status: Extract status and reference point estimates

In cttedwards/bdm: Bayesian biomass dynamics model

Extract status and reference point estimates

Description

These functions can be used to extract output values following a model fit. The status function will look for and return model elements current_biomass, current_depletion and current_harvest_rate. The refpoints function will look for and return model elements msy, depletion_at_msy, biomass_at_msy and harvest_rate_at_msy. These are returned by the default bdm model, but the function will also work if a user-specified model contains potentially different elements in the 'generated quantities {}' block of the code, as long as they are specified in the pars argument.

Usage

status(object, ...)

## S4 method for signature 'bdm'
status(object, pars)

refpoints(object, ...)

## S4 method for signature 'bdm'
refpoints(object, pars)

Arguments

object	a bdm model object
...	additional arguments to the generic function
pars	a character vector specifiying the parameters to be returned

Value

Returns a list containing the specified elements, each of which is a vector equal to the number of posterior samples.

Examples

data(albio)
dat <- bdmData(harvest = albio$catch, index = albio$cpue, time = rownames(albio))

## Not run: 
# initialize and fit default model
mdl <- bdm()
mdl <- compiler(mdl)
mdl <- sampler(mdl, dat)

# get median status estimates
lapply(status(mdl), median)

# get median reference point estimates
lapply(refpoints(mdl), median)

## End(Not run)

cttedwards/bdm documentation built on Oct. 11, 2022, 7:52 p.m.