retro: Retrospective stock assessment in FLR
In FLAssess: Generic classes and methods for stock assessment models

Description Arguments Details Value Generic function Methods Author(s) See Also Examples

WARNING: This method has now been deprecated and is no longer maintained. Users are encouraged to perform retrospective analysis using tapply. See below for an example.

Performs a retrospective stock assessment for the desired years using the stock assessment method specified in the control object (see FLAssess and extended classes)

`FLStock`	An object of type `FLStock` that contains information (catch data, natural mortality etc.) on the stock that is to be assessed
`FLIndices`	An object of type `FLIndices` that contains the tuning data
`control`	A control object of the desired extended `FLAssess` assesment method class, e.g. `FLXSA.control`
`year.range`	Numeric vector of years to perform the assessment
`retro`	An integer that specifies the number of retrospective years. Default value = 0. Only used if year.range is not specified.

The type of assessment method used is determined by the control object, e.g. FLXSA.control, FLICA.control etc. In this way retrospective analysis using different assessment methods can be easily carried out on the same stock and tuning data by using different control classes.

The argument 'year.range' is a numeric vector of years for which the assessment is to be performed. If this is not specified the integer ”retro” is used (default value = 0). If retro = 0 the assessment is run for final year only. If retro = 1, the assessment is run for the penultimate and final year and so on.

The results of the restrospective analysis can be plotted using the generic FLStocks plot() method.

NOTE: This function supercedes the previous retro() function which returned an object of type FLAssess.retro. The FLAssess.retro class is now obsolete and will not be present in future releases. Users are advised to update their scripts to use this new function. The original function is still in the FLAssess package with the name retro.old().

Returns an object of type FLStocks. Each component FLStock object contains the result of each of the retrospective assessments.

retro(stock,indices,control,retro,...)

signature(stock=FLStock,indices=FLIndex,control=ANY,retro=numeric) :: Takes a single index as an FLIndex object.
signature(stock=FLStock,indices=FLIndices,control=ANY,retro=numeric) :: Takes an FLIndices object for multiple indices.

Laurence Kell

FLAssess-class, FLICA, FLXSA

# Using the deprecated retro method
# library(FLXSA)
# data(ple4)
# data(ple4.indices)
# retro(ple4,ple4.indices,FLXSA.control(),4)

# Example using ''tapply'' and specifying the range of years.
# This example uses FLXSA
#ple4 <- ple4+FLXSA(ple4,ple4.indices,FLXSA.control())
#retro.years <- 2004:2008
#ple4.retro  <-tapply(retro.years,1:length(retro.years),function(x)
#return(window(ple4,end=x)+FLXSA(window(ple4,end=x),ple4.indices)))

# coerce into FLStocks object
# ple4.retro <- FLStocks(ple4.retro)
# full retrospective summary plot
# plot(ple4.retro)

# SPECIFIC RETROSPECTIVE PATTERNS
# SSB
#ylab <- 'SSB'
#xlab <- 'Year'
#mainttl <- 'SSB retrospective'
#xyplot(data~year,groups=qname,data=lapply(ple4.retro,ssb),xlab=xlab,ylab=ylab,main=mainttl,type="l")
 
# FBAR
#ylab <- expression(bar(F))
#xlab <- 'Year'
#mainttl <- 'mean F retrospective'
#xyplot(data~year,groups=qname,data=lapply(ple4.retro,fbar),xlab=xlab,ylab=ylab,main=mainttl,type="l")
 
# RECRUITS
#ple4.retro.rec <- list()
#for(i in 1:length(ple4.retro))
#   ple4.retro.rec[[i]] <- stock.n(ple4.retro[[i]])[1,]
#ple4.retro.rec <- FLQuants(mcf(ple4.retro.rec))
#ylab <- 'Recruits'
#xlab <- 'Year'
#mainttl <- 'Recruitment retrospective'
#xyplot(data~year,groups=qname,data=ple4.retro.rec,xlab=xlab,ylab=ylab,main=mainttl,type="l")