runCOSEWIC: COSEWIC MSE run using the correct MPs and projected time...
In DLMtool/DLMtool: Data-Limited Methods Toolkit

Description Usage Arguments Functions Author(s) References

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.

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
)

`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

runCOSEWIC: Calls runMSE with number of projection years for 6x maximum age and uses NFref, FMSYref, and curE MPs.
COSEWIC_Pplot: Projection plots of spawning stock biomass under three scenarios: no catch, FMSY fishing and status quo fishing effort.
COSEWIC_Dplot: Depletion plots evaluate whether significant declines have occurred over three generation times in both historical and projection years.
COSEWIC_Blow: Plots that evaluate the likelihood of declining below Blow, by default, biomass that takes 3 generation times to reach half BMSY with zero fishing
COSEWIC_Hplot: Plots of historical spawning stock relative to unfished and MSY levels.
COSEWIC_report: Create a standard DFO COSEWIC report (provides performance plots to inform COSEWIC processes in Canadian fish stocks).
COSEWIC_tab: Creates a standard COSEWIC performance table:
- P_Cr is the probability of being in the critical zone (less than 20% depletion)
- P_Ct is the probability of being in the cautious zone (between 20% and 40% depletion)
- P_H is the probability of being in the healthy zone (above 40% depletion)
- P_Cr_MSY is the probability of being in the critical zone (less than 40% BMSY)
- P_Ct_MSY is the probability of being in the cautious zone (between 40% and 80% BMSY)
- P_H_MSY is the probability of being in the healthy zone (above 80% BMSY)
- Caut is the probability of being in the cautious zone in the last 10 projected years
- P_A1 is the probability of being designated threatened according to COSEWIC Indicator A1 (Spawning biomass less than 70% that three generation times previously)
- P_A2 is the probability of being designated threatened according to COSEWIC Indicator A2 (Spawning biomass less than 50% that three generation times previously)
- 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
COSEWIC_tab_formatted: A formatted version of the standard COSEWIC performance plot, color coded by thresholds.