% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/DFO.R
\name{runCOSEWIC}
\alias{runCOSEWIC}
\alias{COSEWIC_Pplot}
\alias{COSEWIC_Dplot}
\alias{COSEWIC_Blow}
\alias{COSEWIC_Hplot}
\alias{COSEWIC_report}
\alias{COSEWIC_tab}
\alias{COSEWIC_tab_formatted}
\title{COSEWIC MSE run using the correct MPs and projected time horizon}
\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{
\item{OM}{An operating model object of class OM}

\item{...}{Other named arguments to pass to \code{runMSE}}

\item{MSEobj}{An object of class MSE with \code{MPs = c("NFref", "FMSYref", "curE")}}

\item{syear}{Current year, starting year for projections (e.g. 2017)}

\item{qcol}{Color of shaded regions (bars, quantiles)}

\item{quants}{Quantiles of the shaded regions (vector 5 long e.g. 0.1, 0.2, 0.5, 0.8, 0.9)}

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

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

\item{author}{The person who made this report}

\item{title}{The title of the report}

\item{rnd}{The number of significant figures for rounding.}

\item{GTs}{A vector of mean generation times to evaluate performance metrics over}

\item{Ptab1}{A COSEWIC performance table made by \code{COSEWIC_tab}}

\item{thresh}{A vector of thresholds for each column Health, Yield and Reb are 'greater than threshold' conditions}

\item{ret_thresh}{Logical: if true just the threshold levels are returned}
}
\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.
}
\section{Functions}{
\itemize{
\item \code{runCOSEWIC}: Calls \code{runMSE} with number of projection years for 6x maximum age and
uses \code{NFref}, \code{FMSYref}, and \code{curE} MPs.

\item \code{COSEWIC_Pplot}: Projection plots of spawning stock biomass under three scenarios:
no catch, FMSY fishing and status quo fishing effort.

\item \code{COSEWIC_Dplot}: Depletion plots evaluate whether significant declines have
occurred over three generation times in both historical and projection years.

\item \code{COSEWIC_Blow}: Plots that evaluate the likelihood of declining below \code{Blow},
by default, biomass that takes 3 generation times to reach half BMSY with zero fishing

\item \code{COSEWIC_Hplot}: Plots of historical spawning stock  relative to unfished and MSY levels.

\item \code{COSEWIC_report}: Create a standard DFO COSEWIC report (provides performance plots
to inform COSEWIC processes in Canadian fish stocks).

\item \code{COSEWIC_tab}: Creates a standard COSEWIC performance table:
\itemize{
\item \code{P_Cr} is the probability of being in the critical zone (less than 20\% depletion)
\item \code{P_Ct} is the probability of being in the cautious zone (between 20\% and 40\% depletion)
\item \code{P_H} is the probability of being in the healthy zone (above 40\% depletion)
\item \code{P_Cr_MSY} is the probability of being in the critical zone (less than 40\% BMSY)
\item \code{P_Ct_MSY} is the probability of being in the cautious zone (between 40\% and 80\% BMSY)
\item \code{P_H_MSY} is the probability of being in the healthy zone (above 80\% BMSY)
\item \code{Caut} is the probability of being in the cautious zone in the last 10 projected years
\item \code{P_A1} is the probability of being designated threatened according to COSEWIC Indicator A1 (Spawning biomass less than 70\% that three generation times previously)
\item \code{P_A2} is the probability of being designated threatened according to COSEWIC Indicator A2 (Spawning biomass less than 50\% that three generation times previously)
\item \code{Blow} is the probability that the stock is below the biomass for which it takes 3 generation times to reach 50\% BMSY with zero fishing
}

\item \code{COSEWIC_tab_formatted}: A formatted version of the standard COSEWIC performance plot,
color coded by thresholds.
}}

\references{
\url{http://cosewic.ca/index.php/en-ca/}
}
\author{
T. Carruthers
}
