confint.twoAC: Confidence intervals and profile likelihoods for parameters in 2AC models

Description

Computes confidence intervals from the profiled likelihood and the Wald approximation in the 2AC model, or plots the profile likelihood function for d.prime.

Usage

## S3 method for class 'twoAC':
confint(object, parm, level = 0.95, 
        type = c("profile", "Wald"), ...)

## S3 method for class 'profile.twoAC':
confint(object, parm = "d.prime", level = 0.95, \dots)

## S3 method for class 'twoAC':
profile(fitted, alpha = 1e-3, nSteps = 1e2, range, \dots)

## S3 method for class 'profile.twoAC':
plot(x, level = c(0.95, 0.99), Log = FALSE,
      relative = TRUE, fig = TRUE, n = 1e3, ..., ylim = NULL)

Arguments

object

a fitted twoAC object or a profile.twoAC object.

fitted

a fitted twoAC object.

a profile.twoAC object.

type

the type of confidence interval required. "profile" is the most accurate.

parm

For confint.profile.twoAC: has to be "d.prime". For confint.twoAC: for type = "Wald" a specification of which parameters the confidence interval is required for. Ignored for t

level

the confidence level required.

alpha

determines the range of profiling. By default the likelihood is profiled in the 99.9% Wald confidence interval region.

range

if supplied, d.prime will be profiled between min(range) and max(range). This over-rules the automatic range computation.

nSteps

the number of profile steps.

Log

should the profile likelihood be plotted on the log-scale?

relative

should the relative or the absolute likelihood be plotted?

fig

should the profile likelihood be plotted?

the no. points used in the spline interpolation of the profile likelihood.

ylim

overrules default y-limits on the plot of the profile likelihood.

...

not currently used.

Value

confint: A matrix (or vector) with columns giving lower and upper confidence limits for each parameter. These will be labelled as (1-level)/2 and 1 - (1-level)/2 in % (by default 2.5% and 97.5%). Profile likelihood confindence intervals are only available for d.prime and not tau. profile.twoAC: a data.frame with the profile of d.prime. plot.profile.twoAC invisibly returns the spline approcimation to the profile.

Details

These confint methods call the appropriate profile method, then finds the confidence intervals by interpolation of the profile traces. If the profile object is already available, this should be used as the main argument rather than the fitted model object itself. In plot.profile.twoAC: at least one of Log and relative arguments have to be TRUE.

Examples

Run this code

(fm1 <- twoAC(c(2, 2, 6)))
confint(fm1)
confint(fm1, type = "Wald")

pr1 <- profile(fm1)
confint(pr1)

pr1 <- profile(fm1, alpha = 1e-5)
par(mfrow = c(2,2))
plot(pr1)
plot(pr1, Log = FALSE, relative = TRUE)
plot(pr1, Log = TRUE, relative = TRUE)
plot(pr1, Log = TRUE, relative = FALSE)