simFrogDisease {AHMbook}

Simulate detection data for diseased frogs

Description

Simulates detection data for an amphibian species affected by the fungal pathogen Batrachochytrium dendrobatidis (Lips et al., 2006). Surveys are carried out on multiple occasions each year. Observers count frogs and record whether they were infected or not. Over time, individuals are subject to mortality and there may also be recruitment of new individuals into the population. Individuals transition between the two states: infected frogs may become uninfected (i.e., can shed the fungus) and vice versa. It also seems reasonable to expect that survival probability differs between the two states.

Usage

simFrogDisease(nsites = 100, nyears = 3, nsurveys = 3, alpha.lam = 3,
    omega = c(0.9, 0.7), gamma = c(2,1), p = c(0.8, 0.8, 0.8),
    recovery = 0.1, infection = 0.1)

Arguments

nsites

the number of sites surveyed.

nyears

the number of years of the study.

nsurveys

the number of surveys each year.

alpha.lam

mean abundance per site in the first year.

omega

vector length 2, state-specific survival, noninfected and infected.

gamma

vector length 2, state-specific recruitment, noninfected and infected.

p

vector length nyears, probability of detection of individuals.

recovery

probability of recovery for an infected frog.

infection

probability of infection for a noninfected frog.

Value

A list with the values of the arguments and the following additional elements:

SN

sites x intervals, number of noninfected frogs surviving

SI

sites x intervals, number of infected frogs surviving

GN

sites x intervals, number of noninfected frogs recruited

GI

sites x intervals, number of infected frogs recruited

TrI

sites x intervals, number of infected frogs recovering

TrN

sites x intervals, number of noninfected frogs becoming infected

NN

sites x years, number of noninfected frogs at each site

NI

sites x years, number of infected frogs at each site

yN

sites x years x surveys, number of noninfected frogs detected

yI

sites x years x surveys, number of infected frogs detected

Author(s)

Marc Kéry and Andy Royle

References

Kéry, M. & Royle, J.A. (2021) Applied Hierarchical Modeling in Ecology AHM2 - 2.9.1.

Lips, K.R., Brem, F., Brenes, R., Reeve, J.D., Alford, R.A., Voyles, J., et al., 2006. Emerging infectious disease and the loss of biodiversity in a Neotropical amphibian community. Proc. Natl. Acad. Sci. USA, 103, 3165-3170.

Examples

# Generate a simulated data set with default arguments and look at the structure:
tmp <- simFrogDisease()
str(tmp)