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-rw-r--r--man/kinfit.Rd8
-rw-r--r--man/kinobject.Rd2
-rw-r--r--man/kinobjects.Rd2
-rw-r--r--man/kinplot.Rd4
-rw-r--r--man/kinreport.Rd11
-rw-r--r--man/kinresplot.Rd2
-rw-r--r--man/kinresults.Rd9
-rw-r--r--man/kinwrite.KinGUI.Rd2
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>.

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