| importCol {scape} | R Documentation |
Import Coleraine model results from .res file, and rearrange into a standard format suitable for plotting.
importCol(res.file, info="", Dev=FALSE, CPUE=FALSE, Survey=FALSE,
CAc=FALSE, CAs=FALSE, CLc=FALSE, CLs=FALSE, LA=FALSE,
quiet=TRUE)
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. |
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 |
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).
Arni Magnusson arnima@u.washington.edu.
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.
read.table, readLines, scan,
x.cod, x.ling, x.oreo,
x.sbw.
scape-package gives an overview of the package.
## 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)