for the compounds in mkinmod, and show them in the plot

    • +

  • Use an index.r file to group help topics in static documentation

    • +
+
+
+

+Bug fixes

+
    +
  • +print.summary.mkinfit(): Avoid an error that occurred when printing summaries generated with mkin versions before 0.9-36
    • +
+
+
+
+

+mkin 0.9-40 (2015-07-21)

+
+

+Bug fixes

+
    +
  • +endpoints(): For DFOP and SFORB models, where optimize() is used, make use of the fact that the DT50 must be between DT50_k1 and DT50_k2 (DFOP) or DT50_b1 and DT50_b2 (SFORB), as optimize() sometimes did not find the minimum. Likewise for finding DT90 values. Also fit on the log scale to make the function more efficient.
    • +
+
+
+

+Internal changes

+
    +
  • +DESCRIPTION, NAMESPACE, R/*.R: Import (from) stats, graphics and methods packages, and qualify some function calls for non-base packages installed with R to avoid NOTES made by R CMD check –as-cran with upcoming R versions.
    • +
+
+
+
+

+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.

    • +

  • New function plot.mmkin(): Plots single-row or single-column mmkin objects including residual plots.

    • +
+
+
+

+Bug fixes

+
    +
  • +mkinparplot(): Fix the x axis scaling for rate constants and formation fractions that got confused by the introduction of the t-values of transformed parameters.
    • +
+
+
+
+

+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.

    • +

  • GNUMakefile,vignettes/*: Clean up vignette generation and include table of contents in HTML vignettes.

    • +
+
+
+

+Bug fixes

+
    +
  • +mkinmod(): When generating the C code for the derivatives, only declare the time variable when it is needed and remove the ‘-W-no-unused-variable’ compiler flag as the C compiler used in the CRAN checks on Solaris does not know it.
    • +
+
+
+
+

+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.

    • +

  • If a compiler (gcc) is installed, use a version of the differential equation model compiled from C code, which is a huge performance boost for models where only the deSolve method works.

    • +

  • mkinmod(): Create a list component $cf (of class CFuncList) in the list returned by mkinmod, if a version can be compiled from autogenerated C code (see above).

    • +

  • mkinfit(): Set the default solution_type to deSolve when a compiled version of the model is present, except when an analytical solution is possible.

    • +
+
+
+

+Minor changes

+
    +
  • Added a simple showcase vignette with an evaluation of FOCUS example dataset D
    • +
+
+
+
+

+mkin 0.9-35 (2015-05-15)

+
+

+Major changes

+
    +
  • Switch from RUnit to testthat for testing
    • +
+
+
+

+Bug fixes

+
    +

  • mkinparplot(): Avoid warnings that occurred when not all confidence intervals were available in the summary of the fit

    • +

  • print.summary.mkinfit(): Fix printing the summary for the case that the number of iterations is not available

    • +

  • NAMESPACE: export S3 methods plot.mkinfit, summary.mkinfit and print.summary.mkinfit to satisfy R CMD check on R-devel

    • +

  • mkinparplot(): Avoid warning in R CMD check about undeclared global variable Lower

    • +
+
+
+

+New features

+
    +

  • mkinfit(): Report successful termination when quiet = FALSE. This is helpful for more difficult problems fitted with reweight.method = obs, as no progress is often indicated during the reweighting.

    • +

  • A first test using results established in the expertise written for the German Federal Environmental Agency (UBA) was added.

    • +

  • Add synthetic datasets generated for expertise written for the German Federal Environmental Agency UBA

    • +

  • Add tests based on these datasets

    • +
+
+
+
+

+mkin 0.9-34 (2014-11-22)

+
+

+New features

+
    +

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

    • +

  • Add the possibility to fit indeterminate order rate equation (IORE) models using an analytical solution (parent only) or a numeric solution. Paths from IORE compounds to metabolites are supported when using formation fractions (use_of_ff = ‘max’). Note that the numerical solution (method.ode = ‘deSolve’) of the IORE differential equations sometimes fails due to numerical problems.

    • +

  • Switch to using the Port algorithm (using a model/trust region approach) per default. While needing more iterations than the Levenberg-Marquardt algorithm previously used per default, it is less sensitive to starting parameters.

    • +
+
+
+

+Minor changes

+
    +

  • The formatting of differential equations in the summary was further improved

    • +

  • Always include 0 on y axis when plotting during the fit

    • +
+
+
+
+

+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"

    • +

  • A basic unit test for mkinerrmin() was written

    • +
+
+
+

+Bug fixes

+
    +

  • mkinfit(): The internally fitted parameter for g was named g_ilr even when transform_fractions=FALSE

    • +

  • mkinfit(): The initial value (state.ini) for the parent compound was not set when the parent was not the (only) variable with the highest value in the observed data.

    • +

  • mkinerrmin(): When checking for degrees of freedom for metabolites, check if their time zero value is fixed instead of checking if the observed value is zero. This ensures correct calculation of degrees of freedom also in cases where the metabolite residue at time zero is greater zero.

    • +

  • plot.mkinfit(): Avoid a warning message about only using the first component of ylim that occurred when ylim was specified explicitly

    • +
+
+
+

+Minor changes

+
    +

  • The formatting of differential equations in the summary was improved by wrapping overly long lines

    • +

  • The FOCUS_Z vignette was rebuilt with the above improvement and using a width of 70 to avoid output outside of the grey area

    • +

  • print.summary.mkinfit(): Avoid a warning that occurred when gmkin showed summaries ofinitial fits without iterations

    • +

  • mkinfit(): Avoid a warning that occurred when summarising a fit that was performed with maxitmodFit = 0 as done in gmkin for configuring new fits.

    • +
+
+
+
+

+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.

    • +

  • The default for the initial value for the first state value is now taken from the mean of the observations at time zero, if available.

    • +

  • The kinetic model can alternatively be specified with a shorthand name for parent only degradation models, e.g. SFO, or DFOP.

