bdmData-class: Class containing input data for model run

In cttedwards/bdm: Bayesian biomass dynamics model

Class containing input data for model run

Description

This is an S4 object class that extends the list base type and allows some error checking to be performed during construction to ensure formatting is appropriate for a bdm model run

Usage

bdmData(index, harvest, time, n, sigmao, sigmap, renormalise = FALSE)

Arguments

index	Matrix of abundance index values
harvest	Numeric vector of catch values
time	Character vector of time values
n	Shape parameter for generalised production function
sigmao	Matrix of observation error values with dimensions equal to index
sigmap	Numeric value specifying process error
renormalise	Logical value indicating whether indices should be renormalised to an arithmetic mean of one

Slots

.Data

list containing input data

names

names for each list item

T

Number of discrete time steps in data

I

Number of abundance indices

index

Matrix of abundance index values, with nrow(index)==T and ncol(index)==I.

harvest

Numeric vector of catch values, with length(harvest)==T

time

Character vector of time lables e.g. year values.

n

Shape parameter n for generalised surplus production model.

sigmap

Log-normal process error scale parameter σ_p

sigmao

Matrix of log-normal observation error scale parameters σ_o with dimensions equal to index

See Also

Use sigmao and sigmap to set or extract the σ values. Use shape to set or extract the shape of the production function.

Examples

# load Indian Ocean albacore data
data(albio)

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

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