importCol {scape}R Documentation

Import Coleraine Model Results

Description

Import Coleraine model results from .res file, and rearrange into a standard format suitable for plotting.

Usage

importCol(res.file, info="", Dev=FALSE, CPUE=FALSE, Survey=FALSE,
          CAc=FALSE, CAs=FALSE, CLc=FALSE, CLs=FALSE, LA=FALSE,
          quiet=TRUE)

Arguments

res.file name of Coleraine model results file to import.
info optional string containing information to store with model results.
Dev whether recruitment deviates were estimated in model.
CPUE whether model was fitted to catch-per-unit-effort data.
Survey whether model was fitted to survey abundance index data.
CAc whether model was fitted to commercial catch-at-age data.
CAs whether model was fitted to survey catch-at-age data.
CLc whether model was fitted to commercial catch-at-length data.
CLs whether model was fitted to survey catch-at-length data.
LA whether model was fitted to length-at-age data.
quiet whether to report progress while parsing file.

Value

A list of class scape containing at least N, B, and Sel. The other elements may or may not be included in the list, depending on how importCol was called:

N predicted numbers at age
B predicted biomass, recruitment, and observed landings (year things)
Sel predicted selectivity and observed maturity (age things)
Dev predicted recruitment deviates from the stock-recruitment curve
CPUE, Survey commercial and survey abundance index and fit
CAc, CAs commercial and survey C@A (catch at age) and fit
CLc, CLs commercial and survey C@L (catch at length) and fit
LA observed L@A and fit

Note

This import function is implemented for the Coleraine statistical catch-at-age software, and can serve as a template for scape users who would like to implement import functions for specific stock assessment software.

The example datasets x.cod, x.ling, x.oreo, and x.sbw were generated using importCol.

The functions ll (package gdata) and head are recommended for browsing model results, e.g. ll(x.cod); ll(x.cod$N); head(x.cod$N).

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

read.table, readLines, scan, x.cod, x.ling, x.oreo, x.sbw.

scape-package gives an overview of the package.

Examples

## Not run: 
path <- paste(.find.package("scape"), "/example/cod.res", sep="")
x.cod <- importCol(path, Dev=T, Survey=T, CAc=T, CAs=T)
## End(Not run)

[Package scape version 1.0-8 Index]