    • +

  • Optimisation method, number of model evaluations and time elapsed during optimisation are given in the summary of mkinfit objects.

    • +

  • The maximum number of iterations in the optimisation algorithm can be specified using the argument maxit.modFit to the mkinfit function.

    • +

  • mkinfit gives a warning when the fit does not converge (does not apply to SANN method). This warning is included in the summary.

    • +
+
+
+

+Bug fixes

+
    +

  • Avoid plotting an artifical 0 residual at time zero in mkinresplot

    • +

  • In the determination of the degrees of freedom in mkinerrmin, formation fractions were accounted for multiple times in the case of parallel formation of metabolites. See the new feature described above for the solution.

    • +

  • transform_rates=FALSE in mkinfit now also works for FOMC and HS models.

    • +

  • Initial values for formation fractions were not set in all cases.

    • +

  • No warning was given when the fit did not converge when a method other than the default Levenberg-Marquardt method Marq was used.

    • +
+
+
+

+Minor changes

+
    +

  • Vignettes were rebuilt to reflect the changes in the summary method.

    • +

  • Algorithm Pseudo was excluded because it needs user-defined parameter limits which are not supported.

    • +

  • Algorithm Newton was excluded because of its different way to specify the maximum number of iterations and because it does not appear to provide additional benefits.

    • +
+
+
+
+

+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.
    • +
+
+
+
+

+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().
    • +
+
+
+

+Major changes

+
    +

  • The original and the transformed parameters now have different names (e.g. k_parent and log_k_parent. They also differ in how many they are when we have formation fractions but no pathway to sink.

    • +

  • The order of some of the information blocks in print.summary.mkinfit.R() has been ordered in a more logical way.

    • +
+
+
+

+Minor changes

+
    +

  • The vignette FOCUS_Z has been simplified to use formation fractions with turning off the sink, and slightly amended to use the new versions of DT50 values calculated since mkin 0.9-29.

    • +

  • All vignettes have been rebuilt so they reflect all changes.

    • +

  • The ChangeLog was renamed to NEWS.md and the entries were converted to markdown syntax compatible with the tools::news() function built into R.

    • +

  • The test suite was overhauled. Tests of the DFOP and SFORB models with dataset FOCUS_2006_A were removed, as they were too much dependent on the optimisation algorithm and/or starting parameters, because the dataset is SFO (compare kinfit vignette).

    • +

  • Also, the Schaefer complex case can now be fitted using formation fractions, and with the ‘Port’ optimisation method we also fit A2 in the same way as published in the Piacenza paper.

    • +

  • Some more checks were introduced to mkinfit(), leading to warnings or stopping execution if unsupported combinations of methods and parameters are requested.

    • +
+
+
+
+

+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

    • +
+
+
+

+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

    • +
+
+
+

+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

    • +

  • Possibility to fit without parameter transformations, using bounds as implemented in FME

    • +

  • Add McCall 2,4,5-T dataset

    • +

  • Enable selection of observed variables in plotting

    • +

  • Add possibility to show residual plot in plot.mkinfit

    • +

  • R/mkinparplot.R, man/mkinparplot.Rd: plot parameters with confidence intervals

    • +

  • Change vignette format from Sweave to knitr

    • +

  • Split examples vignette to FOCUS_L and FOCUS_Z

    • +

  • Remove warning about constant formation fractions in mkinmod as it was based on a misconception

    • +

  • Restrict the unit test with the Schaefer data to parent and primary metabolites as formation fraction and DT50 for A2 are higly correlated and passing the test is platform dependent. For example, the test fails in 1 out of 14 platforms on CRAN as of today.

    • +

  • Add Eurofins Regulatory AG copyright notices

    • +

  • Import FME and deSolve instead of depending on them to have clean startup

    • +

  • Add a starter function for the GUI: gmkin()

    • +

  • Change the format of the workspace files of gmkin so they can be distributed and documented in the package

    • +

  • Add gmkin workspace datasets FOCUS_2006_gmkin and FOCUS_2006_Z_gmkin

    • +
+
+
+

+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

    • +
+
+
+

+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

    • +

  • The first successful fits in the not so simple GUI

    • +

  • Fix iteratively reweighted least squares for the case of many metabolites

    • +

  • Unify naming of initial values of state variables

    • +

  • Unify naming in dataframes of optimised and fixed parameters in the summary

    • +

  • Show the weighting method for residuals in the summary

    • +

  • Correct the output of the data in the case of manual weighting

    • +

  • Implement IRLS assuming different variances for observed variables

    • +

  • 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

+
+ + +
+ +
+ + +
+
+

Developed by Johannes Ranke.

+
+ +
+

Site built with pkgdown.

+
+ +
+
+ + + + diff --git a/docs/README.html b/docs/README.html new file mode 100644 index 00000000..98d42ebc --- /dev/null +++ b/docs/README.html @@ -0,0 +1,200 @@ + + + + + + + + +/home/jranke/git/mkin/README.md • mkin + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+
+ + + +
+ +
+
+
+

/home/jranke/git/mkin/README.md

+
+ +
+

+mkin

+

+

The R package mkin provides calculation routines for the analysis of chemical degradation data, including multicompartment kinetics as needed for modelling the formation and decline of transformation products, or if several compartments are involved.

+
+

+Installation

+

You can install the latest released version from CRAN from within R:

+
install.packages("mkin")
+
+
+

+Background

+

In the regulatory evaluation of chemical substances like plant protection products (pesticides), biocides and other chemicals, degradation data play an important role. For the evaluation of pesticide degradation experiments, detailed guidance and helpful tools have been developed as detailed in ‘Credits and historical remarks’ below.

+
+
+

+Usage

+

For a start, have a look a the code examples provided for plot.mkinfit and plot.mmkin, and at the package vignettes FOCUS L and FOCUS D.

+
+
+

+Documentation

+

The HTML documentation is available at jrwb.de, at github and at R-Forge.

