simGLData: Simulate geolocator (GL) migratory movement data

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

Simulate geolocator (GL) migratory movement data

Description

Simulate geolocator (GL) migratory movement data

Usage

simGLData(
  psi,
  originRelAbund = NULL,
  sampleSize,
  originSites = NULL,
  targetSites = NULL,
  geoBias = NULL,
  geoVCov = NULL,
  geoBiasOrigin = geoBias,
  geoVCovOrigin = geoVCov,
  S = 1,
  p = list(1, 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.
originRelAbund	Relative abundances at B origin sites. Numeric vector of length B that sums to 1.
sampleSize	List of length two. The first element is either a vector of length B with the number of simulated animals to release with geolocators at each of the B origin sites, a single integer with the total number of simulated animals to release with geolocators at origin sites (in which case, the origin sites will be sampled according to the relative abundance), or NULL if all animals are released at target sites. The second element is either a vector of length W with the number of simulated animals to release with geolocators at each of the W target sites, a single integer with the total number of simulated animals to release with geolocators at target sites (in which case, the target sites will be sampled according to their relative abundance), or NULL if all animals are released at origin sites.
originSites	A polygon spatial layer (sf - MULTIPOLYGON) defining the geographic representation of sites in the origin season.
targetSites	A polygon spatial layer (sf - MULTIPOLYGON) defining the geographic representation of sites in the target season.
geoBias	Vector of length 2 indicating expected bias in longitude and latitude of animals captured and released at origin sites, in targetSites units.
geoVCov	2x2 matrix with expected variance/covariance in longitude and latitude of animals captured and released at origin sites, in targetSites units.
geoBiasOrigin	Vector of length 2 indicating expected bias in longitude and latitude of animals captured and released at target sites, in originSites units.
geoVCovOrigin	2x2 matrix with expected variance/covariance in longitude and latitude of animals captured and released at target sites, in originSites units.
S	Survival probabilities of released geolocator animals. 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 animals with geolocators survive a year).
p	Recapture probabilities of released geolocator animals; list of length two. The first element is either a vector of length B (if recapture depends on origin site), or a single number (if recapture is the same for all animals released on origin sites). The second element is either a vector of length W (if recapture depends on target site), or a single number (if recapture is the same for all animals released on target sites). Default list(1, 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 or estMC not throw an error. Default FALSE.

Value

simGLData 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 for animals captured at origin sites 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 for animals captured at target sites 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.