addSightings {secr} | R Documentation

## Mark-resight Data

### Description

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

### Usage

    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

- a single integer, the sum of all counts*

- a matrix of the count on each occasion at each detector (dimensions K x S, where K is the number of detectors and S is the total number of occasions). Columns corresponding to marking occasions should be all-zero.

- for multi-session data, a list with components as above

- a character value with the name of a text file containing the data; the file will be read with `read.table`. The ... argument allows some control over how the file is read. The data format comprises at least S+1 columns. The first is a session identifier used to split the file when the data span multiple sessions; it should be constant for a single-session capthist. The remaining S columns contain the counts for occasions 1:S, one row per detector. Further columns may be present; they are ignored at present.

* 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

    ## 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)

[Package secr version 3.2.1 Index]