+
+
+

+Features

+
    +
  • Highly flexible model specification using mkinmod, including equilibrium reactions and using the single first-order reversible binding (SFORB) model, which will automatically create two latent state variables for the observed variable.
    • +
  • As of version 0.9-39, fitting of several models to several datasets, optionally in parallel, is supported, see for example plot.mmkin.
    • +
  • Model solution (forward modelling) in the function mkinpredict is performed either using the analytical solution for the case of parent only degradation, an eigenvalue based solution if only simple first-order (SFO) or SFORB kinetics are used in the model, or using a numeric solver from the deSolve package (default is lsoda).
    • +
  • If a C compiler is installed, the kinetic models are compiled from automatically generated C code, see vignette compiled_models. The autogeneration of C code was inspired by the ccSolve package. Thanks to Karline Soetaert for her work on that.
    • +
  • By default, kinetic rate constants and kinetic formation fractions are transformed internally using transform_odeparms so their estimators can more reasonably be expected to follow a normal distribution. This has the side effect that no constraints are needed in the optimisation. Thanks to René Lehmann for the nice cooperation on this, especially the isometric logration transformation that is now used for the formation fractions.
    • +
  • A side effect of this is that when parameter estimates are backtransformed to match the model definition, confidence intervals calculated from standard errors are also backtransformed to the correct scale, and will not include meaningless values like negative rate constants or formation fractions adding up to more than 1, which can not occur in a single experiment with a single defined radiolabel position.
    • +
  • The usual one-sided t-test for significant difference from zero is nevertheless shown based on estimators for the untransformed parameters.
    • +
  • Summary and plotting functions. The summary of an mkinfit object is in fact a full report that should give enough information to be able to approximately reproduce the fit with other tools.
    • +
  • The chi-squared error level as defined in the FOCUS kinetics guidance (see below) is calculated for each observed variable.
    • +
  • Iteratively reweighted least squares fitting is implemented in a similar way as in KinGUII and CAKE (see below). Simply add the argument reweight.method = "obs" to your call to mkinfit and a separate variance componenent for each of the observed variables will be optimised in a second stage after the primary optimisation algorithm has converged.
    • +
  • Iterative reweighting is also possible using the two-component error model for analytical data of Rocke and Lorenzato using the argument reweight.method = "tc".
    • +
  • When a metabolite decline phase is not described well by SFO kinetics, SFORB kinetics can be used for the metabolite.
    • +
+
+
+

+GUI

+

There is a graphical user interface that I consider useful for real work. Please refer to its documentation page for installation instructions and a manual.

+
+
+

+News

+

There is a ChangeLog, for the latest CRAN release and one for the github master branch.

+
+
+

+Credits and historical remarks

+

mkin would not be possible without the underlying software stack consisting of R and the packages deSolve and FME, to say the least.

+

It could not have been written without me being introduced to regulatory fate modelling of pesticides by Adrian Gurney during my time at Harlan Laboratories Ltd (formerly RCC Ltd). mkin greatly profits from and largely follows the work done by the FOCUS Degradation Kinetics Workgroup, as detailed in their guidance document from 2006, slightly updated in 2011 and in 2014.

+

Also, it was inspired by the first version of KinGUI developed by BayerCropScience, which is based on the MatLab runtime environment.

+

The companion package kinfit (now deprecated) was started in 2008 and first published on CRAN on 01 May 2010.

+

The first mkin code was published on 11 May 2010 and the first CRAN version on 18 May 2010.

+

In 2011, Bayer Crop Science started to distribute an R based successor to KinGUI named KinGUII whose R code is based on mkin, but which added, amongst other refinements, a closed source graphical user interface (GUI), iteratively reweighted least squares (IRLS) optimisation of the variance for each of the observed variables, and Markov Chain Monte Carlo (MCMC) simulation functionality, similar to what is available e.g. in the FME package.

+

Somewhat in parallel, Syngenta has sponsored the development of an mkin and KinGUII based GUI application called CAKE, which also adds IRLS and MCMC, is more limited in the model formulation, but puts more weight on usability. CAKE is available for download from the CAKE website, where you can also find a zip archive of the R scripts derived from mkin, published under the GPL license.

+

Finally, there is KineticEval, which contains a further development of the scripts used for KinGUII, so the different tools will hopefully be able to learn from each other in the future as well.

+
+
+

+Development

+

Contributions are welcome! Your mkin fork is just a mouse click away… The master branch on github should always be in good shape, I implement new features in separate branches now. If you prefer subversion, project members for the r-forge project are welcome as well. Generally, the source code of the latest CRAN version should be available there. You can also browse the source code at cgit.jrwb.de/mkin.

+
+
+ +
+ +
+ + +
+
+

Developed by Johannes Ranke.

+
+ +
+

Site built with pkgdown.

+
+ +
+
+ + + + diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html index d85246f8..a8002acd 100644 --- a/docs/articles/FOCUS_D.html +++ b/docs/articles/FOCUS_D.html @@ -9,7 +9,10 @@ - @@ -77,7 +80,7 @@

