Now the weibull model has an automatic choice of starting values, fixing a bug that prevented

fitting the weibull function in most cases in the last version. Also, the log EC50 is reported
as estimated with nlm from the fitted weibull model. Because of the important changes, mainly 
in naming the different models which leads to incompatibility with the old drfit syntax,
I am increasing the minor version number to 0.04 with this release.



git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@30 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc

3 files changed, 20 insertions, 17 deletions

diff --git a/DESCRIPTION b/DESCRIPTION
index 6b1b85b..ce7412f 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: drfit
-Version: 0.03-29
-Date: 2005-07-16
+Version: 0.04-30
+Date: 2005-07-17
 Title: Dose-response data evaluation
 Author: Johannes Ranke <jranke@uni-bremen.de>
 Maintainer: Johannes Ranke <jranke@uni-bremen.de>
@@ -8,14 +8,15 @@ Depends: R (>= 2.1.0),stats,RODBC
 Description: drfit provides basic functions for fitting dose-response curves to
 	dose-response data, calculating some (eco)toxicological parameters and
 	plotting the results. Functions that are fitted are the cumulative densitiy
-	function of the lognormal distribution, of the logistic distribution and a
-	linear-logistic model, derived from the latter, which is used to describe
-	data showing stimulation at low doses (hormesis). In addition, functions
-	checking, plotting and retrieving dose-response data of the UFT Bremen,
-	Department of Bioorganic Chemistry, are provided. 
-	I would be delighted if you would join in this effort of creating useful
-	and useable tools for dealing with dose-response data from biological
-	testing.
+	function of the lognormal distribution (probit fit), of the logistic
+	distribution (logit fit), of the weibull distribution (weibull fit) and
+	a linear-logistic model ("linlogit" fit), derived from the latter,
+	which is used to describe data showing stimulation at low doses
+	(hormesis). In addition, functions checking, plotting and retrieving
+	dose-response data of the UFT Bremen, Department of Bioorganic
+	Chemistry, are provided.  I would be delighted if you would join in
+	this effort of creating useful and useable tools for dealing with
+	dose-response data from biological testing.
 License: GPL version 2 or newer
 URL: http://www.r-project.org, 
 	http://www.uft.uni-bremen.de/chemie/ranke,
diff --git a/R/drfit.R b/R/drfit.R
index 603cf94..527b756 100644
--- a/R/drfit.R
+++ b/R/drfit.R
@@ -39,7 +39,7 @@ linlogitf <- function(x,k,f,mu,b)
 drfit <- function(data, startlogEC50 = NA, chooseone=TRUE,
         probit = TRUE, logit = FALSE, weibull = FALSE,
         linlogit = FALSE, linlogitWrong = NA, allWrong = NA,
-        b0 = 2, f0 = 0)
+        s0 = 0.5, b0 = 2, f0 = 0)
 {
     if(!is.null(data$ok)) data <- subset(data,ok!="no fit") # Don't use data where ok 
                                                             # was set to "no fit"
@@ -130,7 +130,7 @@ drfit <- function(data, startlogEC50 = NA, chooseone=TRUE,
                     length(subset(allWrong,allWrong == i))==0) {
                     m <- try(nls(response ~ pweibull(-log10(dose)+location,shape),
                             data=tmp,
-                            start=list(location=-0.16,shape=0.4659)))
+                            start=list(location=startlogEC50[[i]],shape=s0)))
                     if (chooseone==FALSE || fit==FALSE) {
                         if (!inherits(m, "try-error")) {
                             fit <- TRUE
@@ -179,7 +179,8 @@ drfit <- function(data, startlogEC50 = NA, chooseone=TRUE,
                             rlld[[ri]] <- log10(lowestdose)
                             rlhd[[ri]] <- log10(highestdose)
                             mtype[[ri]] <- "logit"
-                            logEC50[[ri]] <- coef(m)[["logEC50"]]
+                            logEC50[[ri]] <- a[[ri]] <- coef(m)[["logEC50"]]
+                            b[[ri]] <- coef(m)[["scale"]]
                             c[[ri]] <- NA
                             if (logEC50[[ri]] > rlhd[[ri]]) {
                                 logEC50[[ri]] <- NA
@@ -188,8 +189,6 @@ drfit <- function(data, startlogEC50 = NA, chooseone=TRUE,
                                 b[[ri]] <- NA
                             } else {
                                 stderrlogEC50[[ri]] <- s$parameters["logEC50","Std. Error"]
-                                a[[ri]] <- coef(m)[["logEC50"]]
-                                b[[ri]] <- coef(m)[["scale"]]
                             }
                         }
                     }
diff --git a/man/drfit.Rd b/man/drfit.Rd
index 0d9ee6f..35d6d94 100644
--- a/man/drfit.Rd
+++ b/man/drfit.Rd
@@ -8,7 +8,7 @@
 \usage{
   drfit(data, startlogEC50 = NA, chooseone = TRUE, probit = TRUE, logit = FALSE,
     weibull = FALSE, linlogit = FALSE, linlogitWrong = NA, allWrong = NA, 
-    b0 = 2, f0 = 0)
+    s0 = 0.5, b0 = 2, f0 = 0)
 }
 \arguments{
   \item{data}{
@@ -55,9 +55,12 @@
     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{s0}{
+    If the weibull model is fitted, s0 gives the possibility to adjust the
+    starting value for the shape parameter of \code{\link{pweibull}}.}
   \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.}
+    adjust the starting values for the parameters b and f.}
 }
 \value{
   \item{results}{