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-rw-r--r--DESCRIPTION4
-rw-r--r--R/drfit.R17
-rw-r--r--inst/doc/index.html2
-rw-r--r--man/drfit-package.Rd6
-rw-r--r--man/drfit.Rd18
-rw-r--r--tests/XY.R2
-rw-r--r--tests/XY.Rout.save13
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
>

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