Example evaluation of FOCUS Example Dataset D

Johannes Ranke

-

2018-03-09

+

2018-03-11

@@ -152,8 +155,8 @@ 
summary(fit)
## mkin version:    0.9.46.3 
 ## R version:       3.4.3 
-## Date of fit:     Fri Mar  9 23:09:48 2018 
-## Date of summary: Fri Mar  9 23:09:48 2018 
+## Date of fit:     Sun Mar 11 22:11:56 2018 
+## Date of summary: Sun Mar 11 22:11:57 2018 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -161,7 +164,7 @@
 ## 
 ## Model predictions using solution type deSolve 
 ## 
-## Fitted with method Port using 153 model solutions performed in 0.99 s
+## Fitted with method Port using 153 model solutions performed in 0.984 s
 ## 
 ## Weighting: none
 ## 
diff --git a/docs/articles/FOCUS_L.R b/docs/articles/FOCUS_L.R
deleted file mode 100644
index 063e3d57..00000000
--- a/docs/articles/FOCUS_L.R
+++ /dev/null
@@ -1,86 +0,0 @@
-## ---- include = FALSE----------------------------------------------------
-library(knitr)
-opts_chunk$set(tidy = FALSE, cache = FALSE)
-
-## ------------------------------------------------------------------------
-library("mkin", quietly = TRUE)
-FOCUS_2006_L1 = data.frame(
-  t = rep(c(0, 1, 2, 3, 5, 7, 14, 21, 30), each = 2),
-  parent = c(88.3, 91.4, 85.6, 84.5, 78.9, 77.6,
-             72.0, 71.9, 50.3, 59.4, 47.0, 45.1,
-             27.7, 27.3, 10.0, 10.4, 2.9, 4.0))
-FOCUS_2006_L1_mkin <- mkin_wide_to_long(FOCUS_2006_L1)
-
-## ------------------------------------------------------------------------
-m.L1.SFO <- mkinfit("SFO", FOCUS_2006_L1_mkin, quiet = TRUE)
-summary(m.L1.SFO)
-
-## ----fig.width = 6, fig.height = 5---------------------------------------
-plot(m.L1.SFO, show_errmin = TRUE, main = "FOCUS L1 - SFO")
-
-## ----fig.width = 6, fig.height = 5---------------------------------------
-mkinresplot(m.L1.SFO, ylab = "Observed", xlab = "Time")
-
-## ----fig.width = 6, fig.height = 5---------------------------------------
-m.L1.FOMC <- mkinfit("FOMC", FOCUS_2006_L1_mkin, quiet=TRUE)
-plot(m.L1.FOMC, show_errmin = TRUE, main = "FOCUS L1 - FOMC")
-summary(m.L1.FOMC, data = FALSE)
-
-## ------------------------------------------------------------------------
-FOCUS_2006_L2 = data.frame(
-  t = rep(c(0, 1, 3, 7, 14, 28), each = 2),
-  parent = c(96.1, 91.8, 41.4, 38.7,
-             19.3, 22.3, 4.6, 4.6,
-             2.6, 1.2, 0.3, 0.6))
-FOCUS_2006_L2_mkin <- mkin_wide_to_long(FOCUS_2006_L2)
-
-## ----fig.width = 7, fig.height = 6---------------------------------------
-m.L2.SFO <- mkinfit("SFO", FOCUS_2006_L2_mkin, quiet=TRUE)
-plot(m.L2.SFO, show_residuals = TRUE, show_errmin = TRUE,
-     main = "FOCUS L2 - SFO")
-
-## ----fig.width = 7, fig.height = 6---------------------------------------
-m.L2.FOMC <- mkinfit("FOMC", FOCUS_2006_L2_mkin, quiet = TRUE)
-plot(m.L2.FOMC, show_residuals = TRUE,
-     main = "FOCUS L2 - FOMC")
-summary(m.L2.FOMC, data = FALSE)
-
-## ----fig.width = 7, fig.height = 6---------------------------------------
-m.L2.DFOP <- mkinfit("DFOP", FOCUS_2006_L2_mkin, quiet = TRUE)
-plot(m.L2.DFOP, show_residuals = TRUE, show_errmin = TRUE,
-     main = "FOCUS L2 - DFOP")
-summary(m.L2.DFOP, data = FALSE)
-
-## ------------------------------------------------------------------------
-FOCUS_2006_L3 = data.frame(
-  t = c(0, 3, 7, 14, 30, 60, 91, 120),
-  parent = c(97.8, 60, 51, 43, 35, 22, 15, 12))
-FOCUS_2006_L3_mkin <- mkin_wide_to_long(FOCUS_2006_L3)
-
-## ----fig.height = 8------------------------------------------------------
-# Only use one core here, not to offend the CRAN checks
-mm.L3 <- mmkin(c("SFO", "FOMC", "DFOP"), cores = 1,
-               list("FOCUS L3" = FOCUS_2006_L3_mkin), quiet = TRUE)
-plot(mm.L3)
-
-## ----fig.height = 5------------------------------------------------------
-summary(mm.L3[["DFOP", 1]])
-plot(mm.L3[["DFOP", 1]], show_errmin = TRUE)
-
-## ------------------------------------------------------------------------
-FOCUS_2006_L4 = data.frame(
-  t = c(0, 3, 7, 14, 30, 60, 91, 120),
-  parent = c(96.6, 96.3, 94.3, 88.8, 74.9, 59.9, 53.5, 49.0))
-FOCUS_2006_L4_mkin <- mkin_wide_to_long(FOCUS_2006_L4)
-
-## ----fig.height = 6------------------------------------------------------
-# Only use one core here, not to offend the CRAN checks
-mm.L4 <- mmkin(c("SFO", "FOMC"), cores = 1,
-               list("FOCUS L4" = FOCUS_2006_L4_mkin),
-               quiet = TRUE)
-plot(mm.L4)
-
-## ----fig.height = 8------------------------------------------------------
-summary(mm.L4[["SFO", 1]], data = FALSE)
-summary(mm.L4[["FOMC", 1]], data = FALSE)
-
diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html
index 196a0c4f..a23876ec 100644
--- a/docs/articles/FOCUS_L.html
+++ b/docs/articles/FOCUS_L.html
@@ -9,7 +9,10 @@
 
 
 
-
@@ -77,7 +80,7 @@
       
Example evaluation of FOCUS Laboratory Data L1 to L3

                         
Johannes Ranke

             
-            
2018-03-09

+            
2018-03-11

           
 
