R/abundance.R

In jeremiaheb/rvc: A statistical package for the Reef Visual Census

## Abundance function
## Acts as wrappers for density

## PSU abundance
## @export
## @description Number of individuals in each PSU. \strong{Note:} Does
## not take into account detection probability.
## @inheritParams strat_density
## @return A data.frame with abundance per PSU by species, its variance (var),
## the number of SSUs per PSU (m)
psu_abundance = function(x) {
  ## Calculate PSU level density
  pdens = x
  ## Convert density to abundance
  pdens$density = with(pdens, density*m)
  pdens$var = with(pdens, var*m^2)
  ## Rename density and return
  names(pdens)[names(pdens) == "density"] = "abundance"

  return(pdens)
}

## Stratum abundance
## @export
## @description Number of individuals in a stratum based on count. \strong{Note:} Does
## not take into account detection probability.
## @inheritParams strat_density
## @return A data.frame with abundance per stratum by species, its variance (var),
## the number of SSUs per stratum (nm), the number of PSUs per stratum (n), the total
## possible number of SSUs (NM), and the total possible number of PSUs (N)
strat_abundance = function(x, ntot) {
  ## Calculate stratum level density
  sdens = strat_density(x, ntot)
  ## Convert density to abundance
  sdens$density = with(sdens, density*NM)
  sdens$var = with(sdens, var*NM^2)
  ## Rename density and return
  names(sdens)[names(sdens) == "density"] = "abundance"

  return(sdens)
}

## Domain Abundance
## @export
## @description Number of individuals in a sampling domain based on count. \strong{Note:} Does
## not take into account detection probability.
## @inheritParams strat_density
## @return A data.frame with abundance per sampling domain by species, its variance (var),
## the number of SSUs per stratum (nm), the number of PSUs per stratum (n), the total
## possible number of SSUs (NM), and the total possible number of PSUs (N)
domain_abundance = function(x, ntot) {
  ## Calculate domain density
  dabun = domain_density(x, ntot)
  ## Convert density to abundance
  dabun$density = with(dabun, density*NM)
  dabun$var = with(dabun, var*NM^2)
  ## Rename desnity and return
  names(dabun)[names(dabun) == "density"] = "abundance"

  return(dabun)
}