simFrogDisease: Simulate detection data for diseased frogs

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

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)

AHMbook documentation built on Sept. 12, 2024, 6:37 a.m.