Filtering and Assessing Sample Size of Tracking Data

Functions to filter GPS and/or Argos locations, as well as assessing sample sizes for the analysis of animal distributions. The filters remove temporal and spatial duplicates, fixes located at a given height from estimated high tide line, and locations with high error as described in Shimada et al. (2012) and Shimada et al. (2016) . Sample sizes for the analysis of animal distributions can be assessed by the conventional area-based approach or the alternative probability-based approach as described in Shimada et al. (in prep).

Overview

SDLfilter contains a variety of functions to screen GPS and/or Argos locations, and to plot them on a map.

Installation

install.packages("SDLfilter")
 
# Or the development version from GitHub:
install.packages("devtools")
devtools::install_github("TakahiroShimada/SDLfilter")

Usage

There are three main filtering functions.

1. dupfilter removes temporal and spatial duplicates.

2. ddfilter removes locations with high error.

3. depthfilter removes fixes located at a given height from estimated high tide line (e.g. locations on land).

Please see the help pages and Shimada et al. (2012, 2016) for more details.

library(SDLfilter)
 
### Fastloc GPS data obtained from a green turtle
data(turtle)
 
### Remove temporal and spatial duplicates
turtle.dup <- dupfilter(turtle)
 
### Remove biologically unrealistic fixes 
turtle.dd <- ddfilter(turtle.dup, vmax=9.9, qi=4, ia=90, maxvlp=2.0)
 
### Plot the locations on a map
# unfiltered
plotMap(turtle, point.size = 2, line.size = 0.5, axes.lab.size = 0)
 
# filtered
plotMap(turtle.dd, point.size = 2, line.size = 0.5, axes.lab.size = 0,
        bgmap = "satellite", sb.line.col = "white", sb.text.col = "white")

References

If you use the function ddfilter, please cite

Shimada T, Jones R, Limpus C, Hamann M (2012) Improving data retention and home range estimates by data-driven screening. Mar Ecol Prog Ser 457:171-180 http://dx.doi.org/10.3354/meps09747

If you use the functions dupfilter or depthfilter, please cite

Shimada T, Limpus C, Jones R, Hazel J, Groom R, Hamann M (2016) Sea turtles return home after intentional displacement from coastal foraging areas. Mar Biol 163:1-14 http://dx.doi.org/10.1007/s00227-015-2771-0

Current version

1.2.1 (19 February 2019)