project: Projection function

In cttedwards/bdm: Bayesian biomass dynamics model

Projection function

Description

This function can be used to project the default bdm model forward in time assuming a constant catch (harvest) or harvest rate. Multiple alternative scenarios can be run simultaneously.

Usage

project(object, harvest.project, ...)

## S4 method for signature 'bdm,vector'
project(object, harvest.project, time.project, harvest_rate = TRUE)

Arguments

object	a bdm class object containing a fit to the default model
harvest.project	a constant harvest or harvest rate as a vector across alternative scenarios
time.project	number of time steps for future projection
harvest_rate	a logical value indicating whether or not harvest.project refers to the harvest (catch) or harvest rate (catch over biomass)

Details

Model parameter values are sampled from the joint posterior distribution and a projection is performed for each sample. A correlated random walk of process error terms is assumed during the projection.

Value

Returns a list containing the elements:

run

optional run label that will match the corresponding object@run

scenarios

vector of harvest or harvest rate scenarios

time

complete series of time step labels

nsamples

number of posterior samples equal to object@nsamples

biomass

array of biomass values with dimensions: iteration, time, scenario

depletion

array of depletion values with dimensions: iteration, time, scenario

epsilon_p

process error residual matrix

harvest

catch time series array

harvest_rate

harvest rate time series array

Examples

## Not run: 
# get some data
data(haknz)
dat <- bdmData(harvest = haknz$landings, index = cbind(haknz$survey, haknz$cpue))

# initialize and fit default model
mdl <- bdm()
mdl <- compiler(mdl)
mdl <- sampler(mdl, dat, run = 'example_run')

# constant harvest rate projection scenarios
mdl.project <- project(mdl, harvest = c(0.05, 0.10, 0.15), time = 20, harvest_rate = TRUE)

# check label
mdl@run
mdl.project$run

# extract median values
apply(mdl.project$depletion, 2:3, median)
apply(mdl.project$harvest, 2:3, median)
apply(mdl.project$harvest_rate, 2:3, median)

# constant catch projection scenarios
mdl.project <- project(mdl, harvest = c(900, 1200, 1500), time = 20, harvest_rate = FALSE)

# extract median values
apply(mdl.project$depletion, 2:3, median)
apply(mdl.project$harvest, 2:3, median)
apply(mdl.project$harvest_rate, 2:3, median)

## End(Not run)

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