runCOSEWIC {MSEtool}R Documentation

COSEWIC MSE run using the correct MPs and projected time horizon

Description

Dedicated functions for MSE run and reporting for COSEWIC (Committee on the Status of Endangered Wildlife in Canada). MSE projects for 6x maximum age using NFref, FMSYref and curE management procedures.

Usage

runCOSEWIC(OM, ...)

COSEWIC_Pplot(
  MSEobj,
  syear = 2017,
  qcol = "#FFCB62",
  quants = c(0.05, 0.25, 0.5, 0.75, 0.95)
)

COSEWIC_Dplot(
  MSEobj,
  syear = 2017,
  qcol = "#79F48D",
  quants = c(0.05, 0.25, 0.5, 0.75, 0.95),
  nGT = 3
)

COSEWIC_Blow(
  MSEobj,
  syear = 2017,
  qcol = rgb(0.4, 0.8, 0.95),
  quants = c(0.05, 0.25, 0.5, 0.75, 0.95),
  nGT = 3
)

COSEWIC_Hplot(
  MSEobj,
  syear = 2017,
  qcol = rgb(0.4, 0.8, 0.95),
  quants = c(0.05, 0.25, 0.5, 0.75, 0.95)
)

COSEWIC_report(
  MSEobj,
  output_file = NA,
  author = "Author not specified",
  title = NA
)

COSEWIC_tab(MSEobj, rnd = 0, GTs = c(3, 6), syear = 2017, nGT = 3)

COSEWIC_tab_formatted(
  Ptab1,
  thresh = c(20, 40, 40, 20, 40, 40, 40, 30, 5),
  ret_thresh = F
)

Arguments

OM

An operating model object of class OM

...

Other named arguments to pass to runMSE

MSEobj

An object of class MSE with MPs = c("NFref", "FMSYref", "curE")

syear

Current year, starting year for projections (e.g. 2017)

qcol

Color of shaded regions (bars, quantiles)

quants

Quantiles of the shaded regions (vector 5 long e.g. 0.1, 0.2, 0.5, 0.8, 0.9)

nGT

Number of generation times. For COSEWIC_tab, for moving window of SSB chance (metrics A1 and A2). For COSEWIC_Blow and COSEWIC_Dplot, used for projections (the number of projection years should be greater than MaxAge * nGT).

output_file

The directory and filename you wish to use for the report e.g. "C:/temp/myMSEreport.html"

author

The person who made this report

title

The title of the report

rnd

The number of significant figures for rounding.

GTs

A vector of mean generation times to evaluate performance metrics over

Ptab1

A COSEWIC performance table made by COSEWIC_tab

thresh

A vector of thresholds for each column Health, Yield and Reb are 'greater than threshold' conditions

ret_thresh

Logical: if true just the threshold levels are returned

Functions

Author(s)

T. Carruthers

References

https://cosewic.ca/index.php/en/


[Package MSEtool version 3.7.1 Index]