#' @title Fatality simulator (deprecated)
#' @author Mark Otto (FWS)
#'
#' @description This function calculates the annual predicted fatalities at a location. It has been deprecated. Use simFatalCPr() instead
#' @param Emin Total number of eagle minutes observed in pre-construction monitoring
#' @param SmpHrKM2 Total surveyed hours * area surveyed
#' @param ExpFac Expansion factor
#' @param CPrPriors Collision probability priors, either USFWS or Bay. If neither, custom priors must be provided.
#' @param aPriExp Alpha parameter for the exposure prior. Defaults to 0.9776543.
#' @param bPriExp Beta parameter for the exposure prior. Defaults to 2.777427.
#' @param aPriCpr Alpha parameter for the exposure prior. Must be supplied if neither USFWS nor Bay priors are selected.
#' @param bPriCpr Beta parameter for the exposure prior. Must be supplied if neither USFWS nor Bay priors are selected.
#' @export
#' @import rv
### Fatality Functions - 23 Apr 2013 ###
simFatal<-function(EMin,SmpHrKM2,ExpFac,CPrPriors = "USFWS",
aPriExp=0.9776543,bPriExp=2.777427,aPriCPr=NULL, bPriCPr=NULL){
if(CPrPriors == "USFWS"){
aPriCPr=2.31
bPriCPr=396.69
} else if(CPrPriors == "Bay"){
aPriCPr<-9.28
bPriCPr<-3224.51
}
# Update the exposure prior
aPostExp<-aPriExp+EMin
bPostExp<-bPriExp+SmpHrKM2
print(c(aPostExp=aPostExp,bPostExp=bPostExp,aPriCPr=aPriCPr,bPriCPr=bPriCPr))
Exp<-rvgamma(n=1,aPostExp,bPostExp)
CPr<-if(bPriCPr==0){
aPriCPr
} else {
rvbeta(n=1,aPriCPr,bPriCPr)
}
Fatalities<-ExpFac*Exp*CPr
attr(Fatalities,"Exp")<-cbind(Mean=rvmean(Exp),SD=rvsd(Exp))
return(Fatalities)
}
#' @title Fatality simulator with collison probaility
#' @author Joe Statwick (Arcadis)
#' @author Mark Otto (FWS)
#'
#' @description This function calculates the annual predicted fatalities at a location, when post construction mortality monitoring is completed.
#' @param Emin Total number of eagle minutes observed in pre-construction monitoring. Entering a negative value indicates no surveys performed.
#' @param SmpHrKM2 Total surveyed hours * area surveyed in pre-construction monitoring
#' @param EOutmin Total number of eagle carcasses observed in post-construction mortality monitoring. Entering a negative value indicates no surveys performed.
#' @param CprHrKM2 Total surveyed hours * hazardous area surveyed in post-construction mortality monitoring
#' @param ExpFac Expansion factor
#' @param CPrPriors Collision probability priors, either USFWS or Bay. If neither, custom priors must be provided.
#' @param aPriExp Alpha parameter for the exposure prior. Defaults to 0.9776543.
#' @param bPriExp Beta parameter for the exposure prior. Defaults to 2.777427.
#' @param aPriCpr Alpha parameter for the exposure prior. Must be supplied if neither USFWS nor Bay priors are selected.
#' @param bPriCpr Beta parameter for the exposure prior. Must be supplied if neither USFWS nor Bay priors are selected.
#' @export
#' @import rv
simFatalCPr <- function(EMin, EOutMin, SmpHrKM2, CprHrKM2, ExpFac, CPrPriors = "USFWS", aPriExp=0.9776543,bPriExp=2.777427, aPriCPr=NULL, bPriCPr=NULL){
# EMin: observed number of eagle minutes
# EOutMin: annual eagle fatalities on an operational wind facility
# SmpHrKM2:total hr km2 surveyed for eagle minutes
# ExpFac:expansion factor
# aPriExp: alpha parameter for the prior on lambda
# bPriExp: beta parameter for the prior on lambda
# aPriCPr: alpha parameter for the prior on C
# bPriCPr: beta parameter for the prior on C
# Entering a negative value for EMin or EOutMin indicates that no data
# were collected for those model inputs
if(CPrPriors == "USFWS"){
aPriCPr=2.31
bPriCPr=396.69
} else if(CPrPriors == "Bay"){
aPriCPr<-9.28
bPriCPr<-3224.51
}
# Update the exposure prior
if(EMin>=0){
aPostExp <- aPriExp + EMin
bPostExp <- bPriExp + SmpHrKM2
}else{
aPostExp <- aPriExp
bPostExp <- bPriExp}
Exp <- rvgamma(n=1, aPostExp, bPostExp)
nsurveys<-CprHrKM2*Exp #hazardous space-time surveyed times exposure
# Update the collisions prior
if(EOutMin>=0){
aPostCPr <- aPriCPr + EOutMin
bPostCPr <- bPriCPr + nsurveys
}else{
aPostCPr <- aPriCPr
bPostCPr <- bPriCPr}
CPr <- rvbeta(n=1, aPostCPr, bPostCPr)
Fatalities <- ExpFac * Exp * CPr
attr(Fatalities,"Exp") <- c(Mean=rvmean(Exp), SD=rvsd(Exp))
attr(Fatalities,"CPr") <- c(Mean=rvmean(CPr), SD=rvsd(CPr))
return(Fatalities)}
#' @title Fatality plotter
#' @author Mark Otto (FWS)
#'
#' @description This function plots the annual predicted fatalities at a location.
#' @param Fatalities Predicted distribution of fatalities, as generated by simFatalCpr
#' @param probs Desired upper confidence limit(s) on the mean estimate of fatalities. Defaults to 0.8
#' @param ... further arguments passed to the function hist
#' @export
#' @import rv
plotFatal<-function(Fatalities,probs=0.8,PlotHist=TRUE,
xlim=NULL,xlab="Collisions",ylab="Density",# bty="o",
col="red",add=FALSE,...){
Names<-if(is.null(names(Fatalities))) 1:length(Fatalities) else
names(Fatalities)
Smry<-RVSmry(Names,Fatalities,probs=probs)
ColIdx<-grepl("CI",colnames(Smry))
CIs<-Smry[,ColIdx]
if(!add){
if(is.null(xlim)) xlim<-c(0,1.1*rvquantile(Fatalities,probs=0.99))
rvhist(Fatalities,xlab=xlab,ylab=ylab,
xlim=xlim,freq=FALSE,# bty=bty,
...
)
}
lines(density(as.numeric(Fatalities[[1]],bw="sj")),col=if(add) col else "blue")
abline(v=Smry$Mean,col=if(add) col else "black")
abline(v=CIs,col=col)
invisible(NULL)
}
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