     
@@ -100,15 +103,15 @@ FOCUS_2006_L1_mkin <- summary(m.L1.SFO)
## mkin version:    0.9.46.3 
 ## R version:       3.4.3 
-## Date of fit:     Fri Mar  9 23:09:50 2018 
-## Date of summary: Fri Mar  9 23:09:50 2018 
+## Date of fit:     Sun Mar 11 22:11:58 2018 
+## Date of summary: Sun Mar 11 22:11:58 2018 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 37 model solutions performed in 0.264 s
+## Fitted with method Port using 37 model solutions performed in 0.235 s
 ## 
 ## Weighting: none
 ## 
@@ -191,15 +194,15 @@ FOCUS_2006_L1_mkin <- 
summary(m.L1.FOMC, data = FALSE)

 
## mkin version:    0.9.46.3 
 ## R version:       3.4.3 
-## Date of fit:     Fri Mar  9 23:09:52 2018 
-## Date of summary: Fri Mar  9 23:09:52 2018 
+## Date of fit:     Sun Mar 11 22:12:01 2018 
+## Date of summary: Sun Mar 11 22:12:01 2018 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 611 model solutions performed in 1.451 s
+## Fitted with method Port using 611 model solutions performed in 1.458 s
 ## 
 ## Weighting: none
 ## 
@@ -286,15 +289,15 @@ FOCUS_2006_L2_mkin <- 
summary(m.L2.FOMC, data = FALSE)

 
## mkin version:    0.9.46.3 
 ## R version:       3.4.3 
-## Date of fit:     Fri Mar  9 23:09:53 2018 
-## Date of summary: Fri Mar  9 23:09:53 2018 
+## Date of fit:     Sun Mar 11 22:12:01 2018 
+## Date of summary: Sun Mar 11 22:12:01 2018 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 81 model solutions performed in 0.175 s
+## Fitted with method Port using 81 model solutions performed in 0.158 s
 ## 
 ## Weighting: none
 ## 
@@ -357,8 +360,8 @@ FOCUS_2006_L2_mkin <- 
summary(m.L2.DFOP, data = FALSE)

 
## mkin version:    0.9.46.3 
 ## R version:       3.4.3 
-## Date of fit:     Fri Mar  9 23:09:54 2018 
-## Date of summary: Fri Mar  9 23:09:54 2018 
+## Date of fit:     Sun Mar 11 22:12:02 2018 
+## Date of summary: Sun Mar 11 22:12:02 2018 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -367,7 +370,7 @@ FOCUS_2006_L2_mkin <-  
summary(mm.L3[["DFOP", 1]])

 
## mkin version:    0.9.46.3 
 ## R version:       3.4.3 
-## Date of fit:     Fri Mar  9 23:09:55 2018 
-## Date of summary: Fri Mar  9 23:09:55 2018 
+## Date of fit:     Sun Mar 11 22:12:03 2018 
+## Date of summary: Sun Mar 11 22:12:03 2018 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -459,7 +462,7 @@ mm.L3 <-  
summary(mm.L4[["SFO", 1]], data = FALSE)

 
## mkin version:    0.9.46.3 
 ## R version:       3.4.3 
-## Date of fit:     Fri Mar  9 23:09:55 2018 
-## Date of summary: Fri Mar  9 23:09:56 2018 
+## Date of fit:     Sun Mar 11 22:12:04 2018 
+## Date of summary: Sun Mar 11 22:12:04 2018 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 46 model solutions performed in 0.09 s
+## Fitted with method Port using 46 model solutions performed in 0.092 s
 ## 
 ## Weighting: none
 ## 
@@ -610,15 +613,15 @@ mm.L4 <- 
summary(mm.L4[["FOMC", 1]], data = FALSE)

 
## mkin version:    0.9.46.3 
 ## R version:       3.4.3 
-## Date of fit:     Fri Mar  9 23:09:56 2018 
-## Date of summary: Fri Mar  9 23:09:56 2018 
+## Date of fit:     Sun Mar 11 22:12:04 2018 
+## Date of summary: Sun Mar 11 22:12:04 2018 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 66 model solutions performed in 0.134 s
+## Fitted with method Port using 66 model solutions performed in 0.13 s
 ## 
 ## Weighting: none
 ## 
diff --git a/docs/articles/FOCUS_Z.html b/docs/articles/FOCUS_Z.html
index 606121ff..78a00062 100644
--- a/docs/articles/FOCUS_Z.html
+++ b/docs/articles/FOCUS_Z.html
@@ -9,7 +9,10 @@
 
 
 
-
@@ -77,7 +80,7 @@
       
Example evaluation of FOCUS dataset Z

                         
Johannes Ranke

             
-            
2018-03-09

+            
2018-03-11

           
 
     
diff --git a/docs/articles/compiled_models.html b/docs/articles/compiled_models.html
index 915e5474..8923acac 100644
--- a/docs/articles/compiled_models.html
+++ b/docs/articles/compiled_models.html
@@ -9,7 +9,10 @@
 
 
 
-
@@ -77,7 +80,7 @@
       
Performance benefit by using compiled model definitions in mkin

                         
Johannes Ranke

             
-            
2018-03-09

+            
2018-03-11

           
 
     
@@ -115,9 +118,9 @@ SFO_SFO <-  
   
   
+
 
 
 
@@ -134,3 +135,4 @@
 
   
 
+
diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html
index f668b500..7b26b3f1 100644
--- a/docs/articles/mkin.html
+++ b/docs/articles/mkin.html
@@ -9,7 +9,10 @@
 
 
 
-
@@ -77,7 +80,7 @@
       
Introduction to mkin

                         
Johannes Ranke

             
-            
2018-03-09

+            
2018-03-11

           
 
     
diff --git a/docs/articles/twa.html b/docs/articles/twa.html
index e5b68cfe..7f4c941e 100644
--- a/docs/articles/twa.html
+++ b/docs/articles/twa.html
@@ -9,7 +9,10 @@
 
 
 
-
@@ -77,7 +80,7 @@
       
Calculation of time weighted average concentrations with mkin

                         
Johannes Ranke

             
-            
2018-03-09

+            
2018-03-11

           
 
     
diff --git a/docs/authors.html b/docs/authors.html
index af022eab..a9712678 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -27,6 +27,7 @@
 
