Alt_Alg_discont: Application of Alt_Alg to discontinuous data
In SitesInterest: Inferring an Animal's Sites of Interest from High Resolution Data

Description Usage Arguments Details Author(s) References See Also Examples

Calculates the residence times from discontinuous data, which can then be used to identify sites of interest. This could also be used to identify sites for a group of animals, by treating each animal's trajectory as one segment of a discontinuous set.

1	Alt_Alg_discont(Overall_name,Names, t_all, X_all, Y_all, R, s = 10, m = 500, save = 'n')

`Overall_name`	name for the set of separate trajectories
`Names`	list of names for each trajectory
`t_all`	list of arrays, one for each trajectory of times when the positions were recorded
`X_all`	list of arrays, one for each trajectory of x-coordinates
`Y_all`	list of arrays, one for each trajectory of y-coordinates
`R`	radius value to use
`s`	number of time steps between checks for entrances and exits
`m`	estimate of the maximum number of crossings across all circles
`save`	if `'y'`, save the files

This function is used specifically with discontinuous data to calculate the residence times for the trajectories. It works in the same way as for Alt_Alg, by linking together Alt_Alg_mini and combining.

Rhys Munden <rdmunden1@sheffield.ac.uk>

Munden, R., Borger , L., Wilson, R.P., Redcliffe, J., Loison, A., Garel, M. and Potts, J.P. in review. Making sense of ultra-high-resolution movement data: an algorithm for inferring sites of interest.

See also Alt_Alg for the algorithim used on continuous data. Alt_Alg_mini is used to calculate the residence times for a particular set of circles and a particular trajectory, then using combining all the residence times for the same circles are summed.

##Find the current working directory
wd = getwd()
##Set the working directory as the temporary one
setwd(tempdir())
##Load the data
data(OU_14)
t=unlist(OU_14["t"])
X=unlist(OU_14["X"])
Y=unlist(OU_14["Y"])

##Number of path sections
n=5
##Number of recorded locations
N = length(t)

##A list of arrays of the time recoding for the 3 of the trajectory segments
t_all = list(t[seq(1,floor(N/n))], t[seq(floor(N/n)*2,floor(N/n)*3)], 
t[seq(floor(N/n)*4,floor(N/n)*5)])

##A list of arrays of the x-coordinates for the 3 of the trajectory segments
X_all = list(X[seq(1,floor(N/n))], X[seq(floor(N/n)*2,floor(N/n)*3)], 
X[seq(floor(N/n)*4,floor(N/n)*5)])

##A list of arrays of the y-coordinates for the 3 of the trajectory segments
Y_all = list(Y[seq(1,floor(N/n))], Y[seq(floor(N/n)*2,floor(N/n)*3)], 
Y[seq(floor(N/n)*4,floor(N/n)*5)])

##The calculation of the residence time for discontibuous data
Alt_Alg_discont("OU_14_discont",c("OU_14.1","OU_14.3","OU14.5"),t_all,X_all,Y_all,0.3,save='y')

##Reset the original working directory
setwd(wd)