getMDFR.FisheryQuantities: Get estimated/predicted fishery-related quantities from...

In wStockhausen/rTCSAM2013: Functions to run and plot output from TCSAM2013 models.

Description

Function to get estimated/predicted fishery-related quantities from several model runs.

Usage

getMDFR.FisheryQuantities(obj, type = c("bio.retm", "bio.dscm", "bio.totm",
  "prNatZ.ret", "prNatZ.tot", "PRs.ret", "PRs.tot", "mnPrNatZ.ret",
  "mnPrNatZ.tot", "sel_cxz", "sel_yxz", "ret_yxz", "zscores.tot", "zscores.ret",
  "effSS.ret", "effSS.tot", "qFsh_xy", "maxFc_xy", "max rates", "mean rates"),
  ci = 0.8, pdfType = c("norm2", "normal", "lognormal"), verbose = FALSE)

Arguments

obj	- object that can be converted into a list of tcsam2013.resLst objects
type	- fishery-related quantity to retrieve
ci	- confidence interval for error bars on observations
pdfType	- type of error distribution for observations
verbose	- flag (T/F) to print debug info

Details

Potential values for 'type' are:

• 'bio.retm' - retained catch mortality (1000's t)

• 'bio.dscm' - discard catch mortality (1000's t) for males in directed fishery

• 'bio.totm' - total catch mortality (1000's t)

• 'prNatZ.ret' - annual retained catch proportions-at-size

• 'prNatZ.tot' - annual total catch proportions-at-size

• 'PRs.ret' - pearsons residuals for retained catch proportions-at-size

• 'PRs.tot' - pearsons residuals for total catch proportions-at-size

• 'mnPrNatZ.ret' - mean proportions-at-size for retained catch data

• 'mnPrNatZ.tot' - mean proportions-at-size for total catch data

• 'sel_cxz' - fishery selectivity and retention functions, by time period and sex

• 'sel_yxz' - fishery selectivity functions, by year and sex

• 'ret_yxz' - fishery retention functions, by year and sex

• 'zscores.tot' - annual z-scores for fits to total catch biomass

• 'zscores.ret' - annual z-scores for fits to retained catch biomass

• 'effSS.tot' - effective (and input) sample sizes for total catch size comps

• 'effSS.ret' - effective (and input) sample sizes for retained catch size comps

• 'qFsh_xy' - annual fishery catchabilities

• 'maxFc_xy' - annual max capture rates

• 'max rates' - max fishing mortality, retained mortality, and capture rates

• 'mean rates' - mean fishing mortality, retained mortality, and capture rates

Requires sqldf package.

Value

dataframe in canonical format

wStockhausen/rTCSAM2013 documentation built on May 3, 2019, 7:13 p.m.