From 3a6b9f52c74d6ef88a8d32c50e42864b3f251719 Mon Sep 17 00:00:00 2001 From: jranke Date: Thu, 15 Mar 2012 15:54:14 +0000 Subject: Update kinfit and mkin to the latest version published on BerliOS. git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/kinfit@17 edb9625f-4e0d-4859-8d74-9fd3b1da38cb --- man/kinfit.Rd | 8 ++++++-- man/kinobject.Rd | 2 +- man/kinobjects.Rd | 2 +- man/kinplot.Rd | 4 +++- man/kinreport.Rd | 11 +++++++++-- man/kinresplot.Rd | 2 +- man/kinresults.Rd | 9 ++++++++- man/kinwrite.KinGUI.Rd | 2 +- 8 files changed, 30 insertions(+), 10 deletions(-) (limited to 'man') diff --git a/man/kinfit.Rd b/man/kinfit.Rd index f0301fd..2e2ceb2 100644 --- a/man/kinfit.Rd +++ b/man/kinfit.Rd @@ -9,12 +9,12 @@ Fit kinetic models to chemical degradation data 2006 are fitted to a given dataframe of chemical degradation data. } \usage{ -kinfit(kindata, kinmodels = c("SFO"), parent.0.user = NA, +kinfit(kindata, kinmodels = c("SFO"), parent.0.user = NA, parent.0.fixed = FALSE, start.SFO = list(parent.0 = NA, k = NA), start.FOMC = list(parent.0 = NA, alpha = NA, beta = NA), start.DFOP = list(parent.0 = NA, k1 = NA, k2 = NA, g = NA), start.HS = list(parent.0 = NA, k1 = NA, k2 = NA, tb = NA), - algorithm = "port") + algorithm = "default") } \arguments{ \item{kindata}{ @@ -30,6 +30,10 @@ kinfit(kindata, kinmodels = c("SFO"), parent.0.user = NA, The user can give a starting estimate for parent.0 here, overriding other potential sources for starting values as specified below. } + \item{parent.0.fixed}{ + If TRUE, the initial value for the observed value will be fixed to the + value specified by \code{parent.0.user}. + } \item{start.SFO}{ A list of starting parameters for fitting the \code{\link{SFO}} model, containing \code{parent.0} and \code{k}. diff --git a/man/kinobject.Rd b/man/kinobject.Rd index cd6f0ca..c5c5f77 100644 --- a/man/kinobject.Rd +++ b/man/kinobject.Rd @@ -15,7 +15,7 @@ Function to initialise an object representing a kinetic experiment or trial. \item{type}{ The type of experiment or trial, optionally with an ID } \item{system}{ System name. Important if several systems were used, e.g. several soils. } \item{layers}{ Optional specification of the layer names in a field trial. } - \item{sampling_times}{ Optional specification of the sampling time pionts. } + \item{sampling_times}{ Optional specification of the sampling time points. } } \value{ A list containing the specified information. diff --git a/man/kinobjects.Rd b/man/kinobjects.Rd index 7c960f3..cbc46aa 100644 --- a/man/kinobjects.Rd +++ b/man/kinobjects.Rd @@ -15,7 +15,7 @@ Function to initialise several objects representing a kinetic experiment or tria \item{type}{ The type of experiment or trial, optionally with an ID } \item{systems}{ An array of the system names } \item{layers}{ Optional specification of the layer names in a field trial. } - \item{sampling_times}{ Optional specification of the sampling time pionts. } + \item{sampling_times}{ Optional specification of the sampling time points. } } \value{ A list of lists containing the specified information. diff --git a/man/kinplot.Rd b/man/kinplot.Rd index b6974ee..eb6363a 100644 --- a/man/kinplot.Rd +++ b/man/kinplot.Rd @@ -8,7 +8,7 @@ Creates a plot of the kinetic fits Function to create a plot for a set of fitted models } \usage{ -kinplot(kinobject, xlab = "Time [days]", ylab = "Parent [\% of applied radioactivity]", ylim = c("auto", "auto"), lpos = "topright") +kinplot(kinobject, main = "", xlab = "Time [days]", ylab = "Parent [\% of applied radioactivity]", ylim = c("auto", "auto"), lpos = "topright") } \arguments{ \item{kinobject}{ @@ -17,6 +17,7 @@ kinplot(kinobject, xlab = "Time [days]", ylab = "Parent [\% of applied radioacti the type of the test system (\code{type}), the name of the specific test system used for generating this dataset (\code{system}), + the input dataset (\code{data}), the list of fitted kinetic models (\code{fits}), as returned by \code{\link{kinfit}}, and the list of results (\code{results}) as returned by \code{\link{kinresults}}. @@ -25,6 +26,7 @@ kinplot(kinobject, xlab = "Time [days]", ylab = "Parent [\% of applied radioacti Optionally also the label position of the test compound (\code{label}) and the source of the data (\code{source}). } + \item{main}{ Title. } \item{xlab}{ Label for the x axis. } \item{ylab}{ Label for the y axis. } \item{ylim}{ An array of length two holding the range for values on the y axis or "auto". } diff --git a/man/kinreport.Rd b/man/kinreport.Rd index de7e632..f1b8111 100644 --- a/man/kinreport.Rd +++ b/man/kinreport.Rd @@ -9,7 +9,7 @@ Function to create a report for a set of fitted models, passing it to the