apply_error_to_spp_occupancy_data: Apply error to species occupancy data.

In langfob/bdpg: Package For Building and Testing Biodiversity Problem Generators

Apply error to species occupancy data.

Description

Walk through the occupancy matrix (PU vs spp) and randomly choose to flip some of the TPs to FNs and TNs to FPs based on the given FP and FN error rates. Update the occupancy matrix (bpm) as you go along, but don't update the PU_spp_pair_indices until you know all locations that have flipped. Update PU_spp_pair_indices at the end so that you don't have to constantly resize this big array as you go along.

Usage

apply_error_to_spp_occupancy_data(
  bpm,
  FP_rates,
  FN_rates,
  num_PUs,
  num_spp,
  random_values,
  no_empty_spp_allowed = TRUE,
  min_allowed_num_occ_per_spp = 1
)

Arguments

bpm	bipartite matrix; integer matrix with one row for each species and one column for each planning unit. Each matrix entry specifies whether that species occupies that planning unit; 1 indicates the species does occupy the planning unit and 0 indicates it does not. Same as occ_matrix.
FP_rates	numeric vector
FN_rates	numeric vector
num_PUs	integer number of planning units
num_spp	integer number of species in the problem
random_values	numeric vector
no_empty_spp_allowed	boolean
min_allowed_num_occ_per_spp	integer

Value

Returns bpm matrix

langfob/bdpg documentation built on Dec. 8, 2022, 5:33 a.m.