create.capt: Creating capture history object.

In b-steve/ascr: Acoustic spatial capture-recapture

Creating capture history object.

Description

Creates a capture history object to use with the function fit.ascr.

Usage

create.capt(
  captures,
  n.traps = NULL,
  n.sessions = NULL,
  traps = NULL,
  mrds.locs = NULL
)

Arguments

captures	A data frame of capture records, see 'Details' for the correct format.
n.traps	The number of traps deployed on each session. If the number of traps varies between sessions, then this must be a vector with the ith element providing the number of traps deployed on the ith session.
n.sessions	The total number of sessions.
traps	A matrix of trap locations, or a list for multi-session models (see fit.ascr). If this argument is provided, there is no need to specify n.traps or n.sessions.
mrds.locs	A matrix of animal locations, or a list for multi-session models. See 'Details'.

Details

The captures argument to this function is intended to be of a similar format to the captures argument to make.capthist in the secr package. That is, users can use the same captures data frame with create.capt and make.capthist, which generate capture histories for use with the ascr and secr packages respectively.

As such, the first, second, and fourth columns should provide the session, the identification number of the detected animal or sound, and the trap number of the trap which made the detection (where the trap number is the row number of the corresponding trap in the matrix of trap locations), respectively. Note that, for the secr package, the third column of the captures data frame provides the 'occassion' of the detection for make.capthist. However, the ascr package does not presently have the capabilities to deal with multi-occassion data, so the third column is ignored by create.capt.

Additional columns can specify the auxiliary information collected over the course of the survey:

• A column named bearing, containing estimated bearings (in radians) from the detector to each detected animal or sound.

• A column named dist, containing the estimated distance between the detected animal or sound.

• A column named ss containing the measured signal strengh of the detected sound.

• A column named toa containing the measured time of arrival (in seconds) since the start of the survey (or some other reference time) of the detected sound (only possible when the detectors are microphones).

If animal or sound locations are known exactly, then a mark-recapture distance sampling (MRDS) model can be fitted. In this case, for single-session models the mrds.loc argument should be a matrix, where each row corresponds to the known x- and y-coordiates of an animal. The row number should match with the individual's ID number in the captures data frame, so for example the animal with an ID of 5 should have their location's x- and y-coordinates in the fifth row of mrds.locs. For multi-session models, the mrds.loc argument should be a list of such matrices, where each component is associated with one of the sessions.

b-steve/ascr documentation built on Aug. 15, 2022, 2:38 p.m.