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Package kobe

March 20, 2013

Type Package

Title Tools for providing advice for the Tuna Regional Fisheries Management Organisations

Version 1.2.2

Date 2012-06-22

Author Laurence Kell

Maintainer Laurence Kell

Description The package reads in results from a variety of fish stock

assessment packages and summarise them in the Kobe Scientific

advice format used within the tuna Regional Fisheries

Management Organisations (tRFMOs).. Advice summarises the

probabilities of biomass being greater than and fishing

mortality less than the levels that can support maximumsustainable yield (MSY) for a range of management options.

License GPL-2

Depends

R(>= 2.15.1), methods, ggplot2, reshape, plyr, grid, MASS,coda, emdbook, tables, RCurl, ellipse

Collate ggplotFL-multiplot.R ggplotFL-theme.R kobe-generics.R

kobePhase.R kobeSmry.R kobe-aspic.R kobe-MFCL.R kobeP.R

kobe-ss.R kobe-2box.R kobe-funcs.R kobePhaseMar.R kobeTrks.R

kobe-read-methods.R kobe-SAM.R kobeShade.R

BuildResaveData xz

NeedsCompilation no

Repository CRAN

Date/Publication 2013-03-20 14:32:44

1

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2 kobe-package

R topics documented:

kobe-package . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2

data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3

k o b e - m e t h o d s . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4kobe2box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4

kobeAspic . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

k o b e I n t e r p - m e t h o d s . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

kobeMFCL . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

kobeP-methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8

k o b e P h a s e - m e t h o d s . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8

kobePhaseMar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

kobeProb . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10

kobeShade-methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

kobeSmry-methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

kobeSS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12

kobeTrks-methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13

multiplot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14theme_ms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

Index 16

kobe-package Tools for Tuna RFMOs in the Kobe

Description

Scientific Advice within the tuna Regional Fisheries Management Organisations (tRFMOs) is based

on a common framework. This requires estimating the probability that fishing mortality is less than

FMSY and SSB greater than BMSY for a range of management options; e.g. a range of total

allowable catchess (TAC).

This package provides methods for summarising stock assessment results (i.e. estimates of stock

status, reference points and projections) in the Kobe advice format.

Details

Package: kobe

Type: Package

Version: 1.0

Date: 2012-06-22

License: GPL-2

Depends: methods, ggplot2, reshape, plyr, grid, MASS, coda, emdbook, tablesCollate: kobe-generics.R kobe-funcs.R kobe-methods.R kobe-aspic.R kobe-2box.R kobe-ss.R kobe-MFCL.R mu

Built: R 2.15.1; ; 2012-10-11 17:37:36 UTC; unix

Index:

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data 3

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 differentprobabiity 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


kobeTrks Calculates confidence intervals for different

Trksabiity levels for pairs of data points.

multiplot Calculates confidence intervals for different


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.

Author(s)

Laurence Kell \ Maintainer: Laurence Kell

References

Use http://www.tuna-org.org/Documents/TRFMO3/K3-REC_ENG.pdf

data Example Datasets
http://www.tuna-org.org/Documents/TRFMO3/K3-REC_ENG.pdfhttp://www.tuna-org.org/Documents/TRFMO3/K3-REC_ENG.pdf

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Description

sims A data.frame with histrorical and projected stock biomass and harvest rate by bootstrap

iteration year and assessment run, derived from ASPIC

assmtA data.frame with histrorical stock biomass and harvest rate by bootstrap iteration yearderived from ASPIC

prj1 A data.frame with histrorical and projected stock biomass and harvest rate by bootstrap

iteration year derived from ASPIC

prj A list of data.frames with example summaries of assessment and projection

Datasets can be loaded by issuing the data command, e.g. data(sims).

References

tRFMO.

kobe-methods ~~ Methods for Function kobe in Package kobe ~~

Description

~~ Methods for function kobe in package kobe ~~

Generic function

kobe(object,method)

Methods

signature(object = "character", method = "character")

signature(object = "data.frame", method = "missing")

kobe2box Reads pro2box projection results and returns stock and harvest rate

relative to MSY reference points or proxies.

