Feature-complete version of the new drfit package that can make use

of the drc package in order to obtain confidence intervals for EDx values.

See ChangeLog for details.



git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@98 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc

6 files changed, 149 insertions, 4 deletions

diff --git a/man/IM1xIPC81.Rd b/man/IM1xIPC81.Rd
index 4f5a1dd..dda0c3b 100644
--- a/man/IM1xIPC81.Rd
+++ b/man/IM1xIPC81.Rd
@@ -21,7 +21,12 @@
   the tested organism (name of the cell line).
 }
 \examples{
-  \dontrun{demo(IM1xIPC81)}
+  rIM1xIPC81 <- drfit(IM1xIPC81, linlogit = TRUE, showED50 = TRUE, EDx = 10)
+
+  rIM1xIPC81.drc <- drcfit(IM1xIPC81, linlogit = TRUE, showED50 = TRUE, EDx = 10)
+
+  print(rIM1xIPC81,digits=4)
+  print(rIM1xIPC81.drc,digits=4)
 }
 \source{
   Ranke J, Mölter K, Stock F, Bottin-Weber U, Poczobutt J,
diff --git a/man/IM1xVibrio.Rd b/man/IM1xVibrio.Rd
index 5315432..cb0bd48 100644
--- a/man/IM1xVibrio.Rd
+++ b/man/IM1xVibrio.Rd
@@ -19,7 +19,13 @@
   regarded valid (\code{ok}).
 }
 \examples{
-  \dontrun{demo(IM1xVibrio)}
+  rIM1xVibrio <- drfit(IM1xVibrio, logit = TRUE, chooseone = FALSE,
+                       showED50 = TRUE, EDx = c(10, 20))
+  print(rIM1xVibrio, digits = 4)
+
+  rIM1xVibrio.drc <- drcfit(IM1xVibrio, logit = TRUE, chooseone = FALSE,
+                            showED50 = TRUE, EDx = c(10, 20))
+  print(rIM1xVibrio.drc, digits = 4)
 }
 \source{
   Ranke J, Mölter K, Stock F, Bottin-Weber U, Poczobutt J, Hoffmann J,
diff --git a/man/antifoul.Rd b/man/antifoul.Rd
index 2aa532e..21ae885 100644
--- a/man/antifoul.Rd
+++ b/man/antifoul.Rd
@@ -15,8 +15,19 @@
   database are also present.
 }
 \examples{
-  \dontrun{demo(antifoul)}
+rantifoul.ED50 <- drfit(antifoul, 
+                        linlogit = TRUE, logit = TRUE, weibull = TRUE,
+                        chooseone = FALSE, 
+                        showED50 = TRUE, EDx = c(10))
+print(rantifoul.ED50, digits = 5)
+
+rantifoul.drc <- drcfit(antifoul, 
+                        linlogit = TRUE, logit = TRUE, weibull = TRUE,
+                        chooseone = FALSE, 
+                        showED50 = TRUE, EDx = c(10))
+print(rantifoul.drc, digits = 5)
 }
+
 \source{
   \url{http://www.uft.uni-bremen.de/chemie}
 }
diff --git a/man/drcfit.Rd b/man/drcfit.Rd
new file mode 100644
index 0000000..2da0418
--- /dev/null
+++ b/man/drcfit.Rd
@@ -0,0 +1,110 @@
+\name{drcfit}
+\alias{drcfit}
+\title{Fit dose-response models using the drc package}
+\description{
+  Fit dose-response relationships to dose-response data and calculate
+  biometric results for (eco)toxicity evaluation using the drc package
+}
+\usage{
+  drcfit(data, chooseone = TRUE, probit = TRUE, logit = FALSE,
+  weibull = FALSE, linlogit = FALSE, level = 0.95, 
+  showED50 = FALSE, EDx = NULL)
+}
+\arguments{
+  \item{data}{
+    A data frame containing dose-response data. The data frame has to contain
+    at least a factor called \dQuote{substance}, a numeric vector \dQuote{dose}
+    with the dose values, a vector called \dQuote{unit} containing the unit
+    used for the dose and a numeric vector \dQuote{response} with the response
+    values of the test system normalized between 0 and 1. Such a data frame can
+    be easily obtained if a compliant RODBC data source is available for use in
+    conjunction with the function \code{\link{drdata}}.
+
+    If there is a column called \dQuote{ok} and it is set to \dQuote{no fit} in
+    a specific line, then the corresponding data point will be excluded from
+    the fitting procedure, although it will be plotted.}
+  \item{probit}{
+    A boolean defining if cumulative density curves of normal distributions
+    \code{\link{pnorm}} are fitted against the decadic logarithm of the dose.
+    Default ist TRUE.
+    Note that the parameter definitions used in the model are different to the
+    ones used in \code{\link{drfit}}. Parameter e from \code{\link{LN.2}} is listed
+    as a here, and parameter b from LN.2 is listed as b.}
+  \item{logit}{
+    A boolean defining if cumulative density curves of logistic distributions
+    \code{\link{plogis}} are fitted to the decadic logarithm of the dose.
+    Default is FALSE.
+    Again the parameter definitions used in the model are different to the
+    ones used in \code{\link{drfit}}. Parameter e from \code{\link{LL.2}} is listed
+    as a here, and parameter b from LL.2 is listed as b.}
+  \item{weibull}{
+    A boolean defining if Weibull dose-response models
+    (\code{\link{W1.2}} are fitted to the untransformed dose. Default is FALSE.
+    Note that the results differ from the ones obtained with
+    \code{\link{drfit}}, due to a different model specification.}
+  \item{linlogit}{
+    A boolean defining if the linear-logistic function
+    \code{\link{linlogitf}} as defined by van Ewijk and Hoekstra 1993 is
+    fitted to the data. Default is FALSE. Obtaining the ED50 (and EDx values
+    in general) uses \code{\link{ED}} internally and does not always give a
+    result.
+  }
+  \item{level}{
+    The level for the confidence interval listed for the log ED50.}
+  \item{chooseone}{
+    If TRUE (default), the models are tried in the order linlogit, probit,
+    logit, weibull, and the first model that produces a valid fit is used.
+    If FALSE, all models that are set to TRUE and that can be fitted will be
+    reported.}
+  \item{EDx}{
+    A vector of inhibition values x in percent for which the corresponding doses
+    EDx should be reported.
+  }
+  \item{showED50}{
+    If set to TRUE, the ED50 and its confidence interval on the original dose
+    scale (not log scale) is included in the output.
+  }
+}
+\value{
+  \item{results}{
+    A data frame containing at least one line for each substance. If the data
+    did not show a mean response < 0.5 at the highest dose level, the
+    modeltype is set to \dQuote{inactive}. If the mean response at the lowest
+    dose is smaller than 0.5, the modeltype is set to \dQuote{active}. In
+    both cases, no fitting procedure is carried out.  Every successful fit is
+    reported in one line. Parameters of the fitted curves are only reported
+    if the fitted ED50 is not higher than the highest dose. 
+
+    \code{ndl} is the number of dose levels in the raw data, \code{n} is the
+    total number of data points in the raw data used for the fit
+    \code{lld} is the decadic logarithm of the lowest dose and
+    \code{lhd} is the decadic logarithm of the highest dose.
+ 
+    If the parameter \code{showED50} was set to TRUE, the ED50 values and their
+    confidence intervals are also included on the original dose scale.
+
+    If one or more response leves were specified in the argument \code{EDx},
+    the corresponding dose levels are given, together with their confidence
+    intervals.
+  }
+}
+\examples{
+data(antifoul)
+r <- drcfit(antifoul, showED50 = TRUE, EDx = c(5, 10, 20))
+format(r, digits = 2)
+}
+\note{There is a demo for each dataset that can be accessed by
+  \code{demo(dataset)}} 
+\seealso{
+  Further examples are given in help pages to the datasets
+  \code{\link{antifoul}}, \code{\link{IM1xIPC81}} and
+  \code{\link{IM1xVibrio}}.
+}
+\author{
+  Johannes Ranke 
+  \email{jranke@uni-bremen.de} 
+  \url{http://www.uft.uni-bremen.de/chemie/ranke}
+}
+\keyword{models}
+\keyword{regression}
+\keyword{nonlinear}
diff --git a/man/drfit.Rd b/man/drfit.Rd
index 7237404..fe84a91 100644
--- a/man/drfit.Rd
+++ b/man/drfit.Rd
@@ -114,6 +114,9 @@
  
