Added the drfit-package help page, a new sample data file

and a preliminary version of the drfit-Rnews article.

R/drfit.R
- the possibility to directly write pdf graphs was added
- the results dataframe now has numbered lines where it didn't

The checkplate and checksubstance functions are now classified
internal in their help files.



git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@57 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc

11 files changed, 133 insertions, 49 deletions

diff --git a/DESCRIPTION b/DESCRIPTION
index f1277e1..11639f2 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: drfit
-Version: 0.04-56
-Date: 2006-02-27
+Version: 0.04-57
+Date: 2006-03-04
 Title: Dose-response data evaluation
 Author: Johannes Ranke <jranke@uni-bremen.de>
 Maintainer: Johannes Ranke <jranke@uni-bremen.de>
diff --git a/R/drfit.R b/R/drfit.R
index 1488cd4..3a9535a 100644
--- a/R/drfit.R
+++ b/R/drfit.R
@@ -48,8 +48,8 @@ drfit <- function(data, startlogED50 = NA, chooseone=TRUE,
         linlogit = FALSE, linlogitWrong = NA, allWrong = NA,
         s0 = 0.5, b0 = 2, f0 = 0)
 {
-    if(!is.null(data$ok)) data <- subset(data,ok!="no fit") # Don't use data where ok 
-                                                            # was set to "no fit"
+    if(!is.null(data$ok)) data <- subset(data,ok!="no fit") # Don't use data with 
+                                                            # ok set to "no fit"
     substances <- levels(data$substance)
 
     ri <- rix <- 0                        # ri is the index over the result rows
@@ -57,7 +57,8 @@ drfit <- function(data, startlogED50 = NA, chooseone=TRUE,
                                           # model result was appended
     rsubstance <- array()                 # the substance names in the results
     rndl <- vector()                      # number of dose levels
-    rn <- vector()                        # mean number of replicates in each dose level
+    rn <- vector()                        # mean number of replicates 
+                                          # in each dose level
     runit <- vector()                     # vector of units for each result row
     rlhd <- rlld <- vector()              # highest and lowest doses tested
     mtype <- array()                      # the modeltypes
@@ -292,13 +293,15 @@ drfit <- function(data, startlogED50 = NA, chooseone=TRUE,
     if (linlogit) {
         results$c <- c
     }
+    rownames(results) <- 1:ri
     return(results)
 }
 
 drplot <- function(drresults, data, 
         dtype = "std", alpha = 0.95, ctype = "none",
         path = "./", fileprefix = "drplot", overlay = FALSE,
-        postscript = FALSE, png = FALSE, bw = TRUE,
+        postscript = FALSE, png = FALSE, pdf = FALSE, 
+        bw = TRUE,
         pointsize = 12,
         colors = 1:8, devoff=T, lpos="topright")
 {
@@ -353,13 +356,19 @@ drplot <- function(drresults, data,
                     paper="special",width=7,height=7,horizontal=FALSE, pointsize=pointsize)
             cat("Created File: ",filename,"\n")
         } 
+        if (pdf) {
+            filename = paste(path,fileprefix,".pdf",sep="")
+            pdf(file=filename,
+                    paper="special",width=7,height=7,horizontal=FALSE, pointsize=pointsize)
+            cat("Created File: ",filename,"\n")
+        } 
         if (png) {
             filename = paste(path,fileprefix,".png",sep="")
             png(filename=filename,
                 width=500, height=500, pointsize=pointsize)
             cat("Created File: ",filename,"\n")
         }
-        if (!postscript && !png) {
+        if (!postscript && !png && !pdf) {
             get(getOption("device"))(width=7,height=7)
         }
             
