R/SS3Biomass.fn.R

In SurveyCode: What the package does (short line)

SS3Biomass.fn <-
function(bio,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))
    xxx <- split(bio[,c("AreaName","MinStratumDepth","MaxStratumDepth","Biomass","BiomassVar")],bio$Year)
    years <- names(xxx)
    bio <- unlist(lapply(xxx,function(x){sum(x$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(Year=years,Season=season,Fleet=fleet,Value=med,seLogB=seLogB)
    }
    else {
        out <- data.frame(Year=years,Season=season,Fleet=fleet,Value=bio,seLogB=seLogB)
    }
    row.names(out) <- NULL
    return(out)
}