Some ad hoc measures of home range size may be calculated in secr from capture–recapture data:
dbar is the mean distance between consecutive capture locations,
pooled over individuals (e.g. Efford 2004).
moves returns the
MMDM (for ‘Mean Maximum Distance Moved’) is the average maximum
distance between detections of each individual i.e. the observed range
length averaged over individuals (Otis et al. 1978).
ARL (or ‘Asymptotic Range Length’) is obtained by fitting an
exponential curve to the scatter of observed individual range length vs
the number of detections of each individual (Jett and Nichols 1987: 889).
RPSV (for ‘Root Pooled Spatial Variance’) is a measure of the 2-D
dispersion of the locations at which individual animals are detected,
pooled over individuals (cf Calhoun and Casby 1958, Slade and Swihart 1983).
moves reports the distance between successive detections of each animal.
centroids reports the averaged coordinates of each animal's detections
ORL reports the observed range length of each animal, the maximum
distance between any two detections.
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dbar(capthist, userdist = NULL, mask = NULL) MMDM(capthist, min.recapt = 1, full = FALSE, userdist = NULL, mask = NULL) ARL(capthist, min.recapt = 1, plt = FALSE, full = FALSE, userdist = NULL, mask = NULL) moves(capthist, userdist = NULL, mask = NULL, names = FALSE) RPSV(capthist, CC = FALSE) ORL(capthist, userdist = NULL, mask = NULL) centroids(capthist)
object of class
function or matrix with user-defined distances
habitat mask passed to userdist function, if required
logical; should results be ordered alphanumerically by row names?
integer minimum number of recaptures for a detection history to be used
logical; if TRUE observed range length is plotted against number of recaptures
logical; set to TRUE for detailed output
logical for whether to use Calhoun and Casby formula
dbar is defined as –
see pdf manual
CC = FALSE,
RPSV is defined as –
see pdf manual
CC = TRUE),
RPSV uses the formula of Calhoun
and Casby (1958) with a different denominator –
see pdf manual
The Calhoun and Casby formula (offered from 2.9.1) correctly estimates σ
when trapping is on an infinite, fine grid, and is preferred
for this reason. The original RPSV
CC = FALSE) is retained as the default for compatibility with
previous versions of secr.
RPSV have a specific role as proxies for
detection scale in inverse-prediction estimation of density (Efford
RPSV is used in
autoini to obtain plausible starting
values for maximum likelihood estimation.
ARL discard data from detection histories
containing fewer than
userdist option is included for exotic non-Euclidean cases
secr.fit details). RPSV is not defined for
capthist comprises standalone telemetry data (all detector 'telemetry')
then calculations are performed on the telemetry coordinates.
Movements are reliably reported by
moves only if there is a maximum of one detection per animal per occasion. The sequence of detections within any occasion is not known; where these occur the sequence used by
moves is arbitrary (sequence follows detector index).
Scalar distance in metres, or a list of such values if
is a multi-session list.
full argument may be used with
return more extensive output, particularly the observed range length for
each detection history.
List with one component for each animal, a vector of distances, or numeric(0) if the animal is detected only once. A list of such lists if
capthist is a multi-session list.
For a single-session capthist, a matrix of two columns, the x- and y-coordinates of the centroid of the detections of each animal. The number of detections is returned as the attribute ‘Ndetections’, a 1-column matrix.
For a multi-session capthist, a 3-D array as before, but with a third dimension for the session. Centroid coordinates are missing (NA) if the animal was not detected in a session. The attribute ‘Ndetections’ with the number of detections per animal and session is a matrix.
All measures are affected by the arrangement of detectors.
is also affected quite strongly by serial correlation in the sampled
dbar with ‘proximity’ detectors raises a problem
of interpretation, as the original sequence of multiple detections
within an occasion is unknown. RPSV is a value analogous to the standard
deviation of locations about the home range centre.
The value returned by
dbar for ‘proximity’ or ‘count’ detectors
is of little use because multiple detections of an individual within an
occasion are in arbitrary order.
Inclusion of these measures in the secr package does not mean they are recommended for general use! It is usually better to use a spatial parameter from a fitted model (e.g., sigma of the half-normal detection function). Even then, be careful that sigma is not ‘contaminated’ with behavioural effects (e.g. attraction of animal to detector) or ‘detection at a distance’.
The argument 'names' was added in 3.0.1. The default
names = FALSE
causes a change in behaviour from that version onwards.
Calhoun, J. B. and Casby, J. U. (1958) Calculation of home range and density of small mammals. Public Health Monograph. No. 55. U.S. Government Printing Office.
Efford, M. G. (2004) Density estimation in live-trapping studies. Oikos 106, 598–610.
Jett, D. A. and Nichols, J. D. (1987) A field comparison of nested grid and trapping web density estimators. Journal of Mammalogy 68, 888–892.
Otis, D. L., Burnham, K. P., White, G. C. and Anderson, D. R. (1978) Statistical inference from capture data on closed animal populations. Wildlife Monographs 62, 1–135.
Slade, N. A. and Swihart, R. K. (1983) Home range indices for the hispid cotton rat (Sigmodon hispidus) in Northeastern Kansas. Journal of Mammalogy 64, 580–590.
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