diff options
| -rw-r--r-- | DESCRIPTION | 21 | ||||
| -rw-r--r-- | R/drfit.R | 9 | ||||
| -rw-r--r-- | man/drfit.Rd | 7 |
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, @@ -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}{ |