From 8f38147e145c66ebd27f5d9fcc6f00172c25872f Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 26 Oct 2016 23:18:20 +0200 Subject: Static documentation rebuilt by pkgdown::build_site() --- docs/news/index.html | 267 ++++++++++++++++++++++++++++++++------------------- 1 file changed, 167 insertions(+), 100 deletions(-) (limited to 'docs/news/index.html') diff --git a/docs/news/index.html b/docs/news/index.html index 4e321474..b30b400f 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -6,14 +6,13 @@ -All news. mkin +All news • mkin - - + @@ -22,6 +21,7 @@ + @@ -34,10 +34,9 @@ -
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mkin 0.9.45

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Change log All releases

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+ mkin 0.9.45

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Minor changes

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+ Minor changes

  • 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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mkin 0.9.44 (2016-06-29)

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+ mkin 0.9.44 (2016-06-29)

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Bug fixes

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+ 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)

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+ mkin 0.9.43 (2016-06-28)

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Major changes

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+ 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

    • @@ -99,7 +112,8 @@

  • 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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+ 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.

    • @@ -108,155 +122,187 @@

  • 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.

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Bug fixes

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+ 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.

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mkin 0.9.42 (2016-03-25)

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+ mkin 0.9.42 (2016-03-25)

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Major changes

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+ 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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Minor changes

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+ 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

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mkin 0.9-41 (2015-11-09)

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

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Minor changes

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+ 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

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Bug fixes

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+ Bug fixes

  • print.summary.mkinfit(): Avoid an error that occurred when printing summaries generated with mkin versions before 0.9-36
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mkin 0.9-40 (2015-07-21)

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

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Bug fixes

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+ 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.
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Internal changes

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+ 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.
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mkin 0.9-39 (2015-06-26)

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+ mkin 0.9-39 (2015-06-26)

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Major changes

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+ 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.

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Bug fixes

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+ 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.
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mkin 0.9-38 (2015-06-24)

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+ mkin 0.9-38 (2015-06-24)

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Minor changes

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+ 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.

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Bug fixes

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+ 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.
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mkin 0.9-36 (2015-06-21)

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+ mkin 0.9-36 (2015-06-21)

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Major changes

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+ 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.

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Minor changes

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+ Minor changes

  • Added a simple showcase vignette with an evaluation of FOCUS example dataset D
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mkin 0.9-35 (2015-05-15)

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

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Major changes

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+ Major changes

  • Switch from RUnit to testthat for testing
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Bug fixes

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+ 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

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New features

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+ 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

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mkin 0.9-34 (2014-11-22)

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

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New features

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+ 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.

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Minor changes

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+ Minor changes

  • 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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+ mkin 0.9-33 (2014-10-22)

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New features

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+ 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

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Bug fixes

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+ 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

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Minor changes

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+ 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.

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mkin 0.9-32 (2014-07-24)

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+ mkin 0.9-32 (2014-07-24)

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New features

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+ 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.

    • @@ -265,7 +311,8 @@

  • 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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+ 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.

    • @@ -273,32 +320,39 @@

  • 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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+ 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.

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mkin 0.9-31 (2014-07-14)

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+ mkin 0.9-31 (2014-07-14)

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Bug fixes

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+ 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)

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+ mkin 0.9-30 (2014-07-11)

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New features

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+ New features

  • 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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+ 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.

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Minor changes

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+ 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.

    • @@ -307,20 +361,23 @@

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

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mkin 0.9-29 (2014-06-27)

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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)

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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)

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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

    • @@ -339,14 +396,16 @@

  • 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

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mkin 0.9-24 (2013-11-06)

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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)

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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

    • @@ -360,32 +419,33 @@

  • 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

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