scape (version 1.0-4)

importRes: Import Coleraine Model Results

Description

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

Usage

importRes(res.file, info="", Dev=FALSE, CPUE=FALSE, Survey=FALSE,
          CAc=FALSE, CAs=FALSE, CLc=FALSE, CLs=FALSE, LA=FALSE,
          verbose=FALSE)

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.

verbose

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 importRes 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., 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

The imported model results can be plotted using plotB, plotCA, plotCL, plotIndex, plotLA, plotN, and plotSel. read.table, readLines, and scan are commonly used to import data from text files.

Examples

path <- paste(.find.package("scape"), "/example/cod.res", sep="")
x.cod <- importRes(path, Dev=T, Survey=T, CAc=T, CAs=T)