Description

Reads in text files generated by pro2box, a stock assessment projection program returns time series

or summaries of B:BMSY and F:FMSY. what specifies how data are returned, i.e. sims bootstraps

for all years; trks percentiles given by prob; year selected year(s) given by pts; smRY probabilities

of being in the kobe quadrants and; wrms bootstraps selected at random. If of length 1 then a

data.frame is returned, if >1 then a list of data.frames

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kobeAspic 5

Usage

kobe2box(object,proxy=c("fmsy","fmax","f.1","f2","f3","f4","f9max","f75max")[3],

what =c("sims","trks","pts","smry","wrms")[1], prob=c(.75,.5,.25),year=

Arguments

object character; directory in which pro2box projection files are found.

proxy character; specifies the form of data returned.

what character; specifies the form of data returned.

prob numeric; probabilities with values in [0,1] for percentiles returned ifwhat["trks"]

selected.

year numeric; year(s) for points ifwhat["pts"] selected.

nwrms numeric; number of trajectories sampled at random to return if what["wrms"]

selected.

See Also

kobeAspic,kobeMFCL,kobeSS

Examples

## Not run:

kobe2box("bft")

## End(Not run)

kobeAspic Reads ASPIC bootstraps and projections and returns stock and harvest

rate relative to MSY reference points

Description

Reads ASPIC output files with bootstrapped assesssment and projections and returns time series or

summaries of B:BMSY and F:FMSY. what specifies how data are returned , i.e. sims bootstraps for

all years; trks percentiles given by prob; year selected year(s) given by pts; smRY probabilities of

being in the kobe quadrants and; wrms bootstraps selected at random. If of length 1 then a data.frame

is returned, if >1 then a list of data.frames.

Usage

kobeAspic(object,prb,dir="",

what=c("sims","trks","pts","smry","wrms")[1], prob=c(.75,.5,.25),year=NULL,nw

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Arguments

object character: ".bio" file with estimates of stock biomass and harvest rate trajectories

for each ASPIC bootstrap trial.

prb character; ".prb" file(s) with projection results, i.e. extension of data in bio forTACs, 1 file per TAC.

dir character; optional argument identifying directory where files are.



selected.



selected.

See Also

kobe2box,kobeMFCL,kobeSS

Examples

## Not run:

#aBio="http://gbyp-sam.googlecode.com/svn/trunk/data/ASPIC/whm/212/noBrazil/aspic.bio"

res=kobeAspic(aBio,what=c("pts","trks"))

kobePhase(res$pts)+

geom_point(aes(stock,harvest))+

geom_path( aes(stock,harvest),data=subset(res$trks,Percentile=="5%"))+

scale_y_continuous(limits=c(,3))

## End(Not run)

kobeInterp-methods Methods to generate the Kobe II Strategy Matrix.

Description

Plot of the Kobe II Strategy Matrix, probabilities of being in the green zone of the Kobe phase plot

by year and management options.

Methods

signature(object = "data.frame")

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kobeMFCL 7

kobeMFCL Reads Multifan-CL assessment results and returns stock and harvest

rate relative to MSY reference points

Description

Reads in text file generated by MFCL and returns time series or summaries of B:BMSY and

F:FMSY. what specifies how data are returned, i.e. sims bootstraps for all years; trks percentiles

given by prob; year selected year(s) given by pts; smRY probabilities of being in the kobe quad-

rants and; wrms bootstraps selected at random. If of length 1 then a data.frame is returned, if >1

then a list of data.frames.

Usage

kobeMFCL(object,dir="",

what=c("sims","trks","pts","smry","wrms")[1], prob=c(.75,.5,.25),year=NULL,nw

Arguments

object character: rep file with results.

dir character; optional argument identifying directory where file is.



selected.



selected.

See Also

kobeAspic,kobe2box,kobeMFCL,kobeSS

Examples

## Not run:

kobeMFCL("bft")

## End(Not run)

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8 kobePhase-methods

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.

Description

kobeP

Usage

kobeP(stock, harvest,...)

Arguments

stock numeric vector representing stock or a data.frame with columns for stock and

harvest

harvest numeric vector resprenting harvest

... other

See Also

kobePhase,kobeInterp,kobeP

Examples

## Not run:

data(sims)

## where is point

res=head(kobeP(sims$stock,sims$harvest))

## End(Not run)

kobePhase-methods Kobe phase plot

Description

A plot of assessment results of F verses biomass which summarises stock status by plotting points

by coloured quadrant, I.e. green quadrant (not overfished, no overfishing), the yellow quadrant

(overfished or overfishing), and the red quadrant (overfished and overfishing).

