The tuna Regional Fisheries Management Organisations (tRFMOs) use a common framework for providing scintific advice, i.e. the Kobe II Framework. This is based on maintaining fishing mortality below FMSY and stock biomass above BMSY. This package provides methods for summarising results from stock assessments and Management Strategy Evaluations in the Kobe format.
| Package: |
| kobe |
| Type: |
| Package |
| Version: |
| 1.0 |
| Date: |
| 2012-06-22 |
| License: |
| GPL-2 |
| Depends: |
| methods, ggplot2, reshape, plyr, grid, MASS, coda, emdbook, tables |
| Collate: |
| kobe-generics.R kobe-funcs.R kobe-methods.R kobe-aspic.R kobe-2box.R kobe-ss.R kobe-MFCL.R multiplot.R kobe-Phase.R kobe-k2sm-ggplot2.R kobe-themes.R |
| Built: |
| R 2.15.1; ; 2012-10-11 17:37:36 UTC; unix |
Index:
kobe-package Provides tools for plotting advice in the tRFMO format
kobe2box Reads pro2box projection results and returns
stock and harvest rate relative to BMSY and
FMSY
kobe2sm Calculates confidence intervals for different
probabiity levels for pairs of data points.
kobeAspic Reads ASPIC bootstrap and projections outputs
and returns stock and harvest rate relative to
BMSY and FMSY
kobeMFCL Reads Multifan-CL assessment results and
returns stock and harvest rate relative to BMSY
and FMSY
kobeP Calculates the probability of being over-fished
or subject to over-fishing and being in one of
the kobe phase plots quadrants.
kobePhase Calculates confidence intervals for different
Phaseabiity levels for pairs of data points.
kobePhaseMar Calculates confidence intervals for different
Phaseabiity levels for pairs of data points.
kobeProb Calculates confidence intervals for different
probabiity levels for pairs of data points.
kobeSS Reads SS assessment results and returns stock
and harvest rate relative to BMSY and FMSY
kobeShade Calculates confidence intervals for different
probabiity levels for pairs of data points.
kobeTrks Calculates confidence intervals for different
Trksabiity levels for pairs of data points.
multiplot Calculates confidence intervals for different
probabiity levels for pairs of data points.
sims kobe datasets
The package can be used to read in stock assessment results as text files from a variety of packages. These can then be summarised and plotted.