summary.capthist: Summarise Detections

In secr: Spatially Explicit Capture-Recapture

Summarise Detections

Description

Concise description of capthist object.

Usage

## S3 method for class 'capthist'
summary(object, terse = FALSE, moves = FALSE, tpa = FALSE, ...)

## S3 method for class 'summary.capthist'
print(x, ...)

counts(CHlist, counts = "M(t+1)")

Arguments

object	capthist object
terse	logical; if TRUE return only summary counts
moves	logical; if TRUE then summary includes detected movements
tpa	logical; if TRUE then summary includes number of detectors per animal
x	summary.capthist object
...	arguments passed to other functions
CHlist	capthist object, especially a multi-session object
counts	character vector of count names

Details

These counts are reported by summary.capthist

n	number of individuals detected on each occasion
u	number of individuals detected for the first time on each occasion
f	number of individuals detected exactly f times
M(t+1)	cumulative number of individuals detected
losses	number of individuals reported as not released on each occasion
detections	number of detections, including within-occasion `recaptures'
traps visited	number of detectors at which at least one detection was recorded
traps set	number of detectors, excluding any `not set' in usage attribute of traps attribute

The last two rows are dropped if the data are nonspatial (object has no traps attribute).

Movements are as reported by moves. When terse = TRUE the number of non-zero moves is reported. The temporal sequence of detections at ‘proximity’ and ‘count’ detectors is not recorded in the capthist object, so the movement statistics are not to be taken too seriously. The problem is minimised when detections are sparse (seldom more than one per animal per occasion), and does not occur with 'single' or 'multi' detectors.

The ‘tpa’ option provides the frequency distribution of detectors per animal. When terse = TRUE the number of animals at >= 2 detectors is reported ('Animal2').

counts may be used to return the specified counts in a compact session x occasion table. If more than one count is named then a list is returned with one component for each type of count.

Value

From summary.capthist, an object of class summary.capthist, a list with at least these components

detector	detector type ("single", "multi", "proximity" etc.)
ndetector	number of detectors
xrange	range of x coordinates of detectors
yrange	range of y coordinates of detectors
spacing	mean distance from each trap to nearest other trap
counts	matrix of summary counts (rows) by occasion (columns). See Details.
dbar	mean recapture distance
RPSV	root pooled spatial variance

or, when terse = TRUE, a vector (single session) or dataframe (multiple sessions) of counts (Occasions, Detections, Animals, Detectors, and optionally Moves and Animals2).

A summary of individual covariates is provided if these are present (from secr 4.0.1).

A summary of interference/non-target captures is provided if there is a nontarget attribute (from secr 4.5.5).

See Also

dbar, RPSV, capthist

Examples

temptrap <- make.grid(nx = 5, ny = 3)
summary(sim.capthist(temptrap))
summary(sim.capthist(temptrap))$counts["n",]
summary(captdata, moves = TRUE)

secr documentation built on Nov. 4, 2024, 9:06 a.m.