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kobePhaseMar 9

Methods


signature(object = "FLlst")

signature(object = "missing")

kobePhaseMar Plots Kobe phase plot with marginal densities.

Description

kobePhaseMar Uses kde2d to calculate a bivariate density, then normalizes the results and calculates

the contour corresponding to a contained volume of Phase of the total volume under the surface (i.e.

a two-dimensional Bayesian credible region).

Usage

kobePhaseMar(pts,trks=NULL,mns=FALSE,size=1,

xlab=expression(B:B[MSY]),

ylab=expression(F:F[MSY]),

maxX=2,maxY=maxX,

col =colorRampPalette(c("orange","blue"),space="Lab"),

shade=.5,col2=grey(shade),col3=grey(shade*1.1))

Arguments

pts numeric vector

trks numeric vector

mns logical:

size numeric:

xlab numeric:

ylab numeric:

maxX numeric:

maxY numeric:

col function:

shade character:

col2 character:

col3 character:

See Also


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10 kobeProb

Examples

####

#data(sims)

#pts=subset(sims,year=21)

#kobePhaseMar(x=pts$stock, y=pst$harvest)

kobeProb Calculates 2 dimenisonal confidence intervals for data pairs.

Description

kobeProb Uses kde2d to calculate a bivariate density, then normalises the results and calculatesthe contour corresponding to a contained volume of the total volume under the surface (i.e. a two-

dimensional Bayesian credible region).

Usage

kobeProb(x, y, prob=c(.5, .75, .95), na.rm=FALSE)

Arguments

x numeric vector

y numeric vector

prob numeric vector of probabilities with values in [0,1].

na.rm logical; if true, any NA and NaNs are removed from x before the quantiles are

computed.

See Also


Examples

## Not run:

data(prj)geom_path(aes(x,y,group=level),colour="blue",

data=kobeProb(prj$pts$stock,prj$pts$harvest,prob=c(.7,.5,.25)))

## End(Not run)

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kobeShade-methods 11

kobeShade-methods Shades matrix depending on value of elements

Description

Kobe II strategy matrices to be prepared by the SCRS should highlight in a similar format as shown

in Annex Table 2 a progression of probabilities over 50 % and in the range of 50-59 %, 60-69 %,

70-79 %, 80-89 % and ??? 90 %.

Methods


signature(object = "matrix")

signature(object = "numeric")

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.

Description

kobeSmry

Usage

kobeSmry(stock,harvest,...)

Arguments

stock numeric vector representing stock or a data.frame with columns for stock and

harvest

harvest numeric vector respresenting harvest

... other

Methods

signature(stock="numeric,"harvest="numeric") takes as input numeric vectors of stock and

harvest

signature(stock="data.frame",harvest="missing") takes as input a data.frame with columns

names as stock and harvest

See Also


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12 kobeSS

Examples

## Not run:

data(sims)

## calculate probabilities

res=ddply(subset(sims, year > 21 & year BMSY

1-cast(res,TAC~year,value="overFished")

## K2SM for F1 then a list of data.frames.

Usage

kobeSS(object,nrows=-1,thin=1,

what=c("sims","trks","pts","smry","wrms")[1], prob=c(.75,.5,.25),year=NULL,nwrm

Arguments

object character: derived posteriors file with MCMC runs.

nrows numeric; if -ve reads all rowss, otherwise takes the 1st nrows from the file.

thin numeric; thinning rate for chain.


prob numeric; probabilities with values in [0,1] for percentiles returned ifwhat["trks"]selected.

year numeric; year(s) for points if what["pts"] selected and years for historical

estimates.


selected.

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kobeTrks-methods 13

See Also

kobeAspic,kobe2box,kobeSS

Examples

## Not run:

kobeSS(...)

## End(Not run)

kobeTrks-methods Calculates confidence intervals for different probabiity levels for pairs

of data points.

Description

kobeTrks Uses kde2d to calculate a bivariate density, normalizes the results and then calculates the

contour(S) corresponding to a contained volume of points of the total volume under the surface (i.e.

a two-dimensional Bayesian credible region).

Usage

kobeTrks(stock,harvest,...)

