confint.eicm {eicm}

Confidence intervals for EICM parameters

Description

Computes the profile (penalized) likelihood confidence intervals for all estimated parameters in a EICM model. If the likelihood profiles are not computed yet, they will be computed first.

Usage

## S3 method for class 'eicm'
confint(
  object,
  parm,
  level = 0.99,
  step = 0.3,
  ncores = parallel::detectCores(),
  ...
)

Arguments

object

the fitted EICM model.

parm

currently unused.

level

the confidence level required.

step

the step increments/decrements at which to compute the likelihood profile points.

ncores

the number of CPU cores to use when computing profiles for all parameters.

...

additional argument(s) for methods

Value

The same model object with a new confint component.

Examples

# load the included parameterized model
data(truemodel)

# realize the model
occurrences <- predict(truemodel, nrepetitions=1)

# fit the model without species interactions
fitted <- eicm(occurrences, n.latent=2, mask.sp=0, do.selection=FALSE)$fitted.model

# compute confidence intervals for all parameters
# this updates the fitted model with the confints
fitted <- confint(fitted, ncores=2)

# plot the confidence intervals
plot(fitted, type="confint")