[R] Fieller's Conf Limits and EC50's
Stephen B. Cox
stephen.cox at ttu.edu
Wed Jul 13 18:42:52 CEST 2005
Folks
I have modified an existing function to calculate 'ec/ld/lc' 50 values
and their associated Fieller's confidence limits. It is based on
EC50.calc (writtien by John Bailer) - but also borrows from the dose.p
(MASS) function. My goal was to make the original EC50.calc function
flexible with respect to 1) probability at which to calculate the
expected dose, and 2) the link function. I would appreciate comments
about the validity of doing so! In particular - I want to make sure
that the confidence limit calculations are still valid when changing the
link function.
ec.calc<-function(obj,conf.level=.95,p=.5) {
# calculates confidence interval based upon Fieller's thm.
# modified version of EC50.calc found in P&B Fig 7.22
# now allows other link functions, using the calculations
# found in dose.p (MASS)
# SBC 19 May 05
call <- match.call()
coef = coef(obj)
vcov = summary.glm(obj)$cov.unscaled
b0<-coef[1]
b1<-coef[2]
var.b0<-vcov[1,1]
var.b1<-vcov[2,2]
cov.b0.b1<-vcov[1,2]
alpha<-1-conf.level
zalpha.2 <- -qnorm(alpha/2)
gamma <- zalpha.2^2 * var.b1 / (b1^2)
eta = family(obj)$linkfun(p) #based on calcs in V&R's dose.p
EC50 <- (eta-b0)/b1
const1 <- (gamma/(1-gamma))*(EC50 + cov.b0.b1/var.b1)
const2a <- var.b0 + 2*cov.b0.b1*EC50 + var.b1*EC50^2 -
gamma*(var.b0 - cov.b0.b1^2/var.b1)
const2 <- zalpha.2/( (1-gamma)*abs(b1) )*sqrt(const2a)
LCL <- EC50 + const1 - const2
UCL <- EC50 + const1 + const2
conf.pts <- c(LCL,EC50,UCL)
names(conf.pts) <- c("Lower","EC50","Upper")
return(conf.pts,conf.level,call=call)
}
Thanks
Stephen Cox
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