@@ -391,13 +400,19 @@ drplot <- function(drresults, data,
                                 paper="special",width=7,height=7,horizontal=FALSE,pointsize=pointsize)
                         cat("Created File: ",filename,"\n")
                     } 
+                    if (pdf) {
+                        filename = paste(path,fileprefix,sub(" ","_",i),".pdf",sep="")
+                        pdf(file=filename,
+                                paper="special",width=7,height=7,horizontal=FALSE,pointsize=pointsize)
+                        cat("Created File: ",filename,"\n")
+                    } 
                     if (png) {
                         filename = paste(path,fileprefix,sub(" ","_",i),".png",sep="")
                         png(filename=filename,
                             width=500, height=500, pointsize=pointsize)
                         cat("Created File: ",filename,"\n")
                     }
-                    if (!postscript && !png) {
+                    if (!postscript && !png && !pdf) {
                          get(getOption("device"))(width=7,height=7)
                     }
                         
@@ -484,14 +499,14 @@ drplot <- function(drresults, data,
                         }
                     }
                 }
-                if (!overlay && (postscript || png)) dev.off()
+                if (!overlay && (postscript || png || pdf)) dev.off()
             } else {
                 cat("No data for ",i,"\n")
             }
         }
     }
     if (overlay) legend(lpos, dsubstances,lty = 1, col = colors, inset=0.05)
-    if (overlay && (postscript || png)) {
+    if (overlay && (postscript || png || pdf)) {
         if (devoff) {
             dev.off()
         }
diff --git a/data/XY.rda b/data/XY.rda
new file mode 100644
index 0000000..158285a
--- /dev/null
+++ b/data/XY.rda
diff --git a/inst/doc/drfit-Rnews.pdf b/inst/doc/drfit-Rnews.pdf
new file mode 100644
index 0000000..6abbcaf
--- /dev/null
+++ b/inst/doc/drfit-Rnews.pdf
diff --git a/inst/doc/index.html b/inst/doc/index.html
new file mode 100644
index 0000000..efdd9bd
--- /dev/null
+++ b/inst/doc/index.html
@@ -0,0 +1,15 @@
+<html>
+<head>
+	<title>R: drfit User Guide</title>
+	<link rel="stylesheet" type="text/css" href="../../R.css">
+</head>
+<body>
+
+<h2>User Guide for package drfit</h2>
+<dl>
+	<dt><a href="drfit-Rnews.pdf">drfit-Rnews.pdf</a>:</dt>
+	<dd> Introductory article on drfit</dd>
+</dl>
+
+</body>
+</html>
diff --git a/man/XY.Rd b/man/XY.Rd
new file mode 100644
index 0000000..ae28e99
--- /dev/null
+++ b/man/XY.Rd
@@ -0,0 +1,16 @@
+\name{XY}
+\docType{data}
+\alias{XY}
+\title{Dose-Response data for two substances X and Y}
+\description{
+  This is just a sample data set for two substances named X and Y.
+}
+\usage{data(antifoul)}
+\format{
+  A dataframe containing dose (concentration) and response data, as well as
+  control values where the dose is zero.
+}
+\source{
+  \url{http://www.uft.uni-bremen.de/chemie}
+}
+\keyword{datasets}
diff --git a/man/checkplate.Rd b/man/checkplate.Rd
index 39eea85..794b3f6 100644
--- a/man/checkplate.Rd
+++ b/man/checkplate.Rd
@@ -30,3 +30,4 @@
   \url{http://www.uft.uni-bremen.de/chemie/ranke}
 }
 \keyword{database}
+\keyword{internal}
diff --git a/man/checksubstance.Rd b/man/checksubstance.Rd
index 3871a87..59759e8 100644
--- a/man/checksubstance.Rd
+++ b/man/checksubstance.Rd
@@ -43,3 +43,4 @@
   \url{http://www.uft.uni-bremen.de/chemie/ranke}
 }
 \keyword{database}
+\keyword{internal}
diff --git a/man/drfit-package.Rd b/man/drfit-package.Rd
new file mode 100644
index 0000000..ac91a35
--- /dev/null
+++ b/man/drfit-package.Rd
@@ -0,0 +1,29 @@
+\name{drfit-package}
+\alias{drfit-package}
+\docType{package}
+\title{
+Dose-response data evaluation
+}
+\description{
+See \url{../DESCRIPTION}
+}
+\details{
+There is an introductory article located in \url{../doc/drfit-Rnews.pdf}.
+}
+\author{
