- mkin 0.9.45.1 (2016-12-20)

+mkin 0.9.45.1 (2016-12-20)

- New features

+New features

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

@@ -113,10 +118,10 @@

- mkin 0.9.45 (2016-12-08)

+mkin 0.9.45 (2016-12-08)

- Minor changes

+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.

- mkin 0.9.44 (2016-06-29)

+mkin 0.9.44 (2016-06-29)

- Bug fixes

+Bug fixes

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

@@ -137,10 +142,10 @@

- mkin 0.9.43 (2016-06-28)

+mkin 0.9.43 (2016-06-28)

- Major changes

+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

- Minor changes

+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Remove an outdated reference to the inline package in the compiled_models vignette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.

- Bug fixes

+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.

- mkin 0.9.42 (2016-03-25)

+mkin 0.9.42 (2016-03-25)

- Major changes

+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

+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

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

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

- Minor changes

+Minor changes

Add an R6 class mkinds representing datasets with a printing method
Add a printing method for mkinmod objects

- Bug fixes

+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)

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

- Bug fixes

+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

+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)

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

- Major changes

+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

+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)

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

- Minor changes

+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

+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)

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

- Major changes

+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.

- Minor changes

+Minor changes

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

@@ -298,17 +303,17 @@

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

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

- Major changes

+Major changes

Switch from RUnit to testthat for testing

- Bug fixes

+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

- New features

+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.

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

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

- New features

+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.

- Minor changes

+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)

+mkin 0.9-33 (2014-10-22)

- New features

+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

+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.

- Minor changes

+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

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

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

- New features

+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.

- Bug fixes

+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.

- Minor changes

+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.

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

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

- Bug fixes

+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.

@@ -429,17 +434,17 @@

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

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

- New features

+New features

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

- Major changes

+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

+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.

- mkin 0.9-29 (2014-06-27)

+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

- mkin 0.9-28 (2014-05-20)

+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

- mkin 0.9-27 (2014-05-10)

+mkin 0.9-27 (2014-05-10)

Fork the GUI into a separate package gmkin
DESCRIPTION, NAMESPACE, TODO: Adapt and add copyright information

- mkin 0.9-24 (2013-11-06)

+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

- mkin 0.9-22 (2013-10-26)

+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