secr (version 2.5.0)

capthist.parts: Dissect Spatial Capture History Object

Description

Extract parts of an object of class `capthist'.

Usage

animalID(object, names = TRUE)
occasion(object)
trap(object, names = TRUE)
alive(object)
alongtransect(object, tol = 0.01)
xy(object)
xy(object) <- value
signalframe(object)
signalframe(object) <- value
signal(object)
signal(object) <- value
noise(object)
noise(object) <- value

Arguments

object

a `capthist' object

names

if FALSE the values returned are numeric indices rather than names

tol

tolerance for snapping to transect line (m)

value

replacement value (see Details)

Value

• For animalID and trap a vector of numeric or character values, one per detection. For alive a vector of logical values, one per detection. For occasion, a vector of numeric values, one per detection. For xy, a dataframe with one row per detection and columns `x' and `y'. For signalframe , a dataframe containing signal data and covariates, one row per detection. The data frame has one row per detection. See signalmatrix for a matrix with one row per cue and columns for different microphones. For signal and noise, a numeric vector with one element per detection. If object has multiple sessions, the result is a list with one component per session.

Details

These functions extract data on detections, ignoring occasions when an animal was not detected. Detections are ordered by occasion, animalID and trap. trap returns polygon or transect numbers if traps(object) has detector type `polygon' or `transect'. alongtransect returns the distance of each detection from the start of the transect with which it is associated. Replacement values must precisely match object in number of detections and in their order. xy<- expects a dataframe of x and y coordinates for points of detection within a `polygon' or `transect' detector.

See Also

capthist, polyID, signalmatrix

Examples

## `captdata' is a demonstration dataset
animalID(captdata)

temp <- sim.capthist(popn = list(D = 1), make.grid(detector
    = "count"))
cbind(ID = as.numeric(animalID(temp)), occ = occasion(temp),
    trap = trap(temp))

## ovensong dataset has very simple signalframe
head(signalframe(signalCH))