simTelemetryData: Simulate telemetry/GPS data

In SMBC-NZP/MigConnectivity: Estimate Migratory Connectivity for Migratory Animals

Simulate telemetry/GPS data

Description

Simulate telemetry/GPS data

Usage

simTelemetryData(
  psi,
  sampleSize,
  originRelAbund = NULL,
  originSites = NULL,
  targetSites = NULL,
  captured = "origin",
  S = 1,
  p = 1,
  requireEveryOrigin = FALSE
)

Arguments

psi	Transition probabilities between B origin and W target sites. A matrix with B rows and W columns where rows sum to 1.
sampleSize	If captured is "origin", either a vector of length B with the number of simulated animals to release with geolocators at each of the B origin sites or a single integer with the total number of simulated animals to release with GPS at origin sites (in which case, the origin sites will be sampled according to the relative abundance). If captured is "target", either a vector of length W with the number of simulated animals to release with GPS at each of the W target sites or a single integer with the total number of simulated animals to release at target sites (in which case, the target sites will be sampled according to their relative abundance).
originRelAbund	Relative abundances at B origin sites. Numeric vector of length B that sums to 1. Optional unless providing target data and/or sample size of length 1.
originSites	A polygon spatial layer (sf - MULTIPOLYGON) defining the geographic representation of sites in the origin season. If left NULL, the simulation won't provide origin points.
targetSites	A polygon spatial layer (sf - MULTIPOLYGON) defining the geographic representation of sites in the target season. If left NULL, the simulation won't provide target points.
captured	Either "origin" (the default) or "target".
S	Survival probabilities of released animals. Probably only relevant for simulating archival tags. Either a matrix with B rows and W columns (if survival depends on both origin site and target site), a vector of length W (if survival depends only on target site), or a single number (if survival is the same for all animals). Default 1 (all tagged animals survive a year).
p	Recapture probabilities of released animals. Only relevant for simulating archival tags. Either a vector of length B (if captured on origin and recapture depends on origin site), a vector of length W (if captured on target and recapture depends on target site), or a single number (if recapture is the same for all animals). Default 1 (all animals that survive are recaptured).
requireEveryOrigin	If TRUE, the function will throw an error if it looks like at least one origin site has no animals released in or migrating to it, or if it can, keep simulating until representation is met. This helps estTransition not throw an error. Default FALSE.

Value

simTelemetryData returns a list with the elements:

originAssignment

Vector with true origin site of each animal

targetAssignment

Vector with true target site of each animal

originPointsTrue

True origin location of each animal, type sf, same projection as originSites

targetPointsTrue

True target location of each animal, type sf, same projection as targetSites

originPointsObs

Observed origin location of each animal that survived and was recaptured, type sf, same projection as originSites. Same as originPointsTrue when S and p==1

targetPointsObs

Observed target location of each animal that survived and was recaptured, type sf, same projection as targetSites. Same as targetPointsTrue when S and p==1

lived

0/1 vector for each animal, indicating which survived

recaptured

0/1 vector for each animal, indicating which were recaptured

input

List containing the inputs to function

SMBC-NZP/MigConnectivity documentation built on March 26, 2024, 4:22 p.m.