importCol: Import Coleraine Model Results

In arnima-github/scape: Statistical Catch-at-Age Plotting Environment

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.

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 functions ll (package gdata) and head are recommended for browsing nested objects, e.g. ll(x.cod), ll(x.cod$N), and head(x.cod$N).

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.

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

importADCAM imports ADCAM model results.

scape-package gives an overview of the package.

Examples

path <- system.file("example/cod.res", package="scape")
cod <- importCol(path, Dev=TRUE, Survey=TRUE, CAc=TRUE, CAs=TRUE)

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