simDat19B: Simulate data for Chapter 19B: Binomial N-mixture Model

In ASMbook: Functions for the Book "Applied Statistical Modeling for Ecologists"

Simulate data for Chapter 19B: Binomial N-mixture Model

Description

Function simulates replicated count data as used in the bonus Chapter 19B in the ASM book. Abundance, detection and count data simulation is undertaken for the approximate elevation of the actual sample of survey sites in the Swiss breeding bird survey "Monitoring Häufige Brutvögel" (MHB). Note there is no nSites argument, since this is given in the MHB survey at 267.

Usage

simDat19B(
  nVisits = 3,
  alpha.lam = -3,
  beta1.lam = 8.5,
  beta2.lam = -3.5,
  alpha.p = 2,
  beta.p = -2,
  show.plot = TRUE
)

Arguments

nVisits	Number of occasions, or visits per site
alpha.lam	Intercept of the regression of log expected abundance on scaled elevation
beta1.lam	Linear effect of scaled elevation on log expected abundance
beta2.lam	Quadratic effect of scaled elevation on log expected abundance
alpha.p	Intercept of the regression of logit detection on scaled elevation
beta.p	Linear effect of scaled elevation on logit detection
show.plot	Show plot of simulated output?

Value

A list of simulated data and parameters.

nSites	Number of sites
nVisits	Number of visits to each site
alpha.lam	Abundance intercept
beta1.lam	Linear effect of elevation on abundance
beta2.lam	Quadratic effect of elevation on abundance
alpha.p	Detection intercept
beta.p	Linear effect of elevation on detection
mhbElev	Elevation covariate values
mhbElevScaled	Scaled elevation covariate values
lambda	Expected abundance for each site
N	True abundance at each site
p	Detection probability at each site
C	Observed repeated counts at each site
nocc.true	True number of occupied sites
nocc.app	Apparent number of occupied sites
psi	True proportion of occupied sites
psi.app	Apparent proportion of occupied sites
opt.elev.true	Optimal elevation value
totalN.true	True total population size
totalN.app	Apparent total population size

Author(s)

Marc Kéry

Examples

# With implicit default function argument values
str(simDat19B())

# With explicit function argument values
str(simDat19B(nVisits = 3, alpha.lam = -3, beta1.lam = 8.5, beta2.lam = -3.5, 
    alpha.p = 2, beta.p = -2, show.plot = TRUE))

# No plots
str(simDat19B(show.plot = FALSE))

# More visits
str(simDat19B(nVisits = 10))

# A single visit at each site
str(simDat19B(nVisits = 1))

# Greater abundance
str(simDat19B(alpha.lam = 0))

# Much rarer abundance
str(simDat19B(alpha.lam = -5))

# No quadratic effect of elevation on abundance (only a linear one)
str(simDat19B(beta2.lam = 0))

# No effect of elevation at all on abundance
str(simDat19B(beta1.lam = 0, beta2.lam = 0))

# Higher detection probability (intercept at 0.9)
str(simDat19B(alpha.p = qlogis(0.9), beta.p = -2))

# Higher detection probability (intercept at 0.9) and no effect of elevation
str(simDat19B(alpha.p = qlogis(0.9), beta.p = 0))

# Perfect detection (p = 1)
str(simDat19B(alpha.p = 1000))

# Positive effect of elevation on detection probability (and lower intercept)
str(simDat19B(alpha.p = -2, beta.p = 2))

ASMbook documentation built on Sept. 11, 2024, 5:38 p.m.