console as well as to a file, if specified. } \usage{ -kinreport(kinobject, file = NA, vcov = FALSE, endpoint.digits = 1) +kinreport(kinobject, file = NA, data = TRUE, R2 = FALSE, vcov = FALSE, endpoint.digits = 1) } \arguments{ \item{kinobject}{ @@ -18,6 +18,7 @@ kinreport(kinobject, file = NA, vcov = FALSE, endpoint.digits = 1) the type of the test system (\code{type}), the name of the specific test system used for generating this dataset (\code{system}), + the input dataset (\code{data}), the list of fitted kinetic models (\code{fits}), as returned by \code{\link{kinfit}}, and the list of results (\code{results}) as returned by \code{\link{kinresults}}. @@ -25,12 +26,17 @@ kinreport(kinobject, file = NA, vcov = FALSE, endpoint.digits = 1) the label position of the test compound (\code{label}) and the source of the data (\code{source}). } \item{file}{ The name of the file to which to write. } + \item{data}{ Boolean specifying if the input data should be printed? } + \item{R2}{ Boolean specifying if the coefficient of determination R2 should + be printed. R2 is calculated from all values (not mean values) as 1 - RSS/TSS where + RSS is the sum of squares of residuals, and TSS ist the total sum of squares, i.e. + the sum of squares of the difference of each observation from the overall mean. } \item{vcov}{ Should the variance-covariance matrix/matrices be reported? } \item{endpoint.digits}{ How many digits should be reported for DT50 and DT90 values? } } \value{ The function is called for its side effect, namely the report being passed -to the R console as well as to a text file. +to the R console as well as to a text file if a filename is specified. } \author{ Johannes Ranke } \examples{ @@ -40,6 +46,7 @@ kinobject <- list( parent = "Compound XY", type = "Degradation in the environment", system = "System 1", + data = FOCUS_2006_A, source = "Synthetic example data from FOCUS kinetics", fits = kinfits, results = kinresults(kinfits)) diff --git a/man/kinresplot.Rd b/man/kinresplot.Rd index 85ec333..fcf0561 100644 --- a/man/kinresplot.Rd +++ b/man/kinresplot.Rd @@ -8,7 +8,7 @@ Creates a plot of the residual for specified kinetic fits Function to create a residual plot for a specified fitted model } \usage{ -kinresplot(kinobject, kinmodel, xlab = "Time [days]", ylab = "Residual [\% of applied radioactivity]", maxabs = "auto") + kinresplot(kinobject, kinmodel, xlab = "Time [days]", ylab = "Residual [\% of applied radioactivity]", maxabs = "auto") } \arguments{ \item{kinobject}{ diff --git a/man/kinresults.Rd b/man/kinresults.Rd index 6ab93a7..9e5bc43 100644 --- a/man/kinresults.Rd +++ b/man/kinresults.Rd @@ -9,7 +9,7 @@ This function collects the parameters and some statistics for the fitted kinetic models. It also generates DT50 and DT90 estimates. } \usage{ -kinresults(kinfits, alpha = 0.05, SFORB = TRUE) +kinresults(kinfits, alpha = 0.05, DTmax = 1000, SFORB = TRUE) } \arguments{ \item{kinfits}{ @@ -19,6 +19,13 @@ have been generated by \code{\link{kinfit}}. \item{alpha}{ The confidence level chosen for the chi-squared test used in the call to \code{\link{kinerrmin}}. +} + \item{DTmax}{ +Upper end of the time interval that will be checked for the iterative determination +of DT50 and DT90 values for the FOMC and the DFOP model. If the DT50 or the +DT90 value is less than 0.1 different from \code{DTmax}, which will generally +be the case if the optimization routine hits the upper end, the respective DT50 or +DT90 value will be reported as \code{NA}. } \item{SFORB}{ Should the results of the \code{\link{DFOP}} model be presented as parameters diff --git a/man/kinwrite.KinGUI.Rd b/man/kinwrite.KinGUI.Rd index f5a5ddc..c0910cf 100644 --- a/man/kinwrite.KinGUI.Rd +++ b/man/kinwrite.KinGUI.Rd @@ -35,7 +35,7 @@ An optional comment that will be integrated in the header of the KinGUI input fi The function is called for its side effect, namely the generation of a text file. } \references{ -Schäfer D, Kikolasch M, Rainbird P and Harvey B (2007). KinGUI: a new kinetic software tool for evaluations according to FOCUS degradation kinetics. In: Del Re AAM, Capri E, Fragoulis G and Trevisan M (Eds.). Proceedings of the XIII Symposium Pesticide Chemistry, Piacenza, 2007, p. 916-923. +Schäfer D, Mikolasch M, Rainbird P and Harvey B (2007). KinGUI: a new kinetic software tool for evaluations according to FOCUS degradation kinetics. In: Del Re AAM, Capri E, Fragoulis G and Trevisan M (Eds.). Proceedings of the XIII Symposium Pesticide Chemistry, Piacenza, 2007, p. 916-923. } \note{ The KinGUI software tool was announced to be freely available on CD from the main author of the paper cited above, Dieter Schäfer . -- cgit v1.2.1