Availability

Estimating geographic space available to animals based on telemetry data.

Installation:

library(devtools)
install_github("AustralianAntarcticDataCentre/availability")

Example usage:

Using the vector-AR method (see [1]):

library(availability)
## load observed track, 2-column matrix of longitude and latitude
## the track points should be equally sampled in time
realtrack=...
arf=surrogateARModel(realtrack) ## fit AR model to track
st=surrogateAR(arf,realtrack) ## simulate new track

Or using the crawl-based track simulator:

library(availability)
library(crawl)
fit=crwMLE(...) ## fit crawl to your raw data
pr=fit$pred ## extract predicted (fitted) track
pr=pr[pr$locType=="p",] ## keep only regularly-interpolated locations
## construct the corresponding transition and covariance matrices of the state space model for time increment `dt`
model=surrogateCrawlModel(fit,dt)
## and finally simulate the track
stcrw=surrogateCrawl(model,as.matrix(pr[,c("mu.x","mu.y","nu.x","nu.y")]),pr$date)

More detailed usage examples will follow soon.

References

[1] Raymond B et al. (2014) Important marine habitat off East Antarctica revealed by two decades of multi-species predator tracking. Ecography 38:121–129. doi:10.1111/ecog.01021