calcTransition: Calculate psi (transition probabilities between sites in two...

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

Calculate psi (transition probabilities between sites in two phases of the annual cycle)

Description

Provides simple maximum-likelihood point estimate of transition probabilities that does not include measures of uncertainty. Incorporates detection heterogeneity where appropriate (band/ring return data), but not location uncertainty. Shared primarily for testing; use of estTransition is recommended instead.

Usage

calcTransition(
  banded = NULL,
  reencountered = NULL,
  counts = NULL,
  originAssignment = NULL,
  targetAssignment = NULL,
  originNames = NULL,
  targetNames = NULL,
  method = "SANN"
)

calcPsi(
  banded = NULL,
  reencountered = NULL,
  counts = NULL,
  originAssignment = NULL,
  targetAssignment = NULL,
  originNames = NULL,
  targetNames = NULL,
  method = "SANN"
)

Arguments

banded	For band return data, a vector of the number of released animals from each origin site (including those never reencountered in a target region)
reencountered	For band return data, a matrix with B rows and W columns. Number of animals reencountered on each target site by origin site they came from
counts	Migration data without target-region detection heterogeneity (i.e., anything but band return data) can be entered one of two ways: either here or with originAssignment and targetAssignment. If here, a matrix with B rows and W columns with counts of animals observed in each combination of origin and target site
originAssignment	Assignment of animals (not including band return data) to origin season sites. A vector of integers (1-B) with length number of animals tracked. Note that these data can either be entered using this argument and targetAssignment or using counts, but not both
targetAssignment	Assignment of animals (not including band return data) to target season sites. A vector of integers (1-W) with length number of animals tracked. Note that these data can either be entered using this argument and originAssignment or using counts, but not both
originNames	Optional, but recommended to keep track. Vector of names for the origin sites. If not provided, the function will either try to get these from another input or provide default names (capital letters)
targetNames	Optional, but recommended to keep track. Vector of names for the target sites. If not provided, the function will either try to get these from another input or provide default names (numbers)
method	See optim. "SANN" is slow but reasonably accurate. "Nelder-Mead" is fast but not accurate here. "BFGS" is also fast but not very stable here

Value

calcTransition returns a list with the element(s):

psi

Matrix with point estimate of transition probabilities

r

Vector containing point estimate of reencounter probabilities at each target site. Not included unless data includes band reencounters

See Also

estTransition, optim

Examples

nOriginSites <- 4
nTargetSites <- 4
originNames <- LETTERS[1:nOriginSites]
targetNames <- 1:nTargetSites
psiTrue <- array(c(0.1, 0.2, 0.3, 0.4,
                   0.2, 0.3, 0.4, 0.1,
                   0.3, 0.4, 0.1, 0.2,
                   0.4, 0.1, 0.2, 0.3),
                 c(nOriginSites, nTargetSites),
                 dimnames = list(originNames, targetNames))
rowSums(psiTrue)
rTrue <- c(0.5, 0.05, 0.3, 0.6)
banded1 <- c(500, 1000, 2000, 3000)
reencountered1 <- simCMRData(psiTrue, banded1, rTrue)$reencountered
psi_r_calc_sloppy <- calcTransition(banded = banded1,
                             reencountered = reencountered1,
                             originNames = originNames,
                             targetNames = targetNames,
                             method = "BFGS")
psi_r_calc_sloppy

psi_r_calc <- calcTransition(banded = banded1,
                             reencountered = reencountered1,
                             originNames = originNames,
                             targetNames = targetNames,
                             method = "SANN")
psi_r_calc
psi_r_mcmc <- estTransition(banded = banded1, reencountered = reencountered1,
                            originNames = originNames,
                            targetNames = targetNames,
                            method = "MCMC",
                            nSamples = 45000, nBurnin = 5000, #reduced for example speed
                            nThin = 1, verbose = 0)
print(psi_r_mcmc)
psi_r_boot <- estTransition(banded = banded1, reencountered = reencountered1,
                            originNames = originNames,
                            targetNames = targetNames,
                            method = "bootstrap",
                            nSamples = 200) #reduced for example speed
print(psi_r_boot)

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