syntPath: Generate synthetic trajectories of fishes from acoustic...

Description Usage Arguments Value

View source: R/syntPath.R

Description

This function generates a stochastic trajectory of a fish by sampling a possible pair of coordinates for each time step. It takes into account the depth of the fish, the probability of being detected as function of the distance to the receiver (including acoustic shadow areas outside the acoustic range), and the topography of the study area.

Usage

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syntPath(track.data, topo, dist.rec, ac.range.mod, max.vel = 1,
  depth.cost.list = NULL, check = FALSE)

Arguments

track.data

data.frame with acoustic telemetry data containing the following columns:

rec.id

ID of the acoustic receiver that registered each detection

time.stamp

date and time of each detection, in POSIXt format

depth

depth of the fish, provided by the acoustic transmitters in the coded signals

tag.id

ID of the tagged individual (Optional)

topo

raster dataset (RasterLayer object) with the topographic information of the study area (bathymetry or elevation).

dist.rec

RasterStack object with the distances between all the cells and a given receiver in each layer. Acoustic shadows and other areas to exclude (e.g. land areas) must be identified with NA values.

ac.range.mod

logistic regression model of the relationship between the detection probability and the distance from the receiver. It must be a glm object.

max.vel

Maximum average velocity at which the animal is supposed to move. This argument is used to limit the maximum space between sampled locations. By default is set to 1 m/s.

depth.cost.list

A list containing TransitionLayer objects, each one excluding the cells placed in areas shallower thant the depth that gives the name to the element in the list.

check

Print a message after sampling each coordinate.

Value

A data.frame containing the time stamp, receiver, coordinates and depth of each sampled location.


aspillaga/fishtrack3d documentation built on Oct. 17, 2018, 11:12 p.m.