Make the logit model work again, by setting a sensible

starting value for the scale argument. Now all models
get separate starting arguments, with hopefully effective
default values.



git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@80 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc

7 files changed, 38 insertions, 24 deletions

diff --git a/DESCRIPTION b/DESCRIPTION
index 7182eda..ee6d4ff 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: drfit
-Version: 0.05-78
-Date: 2006-05-08
+Version: 0.05-80
+Date: 2006-05-22
 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 e3d9d3b..e993c61 100644
--- a/R/drfit.R
+++ b/R/drfit.R
@@ -2,7 +2,8 @@ drfit <- function(data, startlogED50 = NA, chooseone=TRUE,
         probit = TRUE, logit = FALSE, weibull = FALSE,
         linlogit = FALSE, level = 0.95,
         linlogitWrong = NA, allWrong = NA,
-        s0 = 0.5, b0 = 2, f0 = 0)
+        ps0 = 1, ls0 = 0.5, ws0 = 0.5,
+        b0 = 2, f0 = 0)
 {
     require(MASS)
     if(!is.null(data$ok)) data <- subset(data,ok!="no fit") # Don't use data
@@ -114,7 +115,7 @@ drfit <- function(data, startlogED50 = NA, chooseone=TRUE,
                         length(subset(allWrong,allWrong == i))==0) {
                         m <- try(nls(response ~ pnorm(-log10(dose),-logED50,scale),
                                     data=tmp,
-                                    start=list(logED50=startlogED50[[i]],scale=1)))
+                                    start=list(logED50=startlogED50[[i]],scale=ps0)))
                         if (chooseone==FALSE || fit==FALSE) {
                             if (!inherits(m, "try-error")) {
                                 fit <- TRUE
@@ -157,7 +158,7 @@ drfit <- function(data, startlogED50 = NA, chooseone=TRUE,
                         length(subset(allWrong,allWrong == i))==0) {
                         m <- try(nls(response ~ plogis(-log10(dose),-logED50,scale),
                                 data=tmp,
-                                start=list(logED50=startlogED50[[i]],scale=1)))
+                                start=list(logED50=startlogED50[[i]],scale=ls0)))
                         if (chooseone==FALSE || fit==FALSE) {
                             if (!inherits(m, "try-error")) {
                                 fit <- TRUE
@@ -199,7 +200,7 @@ drfit <- function(data, startlogED50 = NA, chooseone=TRUE,
                         length(subset(allWrong,allWrong == i))==0) {
                         m <- try(nls(response ~ pweibull(-log10(dose)+location,shape),
                                 data=tmp,
-                                start=list(location=startlogED50[[i]],shape=s0)))
+                                start=list(location=startlogED50[[i]],shape=ws0)))
                         if (chooseone==FALSE || fit==FALSE) {
                             if (!inherits(m, "try-error")) {
                                 fit <- TRUE
@@ -273,10 +274,10 @@ drfit <- function(data, startlogED50 = NA, chooseone=TRUE,
     }
     results <- data.frame(rsubstance, rndl, rn, rlld, rlhd, mtype, 
         logED50, logED50low, logED50high, runit, sigma, a, b)
-	names(results) <- c("Substance","ndl","n","lld","lhd","mtype","logED50",
-		paste(100*(1-level)/2,"%",sep=""),
-		paste(100*(1+level)/2,"%",sep=""),
-		"unit","sigma","a","b")
+    names(results) <- c("Substance","ndl","n","lld","lhd","mtype","logED50",
+        paste(100*(1-level)/2,"%",sep=""),
+        paste(100*(1+level)/2,"%",sep=""),
+        "unit","sigma","a","b")
 
     if (linlogit) {
         results$c <- c
diff --git a/inst/doc/index.html b/inst/doc/index.html
index d6cedf5..6d27f48 100644
--- a/inst/doc/index.html
+++ b/inst/doc/index.html
@@ -8,7 +8,7 @@
 <h2>User Guide for package drfit</h2>
 <dl>
 	<dt><a href="drfit-Rnews.pdf">drfit-Rnews.pdf</a>:</dt>
-	<dd> Preliminary version of an Introductory article on drfit</dd>
+	<dd>Introductory article on drfit, published in R News</dd>
 </dl>
 