     If the parameter \code{showED50} was set to TRUE, the ED50 values and their
     confidence intervals are also included on the original dose scale.
+
+    If one or more response leves were specified in the argument \code{EDx},
+    the corresponding dose levels are given in addition.
   }
 }
 \examples{
@@ -123,6 +126,11 @@ format(r, digits = 2)
 }
 \note{There is a demo for each dataset that can be accessed by
   \code{demo(dataset)}} 
+\seealso{
+  Further examples are given in help pages to the datasets
+  \code{\link{antifoul}}, \code{\link{IM1xIPC81}} and
+  \code{\link{IM1xVibrio}}.
+}
 \author{
   Johannes Ranke 
   \email{jranke@uni-bremen.de} 
diff --git a/man/drplot.Rd b/man/drplot.Rd
index b2c2745..e9e4dd1 100644
--- a/man/drplot.Rd
+++ b/man/drplot.Rd
@@ -8,7 +8,7 @@
 \usage{
   drplot(drresults, data, dtype, alpha, ctype, path,
      fileprefix, overlay, xlim, ylim, xlab, ylab, axes, frame.plot, postscript,
-     pdf, png, bw, pointsize, colors, ltys, devoff, lpos)
+     pdf, png, bw, pointsize, colors, ltys, pchs, devoff, lpos)
 }
 \arguments{
   \item{drresults}{
@@ -99,6 +99,11 @@
   \item{ltys}{
     This is a vector of line types for the dose-response models, defaulting to 1:8.
     }
+  \item{pchs}{
+    This is a vector of character types for the data. The default uses built-in
+    characters 1:n with n being the number of substances for which data are plotted
+    for overlays, or always 1 when no overlay plot is generated.
+    }
   \item{lpos}{
     An optional argument defaulting to "topright" specifying the position
     of the legend by being passed to the legend function. See the help for the