Nothing
strataBiomass.fn <-
function(bio,theStrata="Year",fleet="EnterFleet",season=1,outputMedian=T) {
#This function outputs a dataframe in the abundance index format needed for SS3
#it calculates the standard error of log(B) by first finding the cv of B
#It can output the median biomass or the mean biomass. Median biomass is bias corrected so that log(Bmedian)=mean(log(B))
#print(bio[,theStrata])
xxx <- split(bio[,c(theStrata,"Biomass","BiomassVar")],bio[,theStrata])
strat <- names(xxx)
bio <- unlist(lapply(xxx,function(x){sum(x$Biomass,na.rm=T)}))
variance <- unlist(lapply(xxx,function(x){sum(x$BiomassVar,na.rm=T)}))
cv <- sqrt(variance)/bio
seLogB <- sqrt(log(cv^2+1))
if(outputMedian==T) {
med <- bio*exp(-0.5*seLogB^2)
out <- data.frame(Stratum=strat,Season=season,Fleet=fleet,Value=med,seLogB=seLogB)
}
else {
out <- data.frame(Stratum=strat,Season=season,Fleet=fleet,Value=bio,seLogB=seLogB)
}
row.names(out) <- NULL
return(out)
}
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