R/make_eggs.R

In danStich/anadrofish: Anadromous Fish Population Responses to Habitat Changes

#' @title Simulate number of eggs per fish
#'
#' @description Function used to simulate number of eggs 
#' produced per female (potential annual fecundity, PAF),
#' for rivers included in \code{\link{get_rivers}}.
#'
#' @param river The river for which eggs will be simulated.
#' 
#' @param species Species for which population dynamics will be simulated.
#' Choices include American shad (\code{"AMS"}), alewife (\code{"ALE"}), and
#' blueback herring (\code{"BBH"}).
#' 
#' @param custom_habitat A dataframe containing columns corresponding to the
#' those in the output from \code{\link{custom_habitat_template}}. The default,
#' \code{NULL} uses the default habitat data set for a given combination of
#' \code{species} and \code{river}.
#' 
#' @section Details:
#' The default method for American shad uses predictive equations from Olney and
#' McBride (2003) to simulate batch fecundity from weight-fecundity relationships
#' using coefficients in \code{\link{olney_mcbride}} for the life-history region
#' corresponding to the specified river. Number of batches for this
#' approach is currently drawn from a random normal distribution
#' with a mean of 6.7 and a standard deviation of 2.1 (McBride et al. 2016).
#' 
#' The default method for river herring calls \code{\link{make_eggs_rh}} with
#' simulation methods and references described therein.
#'
#' @return A vector containing age-specific potential annual 
#' fecundity with \code{length = max_age}. 
#'
#' @examples make_eggs(river="Susquehanna", species = "AMS")
#'
#' @references Olney, J. E. and R. S. McBride. 2003. Intraspecific 
#' variation in batch fecundity of American shad (Alosa sapidissima): 
#' revisiting the paradigm of reciprocal latitudinal trends 
#' in reproductive traits. American Fisheries Society 
#' Symposium 35:185-192.
#' 
#' McBride, R. S., R. Ferreri, E. K. Towle, J. M. Boucher, and 
#' G. Basilone, G. 2016. Yolked oocyte dynamics support agreement 
#' between determinate- and indeterminate-method estimates of annual 
#' fecundity for a northeastern United States population of 
#' American shad. PLoS ONE 11(10): 10.1371/journal.pone.0164203
#' 
#' @export
#'
#' @importFrom truncnorm rtruncnorm
#' 
make_eggs <- function(river, species = c("AMS", "ALE", "BBH"),
                      custom_habitat = NULL){
  
  # Error handling ----
  # Require species to be specified from vector of choices
  if(!missing(species)) species <- match.arg(species, c('AMS', 'ALE', 'BBH'))
  
  # River error handling
  if(missing(river)){
    stop("
    
    Argument 'river' must be specified.
    
    To see a list of available rivers, run get_rivers() or specify river name
    in custom_habitat if used.")    
  }
  
  if(!river %in% get_rivers(species) & is.null(custom_habitat)){
    stop("
    
    Argument 'river' must be one of those included in get_rivers() or in
    custom_habitat if used.
    
    To see a list of available rivers, run get_rivers()")
  }
  
  if(species == "AMS"){
    
    # Get region
    region <- get_region(river = river, species = species, 
                         custom_habitat = custom_habitat) 
    
    # Get maximum age 
    max_age <- anadrofish::max_ages$maxage[
      anadrofish::max_ages$region==region & 
      anadrofish::max_ages$sex=='F']
    
    # Get growth params for region from built-in data
    growth_parms <- get(paste0('vbgf_', region))
    
    # Take one sample from posterior
    growth_parms <- growth_parms[sample(1:nrow(growth_parms), 1), ]
    Linf <- growth_parms[,1]
    K <- growth_parms[,2]
    t0 <- growth_parms[,3]
    
    # Get sequence of ages
    ages <- seq(1, max_age, 1)
    
    # Predict fork length at age
    fl <- Linf * (1 - exp( -K*(ages-t0)))
    
    # Get length-weight regression parameters
    alpha <- anadrofish::length_weight$alpha[
      anadrofish::length_weight$region==region &
      anadrofish::length_weight$sex=="F"]
    beta <- anadrofish::length_weight$beta[
      anadrofish::length_weight$region==region & 
      anadrofish::length_weight$sex=="F"]
  
    # Predict mass (g) from fl (mm)
    mass <- alpha * fl^beta
  
    # Calculate number of eggs per batch based on Olney & McBride (2003)
    fec_alpha = anadrofish::olney_mcbride$alpha[
      anadrofish::olney_mcbride$region==region]
    fec_beta = anadrofish::olney_mcbride$beta[
      anadrofish::olney_mcbride$region==region]
    batch_size <- 10^(fec_alpha + fec_beta*log10(mass))
      
    # Draw number of batches based on McBride et al. (2016)  
    if(region=='NI'){
      n_batches <- rtruncnorm(1, a=0, b=10, mean=6.1, sd=.5)
    }
    if(region=='SI'){
      n_batches <- rtruncnorm(1, a=0, b=12, mean=6.1, sd=.5)
    }
    if(region=='SP'){
      n_batches <- rtruncnorm(1, a=0, b=Inf, mean=6.1, sd=.5)
    }
      
    eggs <- batch_size * n_batches

  }
  
  if(species %in% c("ALE", "BBH")){
    eggs <- anadrofish::make_eggs_rh(river = river, species = species,
                                     custom_habitat = custom_habitat)
  }
  
  return(eggs)
}