Tools for providing advice for the Tuna Regional Fisheries Management Organisations


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Documentation for package ‘kobe’ version 1.2.2

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kobe-package Tools for Tuna RFMOs in the Kobe
assmt Example Datasets
kobe ~~ Methods for Function 'kobe' in Package 'kobe' ~~
kobe-method ~~ Methods for Function 'kobe' in Package 'kobe' ~~
kobe2box Reads pro2box projection results and returns stock and harvest rate relative to MSY reference points or proxies.
kobeAspic Reads ASPIC bootstraps and projections and returns stock and harvest rate relative to MSY reference points
kobeInterp Methods to generate the Kobe II Strategy Matrix.
kobeInterp-method Methods to generate the Kobe II Strategy Matrix.
kobeInterp-methods Methods to generate the Kobe II Strategy Matrix.
kobeMFCL Reads Multifan-CL assessment results and returns stock and harvest rate relative to MSY reference points
kobeP Calculates whether each point corresponds to being over-fished or subject to over-fishing and being in the red, green or yellow regions of the kobe phase plots quadrants.
kobeP-method Calculates whether each point corresponds to being over-fished or subject to over-fishing and being in the red, green or yellow regions of the kobe phase plots quadrants.
kobeP-methods Calculates whether each point corresponds to being over-fished or subject to over-fishing and being in the red, green or yellow regions of the kobe phase plots quadrants.
kobePhase Kobe phase plot
kobePhase-method Kobe phase plot
kobePhase-methods Kobe phase plot
kobePhaseMar Plots Kobe phase plot with marginal densities.
kobeProb Calculates 2 dimenisonal confidence intervals for data pairs.
kobeShade Shades matrix depending on value of elements
kobeShade-method Shades matrix depending on value of elements
kobeShade-methods Shades matrix depending on value of elements
kobeSmry Calculates the probability of being over-fished or subject to over-fishing and being in the red, green or yellow regions of the kobe phase plots quadrants.
kobeSmry-method Calculates the probability of being over-fished or subject to over-fishing and being in the red, green or yellow regions of the kobe phase plots quadrants.
kobeSmry-methods Calculates the probability of being over-fished or subject to over-fishing and being in the red, green or yellow regions of the kobe phase plots quadrants.
kobeSS Reads SS assessment results and returns stock and harvest rate relative to MSY reference points
kobeTrks Calculates confidence intervals for different probabiity levels for pairs of data points.
kobeTrks-method Calculates confidence intervals for different probabiity levels for pairs of data points.
kobeTrks-methods Calculates confidence intervals for different probabiity levels for pairs of data points.
multiplot Calculates confidence intervals for different probabiity levels for pairs of data points.
prj Example Datasets
prj1 Example Datasets
sims Example Datasets
theme_ms ggplot2 theme