importProj {scapeMCMC}R Documentation

Import Coleraine MCMC Projections

Description

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

Usage

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

Arguments

dir directory containing the files ‘strategy.out’, ‘projspbm.pst’ and ‘procatch.pst’.
info optional string containing information to store with MCMC projections.
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 example dataset xproj was generated using importProj.

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

Author(s)

Arni Magnusson arnima@u.washington.edu.

References

Hilborn, R., M. Maunder, A. Parma, B. Ernst, J. Payne, and P. Starr. 2003. Coleraine: A generalized age-structured stock assessment model. User's manual version 2.0. University of Washington Report SAFS-UW-0116. Available at http://fish.washington.edu/research/coleraine/coleraine.pdf.

See Also

importMCMC, read.table, readLines, scan, xproj.

scapeMCMC-package gives an overview of the package.

Examples

## Not run: 
path <- paste(.find.package("scapeMCMC"), "/example", sep="")
xproj <- importProj(path)
## End(Not run)

[Package scapeMCMC version 1.0-3 Index]