 </body>
diff --git a/man/drfit-package.Rd b/man/drfit-package.Rd
index 43334ff..3064787 100644
--- a/man/drfit-package.Rd
+++ b/man/drfit-package.Rd
@@ -8,7 +8,9 @@ Dose-response data evaluation
 See \url{../DESCRIPTION}
 }
 \details{
-There is a preliminary version of an introductory article located in \url{../doc/drfit-Rnews.pdf}.
+There is an introductory article located in \url{../doc/drfit-Rnews.pdf},
+which will be published in the R News special edition on the use
+of R for chemists.
 }
 \author{
 Author and Maintainer: Johannes Ranke <jranke@uni-bremen.de>
@@ -28,5 +30,5 @@ the advantage of my package is its user-friendliness.
 data(antifoul)
 r <- drfit(antifoul)
 format(r,digits=2)
-\dontrun{drplot(r,antifoul,overlay=TRUE,bw=FALSE)}
+drplot(r,antifoul,overlay=TRUE,bw=FALSE)
 }
diff --git a/man/drfit.Rd b/man/drfit.Rd
index 453c0f8..6b98f36 100644
--- a/man/drfit.Rd
+++ b/man/drfit.Rd
@@ -8,7 +8,7 @@
 \usage{
   drfit(data, startlogED50 = NA, chooseone = TRUE, probit = TRUE, logit = FALSE,
   weibull = FALSE, linlogit = FALSE, level = 0.95, linlogitWrong = NA,
-  allWrong = NA, s0 = 0.5, b0 = 2, f0 = 0)
+  allWrong = NA, ps0 = 1, ls0 = 0.5, ws0 = 0.5, b0 = 2, f0 = 0)
 }
 \arguments{
   \item{data}{
@@ -56,12 +56,18 @@
     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{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{ps0}{
+    If the probit model is fitted, \code{ps0} gives the possibility to adjust
+    the starting value for the scale parameter of \code{\link{pnorm}}.}
+  \item{ls0}{
+    If the logit model is fitted, \code{ls0} gives the possibility to adjust
+    the starting value for the scale parameter of \code{\link{plogis}}.}
+  \item{ws0}{
+    If the weibull model is fitted, \code{ws0} 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
-    adjust the starting values for the parameters b and f.}
+    If the linearlogistic model is fitted, \code{b0} and \code{f0} give the
+    possibility to adjust the starting values for the parameters b and f.}
 }
 \value{
   \item{results}{
diff --git a/tests/XY.R b/tests/XY.R
index e295be4..7e3ecb2 100644
--- a/tests/XY.R
+++ b/tests/XY.R
@@ -1,4 +1,4 @@
 library(drfit)
 data(XY)
-rXY <- drfit(XY)
+rXY <- drfit(XY,logit=TRUE,weibull=TRUE,chooseone=FALSE)
 rXY
diff --git a/tests/XY.Rout.save b/tests/XY.Rout.save
index d8098ae..9da519f 100644
--- a/tests/XY.Rout.save
+++ b/tests/XY.Rout.save
@@ -1,6 +1,6 @@
 
 R : Copyright 2006, The R Foundation for Statistical Computing
-Version 2.3.0 (2006-04-24)
+Version 2.3.1 beta (2006-05-18 r38119)
 ISBN 3-900051-07-0
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -19,21 +19,26 @@ Type 'q()' to quit R.
 Loading required package: MASS
 Loading required package: RODBC
 > data(XY)
-> rXY <- drfit(XY)
+> rXY <- drfit(XY,logit=TRUE,weibull=TRUE,chooseone=FALSE)
 
 Control: Fitting data...
 
 Substance X: Fitting data...
 Waiting for profiling to be done...
+Waiting for profiling to be done...
 
 Substance Y: Fitting data...
 > rXY
     Substance ndl  n  lld  lhd    mtype  logED50     2.5%    97.5% unit
 1     Control   1  6 -Inf -Inf inactive       NA       NA       NA mg/L
 2 Substance X   4 12    1    3   probit 2.161905 2.105861 2.214359 mg/L
-3 Substance Y   4 12    1    3   active       NA       NA       NA mg/L
+3 Substance X   4 12    1    3    logit 2.160948 2.112152 2.207912 mg/L
+4 Substance X   4 12    1    3  weibull 2.174365       NA       NA mg/L
+5 Substance Y   4 12    1    3   active       NA       NA       NA mg/L
        sigma        a         b
 1         NA       NA        NA
 2 0.04131746 2.161905 0.5061306
-3         NA       NA        NA
+3 0.03758732 2.160948 0.2991424
+4 0.05723870 3.009640 2.0362368
+5         NA       NA        NA
 >