sighting: Sighting Attributes

In secr: Spatially Explicit Capture-Recapture

Sighting Attributes

Description

Extract or replace the markocc attribute of a traps object that distinguishes marking occasions from sighting occasions. Also, extract or replace the attributes Tu, Tm and Tn of a capthist object, used for storing counts of sightings. All attributes are optional, but Tu, Tm and Tn require markocc to be specified. The attribute marked is the animal-level analogue of markocc: it records, for each animal and occasion, the fraction of the occasion for which the animal can be identified as marked, for example while a telemetry collar was working (telemetry type 'marking').

Usage

markocc(object, ...)
markocc(object) <- value
sighting(object)
Tu(object, ...)
Tu(object) <- value
Tm(object, ...)
Tm(object) <- value
Tn(object, ...)
Tn(object) <- value
marked(object, ...)
marked(object) <- value

Arguments

object	traps object (markocc) or capthist object (Tu, Tm, Tn, marked)
value	numeric matrix of detectors x occasions, or a vector (see Details); for marked a matrix of animals x non-telemetry occasions
...	other arguments (not used)

Details

For replacement of markocc, ‘value’ should be a vector of integers indicating the occasions on which animals are sighted only (0) or marked or recaptured (1).

For replacement of Tu, Tm or Tn, ‘value’ may be a scalar (total count) or a detectors x occasions matrix.

For replacement of marked, ‘value’ is a numeric matrix with one row per animal and one column per non-telemetry occasion (the same columns as for Tu), or NULL. The attribute is analogous to detector usage, which records the extent to which each detector was operating on each occasion: marked records the extent to which each animal was identifiable as marked on each occasion. Each element is a known, non-negative multiplier of the usage of the detectors for that animal on that occasion; usually 0 (e.g. collar not working) or 1, or a fraction if the status changed during the occasion. The default (NULL) is 1 for all animals. In telemetry type 'marking' a collared animal contributes cues to the identified counts and Tm only while marked; at other times its cues are part of the unmarked sightings Tu.

Value

markocc(object) returns the markocc vector of the traps object. markocc(object) may be NULL.

Tu, Tm, Tn and marked return the respective attributes of a capthist object, or NULL if they are unspecified.

sighting(object) returns TRUE if the markocc attribute indicates at least one sighting-only occasion.

See Also

traps, addSightings, sightingPlot, secr-markresight.pdf

secr documentation built on Oct. 11, 2026, 5:06 p.m.