ADePTR: ADePTR: Acoustic Detection Processing and Visualization Tool...

In bsmity13/ADePTR: Acoustic Detection Processing and Visualization Tool in R

Description

ADePTR is package developed to streamline processing and visualization of animal movement data from a passive acoustic array.

Details

This package was designed with the following workflow in mind:

1. Process input files

2. Filter erroneous detections

3. Calculate centers of activity

4. Summarize detections on a grid of the study area

5. Interpolate locations and animate

For each step of the workflow, there are both possible inputs and possible outputs. The package is designed to work well with minimal user input (i.e., most arguments have defaults), but it is also designed to allow a high level of customization. Advanced users should be able to edit the outputs of any step before passsing it to the next step, or alternatively, to enter the workflow with their own data at any point.

Step 1. Process Inputs

The primary functions available for this step are:

• proc_dets() – uses station/receiver information to georeference the detections

• plot_sta_history() – makes a summary plot of detections over time by station

• map_dets() – makes a map showing the number of detections by station

Step 2. Filter

The primary functions available for this step are:

• spd_filter() – filters detections that would imply an unrealistic swim speed

• singleton_filter() – filters single detections of an individual ID at an individual station over a given time period

Step 3. COAs

The primary functions available for this step are:

• coa_locs() – calculates centers of activity (COAs) using either arithmetic or harmonic means

• map_coas() – makes a map showing the COAs on top of detections by station

Step 4. Summarize on Grid

The primary functions available for this step are:

• init_raster() – initializes a template raster for future functions

• rasterize_dets() – converts detection data to counts of detections by raster cells

• raster_pres() – converts a detections raster to a presence-only raster

• raster_overlap() – sums the input presence-only or presence-absence layers to show overlapping individuals or species

Step 5. Interpolate and Animate

The primary functions available for this step are:

• str_paths() – connects locations with straight paths

• lc_paths() – connects locations with least cost paths

• regular_points() – interpolates regular points along a straight path or least cost path

• animate_points() – creates an animation from regular points

More details

For more details on the usage of this package, see the package vignette.

The package has a GitHub repository at https://github.com/bjsmith-usgs/ADePTR.

bsmity13/ADePTR documentation built on Nov. 9, 2019, 12:43 a.m.