knitr::opts_chunk$set(collapse = TRUE, comment = "#>") knitr::opts_chunk$set(dpi=85) #options(width = 650)
This is a prototype of an automatic report that describes the results of a demonstration COSEWIC risk analysis for the Canadian Department of Fisheries and Oceans.
A performance table is produced that provides the probability of stock status in the critical, cautious and healthy zones. Also provided are the A1 and A2 indicators of stock trend and an additional metric determining the probability of dropping below a biomass that takes three mean generation times to recover to half BMSY given zero fishing.
tab<-COSEWIC_tab(params$MSEobj) COSEWIC_tab_formatted(tab)
Cos_thresh_tab(tab)
These plots show the historical trajectory of Spawning stock biomass relative to unfished levels (upper left hand panel) and relative to MSY levels (upper right hand panel). The current status (the final year of the historical trajectories) is further described in a pair of status box and whisker plots in the lower panels.
COSEWIC_Hplot(params$MSEobj)
Future projections of spawning biomass (relative to unfished and MSY levels) are illustrated For three alternarive fishing scenarios.
COSEWIC_Pplot(params$MSEobj)
The COSEWIC indicators A1 and A2 characterize changes in spawning biomass over a moving window of three generation times. Here historical (before the vertical black line) and future spawning biomass changes are plotted for each of the three fishing scenarios.
COSEWIC_Dplot(params$MSEobj)
It can be difficult to describe a biomass level below which a stock can be considered quantitatively extinct (qualitative extinction being rare in exploited marine fish species). In this case we calculate a biomass Blow, for which it would take three generation times of zero fishing to reach 50% of BMSY. The plot below shows the probability of dropping below Blow over future projections for each of the fishing scenarios.
COSEWIC_Blow(params$MSEobj)
This report is subject to ongoing testing. If you find a bug or a problem please send a report to t.carruthers@oceans.ubc.ca so that it can be fixed or report an issue at www.github.com/DLMtool/DLMtool/issues.
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