importADCAM {scape}

Import ADCAM Model Results

Description

Import ADCAM model results into a standard format suitable for plotting.

Usage

importADCAM(dir)

Arguments

dir

directory containing the results files (‘resultsbyyearandage’, ‘resultsbyyear’, ‘resultsbyage’), as well as the input file ‘catchparameters’ specifying selectivity periods.

Value

A list of class scape containing the following elements:

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

Survey

survey abundance index and fit

CAc

commercial C@A (catch at age) and fit

CAs

survey C@A (catch at age) and fit

Note

B$VB is reference biomass.

Survey$CV is 0 to give plotIndex sensible y-axis limits.

CAc$SS and CAs$SS are the log(obs+const) - log(fit+const) residuals used in the ADCAM likelihood.

References

Bjornsson, H. and A. Magnusson. (2009) ADCAM user manual (draft version). ICES CM 2009/ACOM:56, Annex 6.

See Also

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

x.saithe was created using importADCAM.

importCol imports Coleraine model results.

scape-package gives an overview of the package.

Examples

path <- system.file("example/saithe", package="scape")
saithe <- importADCAM(path)