loglogistic {drcte}

Log-logistic distribution of germination times within a seed lot

Description

This function provides the truncated log-logistic cumulative distribution of germination times, to be used to fit time-to-event methods to the time-course of seed germination for a seed lot.

Usage

loglogistic(fixed = c(NA, NA, NA), names = c("b", "d", "e"))
loglogisticSurv(fixed = c(NA, NA, NA), names = c("b", "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. It is often used to fix the 'd' parameter to 1, which provides the usual log-logistic distribution, with no ungerminated fraction.

names

a vector of character strings giving the names of the parameters. The default is reasonable.

Details

The log-logistic distribution of germination times is parameterised as:

P(t) = \frac{d}{(1+\exp( - b(\log(t)-\log(e))))}

where 't' is the time and 'P(t)' is the proportion of germinated seeds at time = t. LogLogisticSurv is parameterised as usual in survival analysis:

P(t) = \frac{d}{(1+\exp( - (\log(t)-e)/exp(b)))}

i.e. with 'e' on a log-scale and a log-link on 'b'. With no cured fraction (d = 1), loglogisticSurv gives same results as 'survereg' in the 'survival package', with 'dist = "loglogistic"'.

Value

The value returned is a list containing the nonlinear function, the self starter function and the parameter names.

Author(s)

Andrea Onofri

References

Kleinbaum, D.G., Klein, M., 2005. Survival analysis. Springer Science, USA.

Examples

library(drcte)
data(chickweed)
modb <- drmte(count ~ start + end,
               data=chickweed,
               fct = loglogistic())