W4: The four-parameter Weibull functions

In MaximeBSanofi/drc2:

Description

'W1.4' and 'W2.4' provide the four-parameter Weibull functions, self starter function and names of the parameters.

Usage

  W1.4(fixed = c(NA, NA, NA, NA), names = c("b", "c", "d", "e"), ...)
  
  W2.4(fixed = c(NA, NA, NA, NA), names = c("b", "c", "d", "e"), ...)

Arguments

fixed	numeric vector. Specifies which parameters are fixed and at what value they are fixed. NAs for parameter that are not fixed.
names	a vector of character strings giving the names of the parameters. The default is reasonable.
...	additional arguments to be passed from the convenience functions.

Details

The equations for the mean functions are given at weibull1.

Value

See weibull1.

Note

This function is for use with the model fitting function drm.

Author(s)

Christian Ritz

References

Seber, G. A. F. and Wild, C. J (1989) Nonlinear Regression, New York: Wiley \& Sons (pp. 330–331).

Ritz, C (2009) Towards a unified approach to dose-response modeling in ecotoxicology To appear in Environ Toxicol Chem.

See Also

Setting c=0 yields W1.3. A more flexible function, allowing fixing or constraining parameters, is available through weibull1.

Examples

## Fitting a four-parameter Weibull (type 1) model
terbuthylazin.m1 <- drm(rgr~dose, data = terbuthylazin, fct = W1.4())
summary(terbuthylazin.m1)

## Fitting a first-order multistage model
## to data from BMDS by EPA
## (Figure 3 in Ritz (2009))
bmds.ex1 <- data.frame(ad.dose=c(0,50,100), dose=c(0, 2.83, 5.67), 
num=c(6,10,19), total=c(50,49,50))

bmds.ex1.m1<-drm(num/total~dose, weights=total, data=bmds.ex1, 
fct=W2.4(fixed=c(1,NA,1,NA)), type="binomial")

modelFit(bmds.ex1.m1)  # same as in BMDS

summary(bmds.ex1.m1)  # same background estimate as in BMDS

logLik(bmds.ex1.m1)

## BMD estimate identical to BMDS result
## BMDL estimate differs from BMDS result (different method)
ED(bmds.ex1.m1, 10, ci="delta")

## Better fit

bmds.ex1.m2<-drm(num/total~dose, weights=total, data=bmds.ex1, 
fct=W1.4(fixed=c(-1,NA,1,NA)), type="binomial")
modelFit(bmds.ex1.m2)
summary(bmds.ex1.m2)

ED(bmds.ex1.m2, 50, ci = "delta")

## Creating Figure 3 in Ritz (2009)
bmds.ex1.m3 <- drm(num/total~dose, weights=total, data=bmds.ex1, 
fct=LL.4(fixed=c(-1,NA,1,NA)), type="binomial")

plot(bmds.ex1.m1, ylim = c(0.05, 0.4), log = "", lty = 3, lwd = 2, 
xlab = "Dose (mg/kg/day)", ylab = "",
cex=1.2, cex.axis=1.2, cex.lab=1.2)

mtext("Tumor incidence", 2, line=4, cex=1.2)  # tailored y axis label

plot(bmds.ex1.m2, ylim = c(0.05, 0.4), log = "", add = TRUE, lty = 2, lwd = 2)

plot(bmds.ex1.m3, ylim = c(0.05, 0.4), log = "", add = TRUE, lty = 1, lwd = 2)

arrows(2.6 , 0.14, 2, 0.14, 0.15, lwd=2)
text(2.5, 0.14, "Weibull-1", pos=4, cex=1.2)

MaximeBSanofi/drc2 documentation built on Feb. 22, 2022, 12:02 a.m.