   
   
+
 
 
 
@@ -106,19 +107,19 @@
 
     
@@ -142,3 +143,4 @@
 
   
 
+
diff --git a/docs/index.html b/docs/index.html
index 88fd4f6d..9caba262 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -9,7 +9,17 @@
 
 
 
-
@@ -159,8 +169,7 @@
 
GPL

 
Developers

 
    
-
  • Johannes Ranke 
     Author, maintainer, copyright holder  
    (0000-0003-4371-6538)
-
    • 
+
  • Johannes Ranke 
     Author, maintainer, copyright holder   
    • 
 
  • All authors...
    • 
 

 
Dev status

diff --git a/docs/news/index.html b/docs/news/index.html
index 39b21d12..f311efe5 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -27,6 +27,7 @@
 
   
   
+
 
 
 
@@ -640,3 +641,4 @@
 
   
 
+
diff --git a/docs/pkgdown.css b/docs/pkgdown.css
index 59b659f2..181fe639 100644
--- a/docs/pkgdown.css
+++ b/docs/pkgdown.css
@@ -100,6 +100,11 @@ a.anchor {
   margin-bottom: 0.5em;
 }
 
+.orcid {
+  height: 16px;
+  vertical-align: middle;
+}
+
 /* Reference index & topics ----------------------------------------------- */
 
 .ref-index th {font-weight: normal;}
@@ -137,6 +142,12 @@ pre, code {
   color: #333;
 }
 
+pre code {
+  overflow: auto;
+  word-wrap: normal;
+  white-space: pre;
+}
+
 pre .img {
   margin: 5px 0;
 }
@@ -151,6 +162,10 @@ code a, pre a {
   color: #375f84;
 }
 
+a.sourceLine:hover {
+  text-decoration: none;
+}
+
 .fl      {color: #1514b5;}
 .fu      {color: #000000;} /* function */
 .ch,.st  {color: #036a07;} /* string */
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
new file mode 100644
index 00000000..974e3585
--- /dev/null
+++ b/docs/pkgdown.yml
@@ -0,0 +1,20 @@
+pandoc: 1.19.2.4
+pkgdown: 0.1.0.9000
+pkgdown_sha: ~
+articles:
+  FOCUS_D: FOCUS_D.html
+  FOCUS_D.html: FOCUS_D.html
+  FOCUS_L: FOCUS_L.html
+  FOCUS_L.html: FOCUS_L.html
+  FOCUS_Z: FOCUS_Z.html
+  FOCUS_Z.html: FOCUS_Z.html
+  FOCUS_Z.pdf: FOCUS_Z.pdf
+  compiled_models: compiled_models.html
+  compiled_models.html: compiled_models.html
+  mkin: mkin.html
+  mkin.html: mkin.html
+  mkin_vignettes.css: mkin_vignettes.css
+  references.bib: references.bib
+  twa: twa.html
+  twa.html: twa.html
+
diff --git a/docs/reference/DFOP.solution.html b/docs/reference/DFOP.solution.html
index f89a66e2..b1b3cf50 100644
--- a/docs/reference/DFOP.solution.html
+++ b/docs/reference/DFOP.solution.html
@@ -27,6 +27,11 @@
 
   
   
+
+
+
+
 
 
 
@@ -182,3 +187,4 @@
 
   
 
+
diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html
index 3b96f9ae..e554432f 100644
--- a/docs/reference/Extract.mmkin.html
+++ b/docs/reference/Extract.mmkin.html
@@ -27,6 +27,10 @@
 
   
   
+
+
+
+
 
 
 
@@ -259,7 +263,7 @@
 #> 
 #> $time
 #>    user  system elapsed 
-#>    0.06    0.00    0.06 
+#>   0.234   0.000   0.234 
 #> 
 #> $mkinmod
 #> <mkinmod> model generated with
@@ -448,8 +452,8 @@
 #>     }
 #>     return(mC)
 #> }
-#> <bytecode: 0x5555599fd348>
-#> <environment: 0x555557684190>
+#> <bytecode: 0x5555578e66e0>
+#> <environment: 0x555559cd9780>
 #> 
 #> $cost_notrans
 #> function (P) 
@@ -471,8 +475,8 @@
 #>         scaleVar = scaleVar)
 #>     return(mC)
 #> }
-#> <bytecode: 0x555559feb960>
-#> <environment: 0x555557684190>
+#> <bytecode: 0x55555acf3f50>
+#> <environment: 0x555559cd9780>
 #> 
 #> $hessian_notrans
 #>                   parent_0 k_parent_sink
@@ -539,7 +543,7 @@
 #> 99.17407 
 #> 
 #> $date
-#> [1] "Fri Mar  9 23:08:11 2018"
+#> [1] "Sun Mar 11 22:10:21 2018"
 #> 
 #> $version
 #> [1] "0.9.47.1"
@@ -582,3 +586,4 @@
 
   
 
+
diff --git a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html
index ed5f29b3..f392bf64 100644
--- a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html
+++ b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html
@@ -27,6 +27,14 @@
 
   
   
+
+
+
+
 
 
 
@@ -167,3 +175,4 @@ in this fit.

 
   
 
+
diff --git a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html
index e3e0d238..6e4c8d64 100644
--- a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html
+++ b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html
@@ -27,6 +27,14 @@
 
   
   
+
+
+
+
 
 
 
@@ -166,3 +174,4 @@ in this fit.

 
   
 
+
diff --git a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html
index be785b0b..ed38ccae 100644
--- a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html
+++ b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html
@@ -27,6 +27,14 @@
 
   
   
+
+
+
+
 
 
 
@@ -167,3 +175,4 @@ in this fit.

 
   
 
+
diff --git a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html
index 6ca8e78e..107f3e5f 100644
--- a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html
+++ b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html
@@ -27,6 +27,14 @@
 
   
   
+
+
+
+
 
 
 
@@ -165,3 +173,4 @@ in this fit.

