IPMbook (version 0.1.5)

simCapHist: Simulates capture histories from a population

Description

Simulates capture histories from a simulated population created by simPop. Capture probabilities may vary among the age classes and with time, and can be different for initial capture vs recapture.

Usage

simCapHist(state, cap = c(0.35, 0.4), recap = NULL, maxAge = NULL, verbose = TRUE)

Value

A list with the arguments used and the following 2 components:

ch

matrix with the capture histories.

age

vector with the age class at first capture for each individual; note that animals marked as newborns/nestlings have age = 1, older individuals have ages from 2 to maxAge.

Arguments

state

an animals x years matrix with the age of each animal in the population (animals born in the current year coded as age = 0), usually the output from simPop.

cap

matrix with age- and time-specific probabilities for initial capture; the first row refers to newborns/nestlings. Input can be abbreviated.

recap

matrix with age- and time-specific probabilities probabilities of REcapture: this has 1 less column than cap (no recaptures in the first year) and 1 less row (animals marked in the youngest class will be older when recaptured). Input can be abbreviated. If recap = NULL, recapture probabilities will be the same as initial capture probabilities.

maxAge

maximum number of age classes that can be identified when the individuals are captured for the first time; if NULL, no upper limit is imposed.

verbose

if TRUE, information is displayed in the console.

Author

Michael Schaub

References

Schaub, M., Kéry, M. (2022) Integrated Population Models, Academic Press, section 5.5.1.

Examples

# Generate a simulated population:
pop <- simPop()
# Simulate capture histories
ch <- simCapHist(pop$state)
str(ch)
ch$cap
ch$recap
ch$age
head(ch$ch)

# Time-varying recapture probabilities, same for all classes:
#  use 1-row matrix
ch <- simCapHist(pop$state, recap=matrix(1:5/10, nrow=1))
ch$recap