capthist: Spatial Capture History Object

In secr: Spatially Explicit Capture-Recapture

Spatial Capture History Object

Description

A capthist object encapsulates all data needed by secr.fit, except for the optional habitat mask.

Details

An object of class capthist holds spatial capture histories, detector (trap) locations, individual covariates and other data needed for a spatially explicit capture-recapture analysis with secr.fit.

A capthist is primarily an array of values with dim(capthist) = c(nc, noccasions, ntraps) where nc is the number of detected individuals. Values maybe binary ({–1, 0, 1}) or integer depending on the detector type.

Deaths during the experiment are represented as negative values.

Ancillary data are retained as attributes of a capthist object as follows:

• traps — object of class traps (required)

• session — session identifier (required)

• covariates — dataframe of individual covariates (optional)

• cutval — threshold of signal strength for detection (‘signal’ only)

• signalframe — signal strength values etc., one row per detection (‘signal’ only)

• detectedXY — dataframe of coordinates for location within polygon (‘polygon’-like detectors only)

• xylist — coordinates of telemetered animals

• Tu — detectors x occasions matrix of sightings of unmarked animals

• Tm — detectors x occasions matrix of sightings of marked but unidentified animals

• Tn — detectors x occasions matrix of sightings with unknown mark status

read.capthist is adequate for most data input. Alternatively, the parts of a capthist object can be assembled with the function make.capthist. Use sim.capthist for Monte Carlo simulation (simple models only). Methods are provided to display and manipulate capthist objects (print, summary, plot, rbind, subset, reduce) and to extract and replace attributes (covariates, traps, xy).

A multi-session capthist object is a list in which each component is a capthist for a single session. The list maybe derived directly from multi-session input in Density format, or by combining existing capthist objects with MS.capthist.

Note

Early versions of secr (before 3.0) used an individual x occasion matrix for data from single-catch and multi-catch traps, instead of a 3-D array. Entries in the matrix corresponded to trap numbers. The function updateCH converts the old format.

References

Borchers, D. L. and Efford, M. G. (2008) Spatially explicit maximum likelihood methods for capture–recapture studies. Biometrics 64, 377–385.

Efford, M. G., Borchers D. L. and Byrom, A. E. (2009) Density estimation by spatially explicit capture-recapture: likelihood-based methods. In: D. L. Thomson, E. G. Cooch and M. J. Conroy (eds) Modeling Demographic Processes in Marked Populations. Springer, New York. Pp. 255–269.

See Also

traps, secr.fit, read.capthist, make.capthist, sim.capthist, subset.capthist, rbind.capthist, MS.capthist, reduce.capthist, mask

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