+Author and Maintainer: Johannes Ranke <jranke@uni-bremen.de>
+}
+\keyword{ package }
+\keyword{ models }
+\keyword{ regression }
+\keyword{ nonlinear }
+\seealso{
+There is another, more sophisticated package with similar functionality
+called \code{\link[drc:drc-package]{drc}
+}
+\examples{
+data(antifoul)
+r <- drfit(antifoul)
+format(r,digits=2)
+\dontrun{drplot(r,antifoul,overlay=TRUE,bw=FALSE)}
+}
diff --git a/man/drfit.Rd b/man/drfit.Rd
index bbe7496..6e9ef47 100644
--- a/man/drfit.Rd
+++ b/man/drfit.Rd
@@ -12,17 +12,17 @@
 }
 \arguments{
   \item{data}{
-    A data frame containing dose-response data. The data frame has to
-    contain at least a factor called "substance", a numeric vector "dose" with
-    the dose values, a vector called "unit" containing the unit used for the
-    dose and a numeric vector "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}}.  
+	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 "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.
+	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{startlogED50}{
     Especially for the linlogit model, a suitable log10 of the ED50 has to be given 
@@ -64,32 +64,34 @@
 }
 \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 "inactive". If the mean response at the lowest dose
-      is smaller than 0.5, the modeltype is set to "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
-      rounded mean of the number of replicates at each dose level in the raw
-      data, \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 logED50, i.e the logED50 is 
-      one of the model parameters that is being fitted, and therefore
-      a standard deviation \code{std} is reported for the logED50. 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.}
-  } 
+	  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
+	  rounded mean of the number of replicates at each dose level in the raw
+	  data, \code{lld} is the decadic logarithm of the lowest dose and
+	  \code{lhd} is the decadic logarithm of the highest dose.  For the
+	  \dQuote{linlogit}, \dQuote{logit} and \dQuote{probit} models, the
+	  parameter \code{a} that is reported coincides with the logED50, i.e the
+	  logED50 is one of the model parameters that is being fitted, and
+	  therefore a standard deviation \code{std} is reported for the logED50. In
+	  the case of the \dQuote(weibull) model, \code{a} is a location parameter.
+	  Parameter \code{b} in the case of the \dQuote(linlogit) fit is the
+	  variable b from the \code{\link{linlogitf}} function. In the case of
+	  \dQuote(probit) fit it is the standard deviation of the fitted normal
+	  distribution, in the case of the \dQuote(logit) fit it is the
+	  \code{scale} parameter in the \code{\link{plogis}} function, and in the
+	  \dQuote(weibull) fit it is the \code{shape} parameter of the fitted
+	  \code{\link{pweibull}} function. Only the \dQuote(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 99f77ab..09a8517 100644
--- a/man/drplot.Rd
+++ b/man/drplot.Rd
@@ -53,13 +53,18 @@
     }
   \item{postscript}{
     If TRUE, (a) postscript graph(s) will be created. Otherwise, and if 
-    the png argument is also FALSE, graphics will be
+    the pdf and png arguments are also FALSE, graphics will be
+    displayed with a screen graphics device.
+    }
+  \item{pdf}{
+    If TRUE, (a) pdf graph(s) will be created. Otherwise, and if 
+    the postscript and png arguments are also FALSE, graphics will be
     displayed with a screen graphics device.
     }
   \item{png}{
     If TRUE, (a) png graph(s) will be created. Otherwise, and if the
-    postscript argument is also FALSE, graphics will be displayed with a
-    screen graphics device.
+	postscript and pdf arguments are also FALSE, graphics will be displayed
+	with a screen graphics device.
     }
   \item{bw}{
     A boolean deciding if the plots will be black and white or not. Default