playRN: Function to play Royle-Nichols (RN) model

In mikemeredith/AHMbook: Functions and Data for the Book 'Applied Hierarchical Modeling in Ecology' Vols 1 and 2

Function to play Royle-Nichols (RN) model

Description

Function generates replicated count data under the binomial N-mixture model of Royle (2004), then 'degrades' the counts to detection/nondetection and fits the Royle-Nichols (RN) model (Royle & Nichols 2003) using unmarked and estimates site-specific abundance.

Usage

playRN(M = 267, J = 3, mean.abundance = 1, mean.detection = 0.3,
    show.plots = TRUE, verbose = TRUE)

Arguments

M	The number of sites.
J	The number of visits to each site.
mean.abundance	Expected abundance at each site.
mean.detection	Expected detection at each survey at each site.
show.plots	choose whether to show plots or not. Set to FALSE when using function in simulations.
verbose	if FALSE, output to the console will be suppressed.

Value

A list with the following elements:

nsites	The number of sites, equal to M in the input
nvisits	The number of visits, equal to J in the input
coef	A named vector of coefficients for the linear models for expected number and detection probability
slope	Slope of the regression of the estimated number on the true number; 1 if the model is perfect

Author(s)

Marc Kéry & Andy Royle

References

Royle, J.A. & Nichols, J.D. (2003) Estimating abundance from repeated presence-absence data or point counts, Ecology, 84, 777-790.

Royle, J.A. (2004) N-mixture models for estimating population size from spatially replicated counts, Biometrics, 60, 108-115.

Kéry, M. & Royle, J.A. (2016) Applied Hierarchical Modeling in Ecology AHM1 - 6.13.1.

Examples

# Run a simulation with the default arguments and look at the results:
playRN()


# Execute the function using various settings
playRN(M = 100, J = 3, mean.abundance = 0.1)  # Increasing abundance
playRN(M = 100, J = 3, mean.abundance = 1)
playRN(M = 100, J = 3, mean.abundance = 5)
playRN(M = 100, J = 3, mean.detection = 0.3)  # Increasing detection
playRN(M = 100, J = 3, mean.detection = 0.5)
playRN(M = 100, J = 3, mean.detection = 0.7)
playRN(M = 100, J = 20)                       # More visits
playRN(M = 1000, J = 3)                       # More sites

mikemeredith/AHMbook documentation built on Dec. 5, 2022, 12:58 p.m.