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

Defines functions domain_abundancestrat_abundancepsu_abundance

```## 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)
}
```
jeremiaheb/rvc documentation built on April 3, 2018, 2:29 a.m.