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

8 files changed, 30 insertions, 10 deletions

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}{

@@ -20,6 +20,13 @@ have been generated by \code{\link{kinfit}}.
 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

 to the Single First-Order Reversible Binding (SFORB) model? }

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 <dieter.schaefer@bayercropscience.com>.