R/assign_phi.R

In DanOvando/GUM: Run Global Upsides Model

#' assign_phi
#'
#' \code{assign_phi} finds the phi in PT model given a BvK ratio
#' @param data data
#' @param taxdata the taxdata
#' @param phidata the phidata
#' @param default_phi default phi
#' @param min_phi minimum possible phi
#'
#' @return the phi that produces target BvK ratio
#' @export
assign_phi <- function(data, taxdata, phidata, default_phi = 0.188, min_phi = .1)
{

  phidata$order <- tolower(phidata$order)

  data$phi <- NA

  for (p in 1:dim(phidata)[1])
  {
    phidata$phi[p] <- pmax(min_phi,find_phi(target_msy_ratio = phidata$msy_ratio[p]))
  }

  data$paste_name <- paste(data$SciName,data$CommName, sep = '-')

  taxdata$paste_name <- paste(taxdata$SciName,taxdata$CommName, sep = '-')

  taxdata <- taxdata[,c('paste_name','order')]

  data <- join(data, taxdata, by = 'paste_name')

  data$order <- tolower(data$order)

  data <- select(data, -phi, -paste_name)

  phidata <- select(phidata,order,phi)

  data <- join(data,phidata, by = 'order')

  data$phi[is.na(data$phi)] <- default_phi

  return(data)

}