 
   
 
+
diff --git a/docs/reference/FOCUS_2006_datasets.html b/docs/reference/FOCUS_2006_datasets.html
index 9ea69f23..cc310ee3 100644
--- a/docs/reference/FOCUS_2006_datasets.html
+++ b/docs/reference/FOCUS_2006_datasets.html
@@ -27,6 +27,10 @@
 
   
   
+
+
+
+
 
 
 
@@ -167,3 +171,4 @@
 
   
 
+
diff --git a/docs/reference/FOMC.solution.html b/docs/reference/FOMC.solution.html
index b5b4c87c..397dc82d 100644
--- a/docs/reference/FOMC.solution.html
+++ b/docs/reference/FOMC.solution.html
@@ -27,6 +27,14 @@
 
   
   
+
+
+
+
 
 
 
@@ -193,3 +201,4 @@
 
   
 
+
diff --git a/docs/reference/HS.solution.html b/docs/reference/HS.solution.html
index 0dc432ef..f633aa67 100644
--- a/docs/reference/HS.solution.html
+++ b/docs/reference/HS.solution.html
@@ -27,6 +27,11 @@
 
   
   
+
+
+
+
 
 
 
@@ -183,3 +188,4 @@
 
   
 
+
diff --git a/docs/reference/IORE.solution.html b/docs/reference/IORE.solution.html
index b055534a..687dee5a 100644
--- a/docs/reference/IORE.solution.html
+++ b/docs/reference/IORE.solution.html
@@ -27,6 +27,11 @@
 
   
   
+
+
+
+
 
 
 
@@ -197,3 +202,4 @@
 
   
 
+
diff --git a/docs/reference/SFO.solution.html b/docs/reference/SFO.solution.html
index eda43e4d..1156c16f 100644
--- a/docs/reference/SFO.solution.html
+++ b/docs/reference/SFO.solution.html
@@ -27,6 +27,10 @@
 
   
   
+
+
+
+
 
 
 
@@ -174,3 +178,4 @@
 
   
 
+
diff --git a/docs/reference/SFORB.solution.html b/docs/reference/SFORB.solution.html
index 2b6b2bc6..6901c435 100644
--- a/docs/reference/SFORB.solution.html
+++ b/docs/reference/SFORB.solution.html
@@ -27,6 +27,14 @@
 
   
   
+
+
+
+
 
 
 
@@ -187,3 +195,4 @@
 
   
 
+
diff --git a/docs/reference/add_err.html b/docs/reference/add_err.html
index 407e1a3e..6d830113 100644
--- a/docs/reference/add_err.html
+++ b/docs/reference/add_err.html
@@ -27,6 +27,12 @@
 
   
   
+
+
+
+
 
 
 
@@ -241,3 +247,4 @@
 
   
 
+
diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html
index 4ab395cb..0f5ba0a4 100644
--- a/docs/reference/endpoints.html
+++ b/docs/reference/endpoints.html
@@ -27,6 +27,13 @@
 
   
   
+
+
+
+
 
 
 
@@ -177,3 +184,4 @@ with the advantage that the SFORB model can also be used for metabolites.

 
   
 
+
diff --git a/docs/reference/geometric_mean.html b/docs/reference/geometric_mean.html
index 7e27c1dc..9d91b5a8 100644
--- a/docs/reference/geometric_mean.html
+++ b/docs/reference/geometric_mean.html
@@ -27,6 +27,10 @@
 
   
   
+
+
+
+
 
 
 
@@ -158,3 +162,4 @@
 
   
 
+
diff --git a/docs/reference/ilr.html b/docs/reference/ilr.html
index 7ed15db5..33d749ce 100644
--- a/docs/reference/ilr.html
+++ b/docs/reference/ilr.html
@@ -27,6 +27,10 @@
 
   
   
+
+
+
+
 
 
 
@@ -182,3 +186,4 @@
 
   
 
+
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 157eaad3..6c05941d 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -27,6 +27,7 @@
 
   
   
+
 
 
 
@@ -453,3 +454,4 @@
 
   
 
+
diff --git a/docs/reference/max_twa_parent.html b/docs/reference/max_twa_parent.html
index 9e1e3974..696ca729 100644
--- a/docs/reference/max_twa_parent.html
+++ b/docs/reference/max_twa_parent.html
@@ -27,6 +27,14 @@
 
   
   
+
+
+
+
 
 
 
@@ -178,3 +186,4 @@ guidance.

 
   
 
+
diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html
index 30aa894e..80cac442 100644
--- a/docs/reference/mccall81_245T.html
+++ b/docs/reference/mccall81_245T.html
@@ -27,6 +27,12 @@
 
   
   
+
+
+
+
 
 
 
@@ -145,8 +151,8 @@
                  fixed_parms = "k_phenol_sink", quiet = TRUE)
   summary(fit.2, data = FALSE)
#> mkin version used for fitting:    0.9.47.1 
 #> R version used for fitting:       3.4.3 
-#> Date of fit:     Fri Mar  9 23:08:18 2018 
-#> Date of summary: Fri Mar  9 23:08:18 2018 
+#> Date of fit:     Sun Mar 11 22:10:30 2018 
+#> Date of summary: Sun Mar 11 22:10:30 2018 
 #> 
 #> Equations:
 #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245
@@ -156,7 +162,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 246 model solutions performed in 1.359 s
+#> Fitted with method Port using 246 model solutions performed in 1.318 s
 #> 
 #> Weighting: none
 #> 
@@ -266,3 +272,4 @@
 
   
 
+
diff --git a/docs/reference/mkin_long_to_wide.html b/docs/reference/mkin_long_to_wide.html
index dc781aaf..3c498a76 100644
--- a/docs/reference/mkin_long_to_wide.html
+++ b/docs/reference/mkin_long_to_wide.html
@@ -27,6 +27,12 @@
 
   
   
+
+
+
+
 
 
 
@@ -192,3 +198,4 @@
 
   
 
