addSightings: Mark-resight Data

Description Usage Arguments Details Value Warning See Also Examples

View source: R/addSightings.R

Description

Add sighting data on unmarked individuals and/or unidentified marked individuals to an existing capthist object.

Usage

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addSightings(capthist, unmarked = NULL, nonID = NULL, uncertain = NULL, verify = TRUE,
    ...)

Arguments

capthist

secr capthist object

unmarked

matrix or list of matrices of sightings of unmarked animals, Tu, or file name (see Details)

nonID

matrix or list of matrices of unidentified sightings of marked animals, Tm, or file name (see Details)

uncertain

matrix or list of matrices of uncertain sightings, Tn, or file name (see Details)

verify

logical; if TRUE then the resulting capthist object is checked with verify

...

other arguments passed to read.table

Details

The capthist object for mark-resight analysis comprises distinct marking and sighting occasions, defined in the markocc attribute of traps(capthist). Add this attribute to traps(capthist) with markocc before using 'addSightings'. See also read.traps and read.capthist.

Mark-resight data may be binary (detector type ‘proximity’) or counts (detector types ‘count’, 'polygon' or 'transect'). The detector type is an attribute of traps(capthist). Values in unmarked and nonID should be whole numbers, and may be greater than 1 even for binary proximity detectors because multiple animals may be detected simultaneously at one place.

Arguments unmarked, nonID, uncertain provide data for attributes ‘Tu’, ‘Tm’, ‘Tn’ respectively. They may take several forms

* although this is convenient, the full matrix of counts provides more flexibility (e.g., when you wish to subset by occasion), and enables modelling of variation across detectors and occasions.

Value

A capthist object with the same structure as the input, but with new sighting-related attributes Tu (sightings of unmarked animals) and/or Tm (unidentified sightings of marked animals). Input values, including NULL, overwrite existing values.

Warning

** Mark-resight data formats and models are experimental in secr 2.10.0 and subject to change **

See Also

markocc, read.capthist, read.traps, sim.resight, Tm, Tu, Tn, secr-markresight.pdf

Examples

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## Not run: 

## suppose CH is a capthist object with detector type proximity,
## attribute 'markocc' is defined for traps(CH), and 
## unmarkedsightings.txt is a text file with a
## compatible K x S array of non-negative integer values.

Tu <- read.table('unmarkedsightings.txt')
CH2 <- addSightings(CH, unmarked = Tu)


## End(Not run)

secr documentation built on Sept. 20, 2017, 5:02 p.m.