kobe (version 1.3.2)

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(0.75,0.5,0.25),year=NULL,nwrms=10)

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 for TACs, 1 file per TAC.

dir

character; optional argument identifying directory where files are.

what

character; specifies the form of data returned.

prob

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

year

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

nwrms

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

See Also

kobe2box,kobeMFCL,kobeSS

Examples

## Not run: 
# 
# #aBio="http://gbyp-sam.googlecode.com/svn/trunk/data/ASPIC/whm/2012/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=="50%"))+
#      scale_y_continuous(limits=c(0,3))
# ## End(Not run)