+
diff --git a/docs/reference/mkin_wide_to_long.html b/docs/reference/mkin_wide_to_long.html
index 2a8d20a3..f40cb7cf 100644
--- a/docs/reference/mkin_wide_to_long.html
+++ b/docs/reference/mkin_wide_to_long.html
@@ -27,6 +27,11 @@
 
   
   
+
+
+
+
 
 
 
@@ -171,3 +176,4 @@
 
   
 
+
diff --git a/docs/reference/mkinds.html b/docs/reference/mkinds.html
index fd707cfd..7f5ec78e 100644
--- a/docs/reference/mkinds.html
+++ b/docs/reference/mkinds.html
@@ -27,6 +27,10 @@
 
   
   
+
+
+
+
 
 
 
@@ -160,3 +164,4 @@ in order to be compatible with mkinfit

 
   
 
+
diff --git a/docs/reference/mkinerrmin.html b/docs/reference/mkinerrmin.html
index 045e5805..f172cba1 100644
--- a/docs/reference/mkinerrmin.html
+++ b/docs/reference/mkinerrmin.html
@@ -27,6 +27,11 @@
 
   
   
+
+
+
+
 
 
 
@@ -195,3 +200,4 @@ chi-squared test as defined in the FOCUS kinetics report from 2006.

 
   
 
+
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index 10052053..991df1cc 100644
--- a/docs/reference/mkinfit.html
+++ b/docs/reference/mkinfit.html
@@ -27,6 +27,20 @@
 
   
   
+
+
+
+
 
 
 
@@ -400,15 +414,15 @@
 fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
 summary(fit)
#> mkin version used for fitting:    0.9.47.1 
 #> R version used for fitting:       3.4.3 
-#> Date of fit:     Fri Mar  9 23:08:20 2018 
-#> Date of summary: Fri Mar  9 23:08:20 2018 
+#> Date of fit:     Sun Mar 11 22:10:32 2018 
+#> Date of summary: Sun Mar 11 22:10:32 2018 
 #> 
 #> Equations:
 #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 #> 
 #> Model predictions using solution type analytical 
 #> 
-#> Fitted with method Port using 64 model solutions performed in 0.148 s
+#> Fitted with method Port using 64 model solutions performed in 0.135 s
 #> 
 #> Weighting: none
 #> 
@@ -477,7 +491,7 @@
   m1 = mkinsub("SFO"))
#> Successfully compiled differential equation model from auto-generated C code.
# Fit the model to the FOCUS example dataset D using defaults
 print(system.time(fit <- mkinfit(SFO_SFO, FOCUS_2006_D,
                            solution_type = "eigen", quiet = TRUE)))
#>    user  system elapsed 
-#>   0.839   0.000   0.840 
coef(fit)
#>          parent_0 log_k_parent_sink   log_k_parent_m1     log_k_m1_sink 
+#>   0.829   0.000   0.829 
coef(fit)
#>          parent_0 log_k_parent_sink   log_k_parent_m1     log_k_m1_sink 
 #>          99.59848          -3.03822          -2.98030          -5.24750 
endpoints(fit)
#> $ff
 #> parent_sink   parent_m1     m1_sink 
 #>    0.485524    0.514476    1.000000 
@@ -585,3 +599,4 @@
 
   
 
+
diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html
index 032fcbb6..7d3c0f94 100644
--- a/docs/reference/mkinmod.html
+++ b/docs/reference/mkinmod.html
@@ -27,6 +27,15 @@
 
   
   
+
+
+
+
 
 
 
@@ -255,3 +264,4 @@
 
   
 
+
diff --git a/docs/reference/mkinparplot.html b/docs/reference/mkinparplot.html
index e416d67c..81f52fc3 100644
--- a/docs/reference/mkinparplot.html
+++ b/docs/reference/mkinparplot.html
@@ -27,6 +27,11 @@
 
   
   
+
+
+
+
 
 
 
@@ -163,3 +168,4 @@
 
   
 
+
diff --git a/docs/reference/mkinplot.html b/docs/reference/mkinplot.html
index e1ee1607..cfd72521 100644
--- a/docs/reference/mkinplot.html
+++ b/docs/reference/mkinplot.html
@@ -27,6 +27,10 @@
 
   
   
+
+
+
+
 
 
 
@@ -158,3 +162,4 @@
 
   
 
+
diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html
index 7354c496..044b2d92 100644
--- a/docs/reference/mkinpredict.html
+++ b/docs/reference/mkinpredict.html
@@ -27,6 +27,12 @@
 
   
   
+
+
+
+
 
 
 
@@ -300,17 +306,17 @@
                 c(parent = 100, m1 = 0), seq(0, 20, by = 0.1),
                 solution_type = "eigen")[201,]))
#>     time   parent       m1
 #> 201   20 4.978707 27.46227
#>    user  system elapsed 
-#>   0.003   0.000   0.003 
  system.time(
+#>   0.002   0.000   0.003 
  system.time(
     print(mkinpredict(SFO_SFO, c(k_parent_m1 = 0.05, k_parent_sink = 0.1, k_m1_sink = 0.01),
                 c(parent = 100, m1 = 0), seq(0, 20, by = 0.1),
                 solution_type = "deSolve")[201,]))
#>     time   parent       m1
 #> 201   20 4.978707 27.46227
#>    user  system elapsed 
-#>   0.002   0.000   0.002 
  system.time(
+#>   0.002   0.000   0.001 
  system.time(
     print(mkinpredict(SFO_SFO, c(k_parent_m1 = 0.05, k_parent_sink = 0.1, k_m1_sink = 0.01),
                 c(parent = 100, m1 = 0), seq(0, 20, by = 0.1),
                 solution_type = "deSolve", use_compiled = FALSE)[201,]))
#>     time   parent       m1
 #> 201   20 4.978707 27.46227
#>    user  system elapsed 
-#>   0.031   0.000   0.031 

+#>   0.029   0.000   0.029