From 3010c9dcbc7f90f15b55c14919f6688d61d14414 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Sat, 4 Mar 2017 09:58:00 +0100 Subject: Mention pkgdown.jrwb.de/mkin in README Add very small twa vignette, update pkgdown docs --- docs/news/index.html | 254 ++++++++++++++++++++++++++++++++++----------------- 1 file changed, 170 insertions(+), 84 deletions(-) (limited to 'docs/news/index.html') diff --git a/docs/news/index.html b/docs/news/index.html index cbf35a73..2e7f0e34 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -100,16 +100,29 @@
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+ mkin 0.9.45.1 (2016-12-20)

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+ New features

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  • 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

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  • 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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    • 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

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Bug fixes

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

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

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    • 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

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Minor changes

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Bug fixes

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@@ -158,15 +179,19 @@

Major changes

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  • 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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  • 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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Minor changes

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@@ -174,17 +199,21 @@

Minor changes

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

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    • 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

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Bug fixes

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Bug fixes

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    • 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.
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Internal changes

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Major changes

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  • 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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    • 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.

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Bug fixes

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@@ -224,15 +261,19 @@

Minor changes

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  • 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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    • 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.

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Bug fixes

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@@ -240,16 +281,20 @@

Major changes

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  • 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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    • 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.

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Minor changes

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@@ -257,97 +302,119 @@

Major changes

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  • Switch from RUnit to testthat for testing
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  • Switch from RUnit to testthat for testing
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Bug fixes

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- New features

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mkin 0.9-34 (2014-11-22)

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- New features

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

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    • 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.

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Minor changes

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

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

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

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mkin 0.9-33 (2014-10-22)

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- New features

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  • 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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    • 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

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Bug fixes

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

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    • 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

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Minor changes

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mkin 0.9-32 (2014-07-24)

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- New features

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  • 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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    • 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.

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Bug fixes

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

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    • 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.

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Minor changes

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@@ -355,52 +422,65 @@

Bug fixes

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  • 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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  • 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)

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- New features

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  • It is now possible to use formation fractions in combination with turning off the sink in mkinmod().
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+ New features +
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  • It is now possible to use formation fractions in combination with turning off the sink in mkinmod().
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Major changes

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  • 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.

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    • 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.

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Minor changes

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mkin 0.9-29 (2014-06-27)

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mkin 0.9-28 (2014-05-20)

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mkin 0.9-27 (2014-05-10)

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mkin 0.9-24 (2013-11-06)

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mkin 0.9-22 (2013-10-26)

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

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