Arguments

stock numeric vector representing stock or a data.frame with columns for stock andharvest

harvest character

... character

Methods

signature(stock="data.frame")

signature(stock="numeric",harvest="numeric")

Examples

#data(sims)

#pts=subset(sims,year==21)

#kobeTrks(x=pts$stock, y=pts$harvest)

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multiplot Calculates confidence intervals for different probabiity levels for pairs

of data points.

Description

A multiple plot function, allowing ggplot2 objects to be plotted together. If the layout is something

like matrix(c(1,2,3,3), nrow=2, by.row=TRUE), then plot 1 will go in the upper left, 2 will go in the

upper right, and 3 will go all the way across the bottom.

Borrowed with thanks from http://wiki.stdout.org/rcookbook/Graphs/Multiple

Usage

multiplot(..., plotlist=NULL, file, cols=1, layout=NULL)

Arguments

... ggplot2 objects

plotlist list ofggplot2 objects

file character

cols numeric; number of columns in layout

layout numeric; A matrix specifying the layout. If present, cols is ignored

See Also


Examples

## Not run:

a=ggplot(data.frame(x=1:1,y=1:1))+geom_point(aes(x,y))

multiplot(a,a)

## End(Not run)

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theme_ms 15

theme_ms ggplot2 theme

Description

A ggplot2 theme for presentation of plots

Usage

theme_ms(base_size=12, base_family="", ...)

Arguments

base_size numeric: default font size.

base_family character; default font.

... any other arguments.

Details

The ggplot2 "grammar of graphics" package includes "Themes" for ggplot2 charts, making it pos-

sible to define and re-use your own preferences for title fonts and sizes, tick marks, grid color,

etc.

Source

see https://github.com/hadley/ggplot2/wiki/Themes

Examplesdata(prj)

ggplot(subset(prj$trks, Percentile=="5%")) +

geom_line(aes(year,stock,group=TAC,col=TAC)) +

theme_ms()

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Index

Topic \textasciitilde\textasciitildeother possible keyword(s)

\textasciitilde\textasciitildekobeInterp-methods, 6

kobePhase-methods, 8

kobeShade-methods, 11

Topic datasetsdata, 3

Topic ggplot2theme_ms, 15

Topic kobePhasekobe-methods, 4

Topic methodskobe-methods, 4

kobeInterp-methods, 6



Topic packagekobe-package, 2

Topic plottheme_ms, 15

Topic themetheme_ms, 15

assmt (data), 3

data, 3

kobe (kobe-methods), 4

kobe,character,character-method

(kobe-methods), 4

kobe,data.frame,missing-method

(kobe-methods), 4

kobe-method (kobe-methods), 4

kobe-methods, 4

kobe-package, 2

kobe2box, 4, 6, 7, 13

kobeAspic, 5, 5, 7, 13

kobeInterp, 811, 14

kobeInterp (kobeInterp-methods), 6

kobeInterp,data.frame-method

(kobeInterp-methods), 6

kobeInterp-methods, 6

kobeMFCL, 57, 7

kobeP, 811, 14

kobeP (kobeP-methods), 8

kobeP,data.frame,missing-method

(kobeP-methods), 8

kobeP,numeric,numeric-method

(kobeP-methods), 8

kobeP-methods, 8

kobePhase, 811, 14

kobePhase (kobePhase-methods), 8

kobePhase,data.frame-method

(kobePhase-methods), 8

kobePhase,list-method


kobePhase,missing-method



kobePhaseMar, 9kobeProb, 10

kobeShade (kobeShade-methods), 11

kobeShade,cast_df-method

(kobeShade-methods), 11

kobeShade,data.frame-method


kobeShade,matrix-method


kobeShade,numeric-method



kobeSmry (kobeSmry-methods), 11

kobeSmry,data.frame,missing-method

(kobeSmry-methods), 11

kobeSmry,numeric,numeric-method

(kobeSmry-methods), 11

kobeSmry-methods, 11

kobeSS, 57, 12, 13

16

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INDEX 17

kobeTrks (kobeTrks-methods), 13

kobeTrks,data.frame,missing-method

(kobeTrks-methods), 13

kobeTrks,numeric,numeric-method

(kobeTrks-methods), 13kobeTrks-methods, 13

multiplot, 14

prj (data), 3

prj1 (data), 3

sims (data), 3

theme_ms, 15