capthistfn: Dissect Spatial Capture History Object

In secr: Spatially Explicit Capture-Recapture

Dissect Spatial Capture History Object

Description

Extract parts of an object of class ‘capthist’.

Usage

animalID(object, names = TRUE, sortorder = c("snk", "ksn"))
occasion(object, sortorder = c("snk", "ksn"))
trap(object, names = TRUE, sortorder = c("snk", "ksn"))
alive(object, sortorder = c("snk", "ksn"))
alongtransect(object, tol = 0.01)
xy(object)
xy(object) <- value
telemetryxy(object, includeNULL = FALSE)
telemetryxy(object) <- value
telemetered(object)

Arguments

object	a ‘capthist’ object
names	if FALSE the values returned are numeric indices rather than names
sortorder	character code for sort order (see Details)
tol	tolerance for snapping to transect line (m)
value	replacement value (see Details)
includeNULL	logical; if TRUE a NULL component is included for untelemetered animals

Details

These functions extract data on detections, ignoring occasions when an animal was not detected. By default, detections are ordered by occasion, animalID and trap (sortorder = "snk"). The alternative is to order by trap, occasion and animalID (sortorder = "ksn"). (‘n’, ‘s’ and ‘k’ are the indices used internally for animals, occasions and traps respectively).

For historical reasons, "ksn" is used for locations within polygons and similar (xy).

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. telemetryxy<- expects a list of dataframes, one per telemetered animal.

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’.

If object has multiple sessions, the result is a list with one component per session.

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))

secr documentation built on Oct. 18, 2023, 1:07 a.m.