#' Return the right whale population level health as a data frame
#'
#' @param ngg A scalar corresponding to the number of Gibbs steps
#' @param tIndex A vector containing values 1:nt
#' @param monYr An nt by 2 matrix containing months in the first column and years in the second
#' @param newgibbsMales A matrix containing the estimates of right whale health for Adult Males
#' @param newgibbsJuvs1 A matrix containing the estimates of right whale health for Young Juveniles
#' @param newgibbsJuvs3 A matrix containing the estimates of right whale health for Old Juveniles
#' @param newgibbsMales2 A matrix containing the estimates of standard deviation of right whale health for Adult Males
#' @param newgibbsJuvs12 A matrix containing the estimates of standard deviation of right whale health for Young Juveniles
#' @param newgibbsJuvs32 A matrix containing the estimates of standard deviation of right whale health for Old Juveniles
#'
#' @return A data frame of right whale population level health, comprised of median health between Adult males, and young and old juveniles
#' @export
#' @examples
#' \dontrun{
#' returnPophealth()
#' }
#'
returnPophealth <- function() {
healthmeanM <- newhgibbsMales / ngg
healthmeanJ1 <- newhgibbsJuvs1 / ngg
healthmeanJ2 <- newhgibbsJuvs3 / ngg
healthmeanMSD <- newhgibbsMales2 / ngg
healthmeanJ1SD <- newhgibbsJuvs12 / ngg
healthmeanJ2SD <- newhgibbsJuvs32 / ngg
for(i in 1:nrow(healthmean)){
healthmeanM[i, 1:firstSight[i]] <- NA
healthmeanJ1[i, 1:firstSight[i]] <- NA
healthmeanJ2[i, 1:firstSight[i]] <- NA
healthmeanMSD[i, 1:firstSight[i]] <- NA
healthmeanJ1SD[i, 1:firstSight[i]] <- NA
healthmeanJ2SD[i, 1:firstSight[i]] <- NA
}
newPopCat <- rbind(healthmeanM, healthmeanJ1, healthmeanJ2)
newPopMedian <- apply(newPopCat, 2, median, na.rm = TRUE)
newPopAllVar <- rbind(healthmeanMSD, healthmeanJ1SD, healthmeanJ2SD)
newPopvar <- newPopAllVar - newPopCat ^ 2
newpopsd <- sqrt(newPopvar)
newpopsdmean <- apply(newpopsd, 2, median, na.rm = TRUE)
popplot <- data.frame(time = tIndex,
popHealth = newPopMedian,
hsd = newpopsdmean,
date = makeYearmon(monYr))
popplot
}
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