scape (version 2.2-0)

importCol: 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, 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.

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.

...

passed to data.frame, e.g. stringsAsFactors=FALSE.

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

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. Available at http://fish.washington.edu/research/coleraine/pdf/coleraine.pdf.

See Also

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

x.cod, x.ling, x.oreo, and x.sbw were created using importCol.

scape-package gives an overview of the package.

Examples

## Not run: 
# path <- system.file("example/cod.res", package="scape")
# x.cod <- importCol(path, Dev=TRUE, Survey=TRUE, CAc=TRUE, CAs=TRUE)
# ## End(Not run)