wiqid (version 0.3.3)

occ2sps: Single-season two-species occupancy estimation

Description

Estimates occupancy and probability of detection for two species, where one (dominant) species affects the occupancy or detection of the other (subordinate) species (see Richmond et al, 2010). The model has the following parameters:

psiA	probability of occupancy of species A
psiBa	probability of occupancy of B if A is absent
psiBA	probability of occupancy of B if A is present
pA	probability of detection of species A if B is absent
rA	probability of detection of species A if both are present
pB	probability of detection of species B if A is absent
rBa	probability of detection of species B if both are present but A was not detected
rBA	probability of detection of species B if both are present and A was detected

Usage

occ2sps(DHA, DHB, model=NULL, data=NULL, ci = 0.95, verify=TRUE)

Value

Returns an object of class wiqid, see wiqid-class for details.

Arguments

DHA

a 1/0/NA matrix (or data frame) of detection histories, sites x occasions, for the dominant species.

DHB

detection histories for the subordinate species in the same format as DHA.

model

a list of formulae symbolically defining a linear predictor for any of the parameters in the model. The default, NULL, is equivalent to list(psiA~1, psiBa~1, pA~1, pB~1); parameters not included in the list are given the following values: psiBA <- psiBa, rA <- pA, rBa <- pB, rBA <- rBa.

data

a data frame containing the variables in the model. If data = NULL, a faster algorithm is used, and any covariates in the model will be ignored.

ci

the confidence interval to use.

verify

if TRUE, the data provided will be checked.

Benchmarks

Output has been checked against output from PRESENCE (Hines 2006) v.5.5 for the railSims data set. Real values are the same to 4 decimal places, and AICs are the same.

Author

Mike Meredith

References

Richmond, Hines, Beissinger (2010) Two-species occupancy models: a new parameterization applied to co-occurrence of secretive rails. Ecological Applications 20(7):2036-2046

MacKenzie, D I; J D Nichols; A J Royle; K H Pollock; L L Bailey; J E Hines 2006. Occupancy Estimation and Modeling : Inferring Patterns and Dynamics of Species Occurrence. Elsevier Publishing.

See Also

See the example data set railSims. See occSS for single-season single-species occupancy estimation.

Examples

data(railSims)
# Extract the two detection histories
DHA <- railSims[, 1:3]
DHB <- railSims[, 4:6]

# Default model (no interaction)
occ2sps(DHA, DHB)

  
# Add a submodel for psiBA, so that psiBA and psiBa are separated:
occ2sps(DHA, DHB, model = psiBA ~ 1)

# Add covariates for psiA and psiBA; only display beta coefficients:
occ2sps(DHA, DHB, model = list(psiA ~ logArea, psiBA ~ reeds), data=railSims)$beta

# Model corresponding to the data generation model
occ2sps(DHA, DHB, list(psiA ~ logArea, psiBA ~ reeds, rBA ~ 1), data=railSims)$beta