Several changes in this revision:

- Addition of the weibull fit
- Renaming of lognorm to probit, logis to logit, and linearlogis to linlogit
- Fix of a bug that prevented the logis fit to work in recent version
- Different way of listing parameters in the output.
- Documentation of changes



git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@29 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc

3 files changed, 60 insertions, 35 deletions

diff --git a/man/drfit.Rd b/man/drfit.Rd
index 2ec4a73..0d9ee6f 100644
--- a/man/drfit.Rd
+++ b/man/drfit.Rd
@@ -6,58 +6,84 @@
   biometric results for (eco)toxicity evaluation
 }
 \usage{
-  drfit(data, startlogEC50 = NA, chooseone = TRUE, lognorm = TRUE, logis = FALSE, 
-    linearlogis = FALSE, linearlogisWrong = NA, allWrong = NA, b0 = 2, f0 = 0)
+  drfit(data, startlogEC50 = NA, chooseone = TRUE, probit = TRUE, logit = FALSE,
+    weibull = FALSE, linlogit = FALSE, linlogitWrong = NA, allWrong = NA, 
+    b0 = 2, f0 = 0)
 }
 \arguments{
   \item{data}{
-    A data frame as returned from \code{\link{drdata}}.  The data frame has to
+    A data frame containing dose-response data. The data frame has to
     contain at least a factor called "substance", a vector called "unit"
     containing the unit used for the dose, a column "response" with the
     response values of the test system normalized between 0 and 1 and a column
-    "dose" with the numeric dose values. For later use of the
-    \code{\link{drplot}} function, a factor called "dosefactor" also has to be
-    present, containing the dose as a factor. If there is a column called "ok"
-    and it is set to "no fit", then the corresponding data point will be excluded
-    from the fitting procedure.
+    "dose" with the numeric dose values. 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 "ok" and it is set to "no fit" in a specific
+    line, then the corresponding data point will be excluded from the fitting
+    procedure, although it will be plotted.
     }
   \item{startlogEC50}{
-    Especially for the linearlogis model, a suitable log10 of the EC50 has to be given 
+    Especially for the linlogit model, a suitable log10 of the EC50 has to be given 
     by the user, since it is not correctly estimated for data showing hormesis with
     the default estimation method.}
-  \item{lognorm}{
+  \item{probit}{
     A boolean defining if cumulative density curves of normal distributions
-    are fitted to the data. Default ist TRUE.} 
-  \item{logis}{
-    A boolean defining if cumulative densitiy curves of logistic distributions
-    are fitted to the data. Default is FALSE.} 
-  \item{linearlogis}{
+    \code{\link{pnorm}} are fitted against the decadic logarithm of the dose.
+    Default ist TRUE.} 
+  \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.} 
+  \item{weibull}{
+    A boolean defining if the cumulative density curves of weibull distributions
+    (\code{\link{pweibull}} with additionall location parameter and scale=1)
+    are fitted to the decadic logarithm of the dose. Default is FALSE.}
+  \item{linlogit}{
     A boolean defining if the linear-logistic function
-    \code{\link{linearlogisf}} as defined by van Ewijk and Hoekstra 1993 is
+    \code{\link{linlogitf}} as defined by van Ewijk and Hoekstra 1993 is
     fitted to the data. Default is FALSE.}
-  \item{linearlogisWrong}{
+  \item{linlogitWrong}{
     An optional vector containing the names of the substances for which the
-    linearlogis function produces a wrong fit.}
+    linlogit function produces a wrong fit.}
   \item{allWrong}{
     An optional vector containing the names of the substances for which all
-    functions produces a wrong fit.}
+    functions produce a wrong fit.}
   \item{chooseone}{
-    If TRUE (default), the models are tried in the order linearlogis, logis and lognorm,
-    and the first model that produces a valid fit is used. Usually this will be the one 
-    with the lowest residual standard deviation. If FALSE, all models that are set to TRUE
-    and that can be fitted will be reported.}
+    If TRUE (default), the models are tried in the order linlogit, weibull,
+    logit, probit, 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{b0,f0}{
     If the linearlogistic model is fitted, b0 and f0 give the possibility to
     adapt the starting values for the parameters b and f.}
 }
 \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 "none".
-      Every successful fit is reported in one line. Parameters of the fitted curves are only
-      reported if the fitted EC50 is not higher than the highest dose.}
-    
-} 
+      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 "none".
+      Every successful fit is reported in one line. Parameters of the fitted
+      curves are only reported if the fitted EC50 is not higher than the
+      highest dose. 
+      \code{n} is the number of dose-response curves in the raw data (repetitions
+      in each point), \code{lld} is the decadic logarithm of the lowest dose and
+      \code{lhd} is the decadic logarithm of the highest dose.
+      For the "linlogit", "logit" and "probit" models, the parameter
+      \code{a} that is reported coincides with the logEC50, i.e the logEC50 is 
+      one of the model parameters that is being fitted, and therefore
+      a standard deviation \code{std} is reported for the logEC50. In the 
+      case of the "weibull" model, \code{a} is a location parameter.
+      Parameter \code{b} in the case of the "linlogit" fit is the variable
+      b from the \code{\link{linlogitf}} function. In the case of "probit" fit
+      it is the standard deviation of the fitted normal distribution, in the case
+      of the "logit" fit it is the \code{scale} parameter in the \code{\link{plogis}}
+      function, and in the "weibull" fit it is the \code{shape} parameter of the
+      fitted \code{\link{pweibull}} function. Only the "linlogit" fit produces a 
+      third parameter \code{c} which is the variable f from the
+      \code{\link{linlogitf}} function.}
+  } 
 \examples{
 data(antifoul)
 r <- drfit(antifoul)
diff --git a/man/drplot.Rd b/man/drplot.Rd
index ecd6895..e5201a2 100644
--- a/man/drplot.Rd
+++ b/man/drplot.Rd
@@ -80,9 +80,8 @@
     
 } 
 \note{
-  Treatment of legends is not really well solved. Be sure all devices are
-  closed (e.g. by calling \code{dev.off()}) before calling \code{drplot}
-  again after a failure.
+  Be sure all devices are closed (e.g. by calling \code{dev.off()}) before
+  calling \code{drplot} again after a failure.
 }
 \examples{
 data(antifoul)
diff --git a/man/linearlogisf.Rd b/man/linlogitf.Rd
index 1ebe8be..2eca8c4 100644..100755
--- a/man/linearlogisf.Rd
+++ b/man/linlogitf.Rd
@@ -1,12 +1,12 @@
-\name{linearlogisf}
-\alias{linearlogisf}
+\name{linlogitf}
+\alias{linlogitf}
 \title{Linear-logistic function}
 \description{
   Helper function describing a special type of dose-response curves, showing a stimulus
   at subtoxic doses.
 }
 \usage{
-  linearlogisf(x,k,f,mu,b)
+  linlogitf(x,k,f,mu,b)
 }
 \arguments{
   \item{x}{