density_ratio: Density ratio

In vquennessen/densityratio: Using Density Ratios to Help Manage Fisheries In And Around Marine Reserves

Density ratio

Description

density_ratio estimates the density ratio for a stock in line with a specific control rule.

Usage

density_ratio(
  t,
  cr,
  fdr,
  A,
  Count,
  Years_sampled = 1,
  Areas_sampled = "all",
  Ind_sampled = "all",
  Transects = 24,
  Inside,
  Outside
)

Arguments

t	temporary numeric value, the current time step.
cr	temporary numeric value, the current control rule.
fdr	temporary numeric value, the current final target density ratio.
A	numeric value, the number of total areas in the model. Default value is 5.
Count	numeric array, the number of individuals estimated to be in each area, at each timestep, under each control rule, for each estimate of natural mortality, for both all individuals and just mature individuals.
Years_sampled	numeric value, the number of years of sampling upon which to base the estimate of density ratio. Default value is 1.
Areas_sampled	character value, the areas to be sampled to calculate density ratio. Values can be: 'all' - sample all areas. 'far' - sample only the first and last areas (assuming the reserve is somewhere in the middle. Default value is 'all'.
Ind_sampled	character value, the individuals to be sampled to calculate density ratio. Values can be: 'all' - sample all individuals. 'mature' - sample only mature individuals. Default value is 'all'.
Transects	numeric value, the number of sampling transects conducted in each area to estimate density ratio. Default value is 24.
Inside	numeric vector, the area(s) inside the marine reserve. Default is c(3).
Outside	numeric vector, the area(s) outside the marine reserve. Default is c(1, 2, 4, 5).

Value

numeric value, the calculated density ratio for a specific timestep, under a specific control rule, with a specific estimate of natural mortality.

Examples

A = 5; TimeT = 70; CR = 6; FDR = 4; Transects = 24
Count <- array(rep(5, A*TimeT*Transects*2*CR*FDR),
   c(A, TimeT, Transects, 2, CR, FDR))
density_ratio(t = 51, cr = 1, fdr = 1, A = 5, Count,
   Years_sampled = 1, Areas_sampled = 'all', Ind_sampled = 'all',
   Transects = 24, Inside = 3, Outside = c(1, 2, 4, 5))

vquennessen/densityratio documentation built on Aug. 28, 2022, 5:36 p.m.