combining: Combines the residence times for the same set of circles and...

In SitesInterest: Inferring an Animal's Sites of Interest from High Resolution Data

Description

Combines the residence times for the same set of circles and different trajectories and also for the entire set.

Usage

combining(Overall_name, Circle_names, Path_names, R, save = 'n')

Arguments

Overall_name	name for the set of separate trajectories
Circle_names	the list of names for each set of circles
Path_names	the list of names for each trajectory
R	radius value to use
save	if 'y', save the files

Details

This function combines the already calculated residence times for each of the path segments as well as combining the residence times of all path segments across the same set of circles. The results are stored in a csv file named 'Overall_name'_combined_UD_alt_R'R'.csv.

Author(s)

Rhys Munden <[e-mail]>

References

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

See also Alt_Alg_mini for how to calculate the residence times for a particular set of circles and a particular trajectory. Alt_Alg_discont is used to calculate the residence times across a whole set of discontinuous trajectories.

Examples

##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 path 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 path 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 path 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 names of each path segment
Names = c("OU_14.1","OU_14.3","OU_14.5")

##Calculates the residence time for each path segment individually
Alt_Alg("OU_14.1",unlist(t_all[1]),unlist(X_all[1]),unlist(Y_all[1]),0.3,first='y',save='y')
Alt_Alg("OU_14.3",unlist(t_all[2]),unlist(X_all[2]),unlist(Y_all[2]),0.3,first='y',save='y')
Alt_Alg("OU_14.5",unlist(t_all[3]),unlist(X_all[3]),unlist(Y_all[3]),0.3,first='y',save='y')

Circle_names = Names
Path_names = Names

##Calculate the residence time for each set of circles and each path segment
for (Circles_name in Circle_names){
  df = read.csv(paste(Circles_name,"_UD_alt_R",0.3,".csv",sep=''))
  t_centers_list = df[1]
  X_centers_list = df[2]
  Y_centers_list = df[3]
  t_centers = unlist(t_centers_list)
  X_centers = unlist(X_centers_list)
  Y_centers = unlist(Y_centers_list)
  for (Path_name in Path_names){
  if (Circles_name != Path_name){
       index = match(Path_name,Names)
       Alt_Alg_mini(Circles_name, t_centers, X_centers, Y_centers, Path_name, 
       unlist(t_all[index]),unlist(X_all[index]),unlist(Y_all[index]),0.3,s=10,m=500,save='y')}}}

##Combine all the residence times for the same circles
combining("OU_14_discont", Circle_names, Path_names, 0.3,save='y')

##Reset the original working directory
setwd(wd)

SitesInterest documentation built on May 2, 2019, 4:25 a.m.