importProj: Import Coleraine MCMC Projections

View source: R/importProj.R

importProjR Documentation

Import Coleraine MCMC Projections

Description

Import Coleraine MCMC traces for spawning biomass and catch, projected into the near future.

Usage

importProj(dir, coda=FALSE, quiet=TRUE)

Arguments

dir

directory containing the files ‘strategy.out’, ‘projspbm.pst’ and ‘procatch.pst’.

coda

whether data frames should be coerced to class mcmc using the coda package.

quiet

whether to report progress while parsing files in directory.

Value

A list containing:

B

biomass by catch policy and year

Y

catch by catch policy and year

as lists of data frames, or mcmc objects if coda=TRUE.

Note

MCMC projections can be used to evaluate the short-term outcome of harvest policies (constant catch or constant harvest rate), given the uncertainty about parameter values and random future recruitment.

The functions ll (package gdata) and head are recommended for browsing nested objects, e.g. ll(xproj), ll(xproj$B), ll(xproj$B$"0.2"), and head(xproj$B$"0.2").

The plotMCMC package is recommended for plotting MCMC diagnostics and posteriors.

References

Hilborn, R., Maunder, M., Parma, A., Ernst, B., Payne, J., and Starr, P. (2003). Coleraine: A generalized age-structured stock assessment model. User's manual version 2.0. University of Washington Report SAFS-UW-0116.

See Also

read.table, readLines, and scan import any data.

importMCMC and importProj import Coleraine MCMC results.

xproj was created using importProj.

scape-package gives an overview of the package.

Examples

path <- system.file("example/mcmc", package="scape")
proj <- importProj(path)

arnima-github/scape documentation built on Jan. 17, 2024, 2:39 p.m.