SitesInterest (version 1.0)

plot_bars_and_hoops: Plots both the bar chart and hoops plot in one figure

Description

The bar chart is the plot of the ranked non-overlapping residence times and the hoops plot shows where along the trajectory these different circles are located.

Usage

plot_bars_and_hoops(x, y, Name, R, colours = c('orange','darkgreen','red'), lwds = 
c(2,2,2), number_sites=-1, first='n')

Arguments

x

array of the x-coordinates describing the trajectory

y

array of the y-coordinates describing the trajectory

Name

the name of the data used to save the files and also in the title of the plot

R

radius value to use

colours

list of colours used for the bars and hoops

lwds

list of the widths of the circles

number_sites

number of sites to manually show the results for

first

if 'y', the algorithm will look for the second greatest maximum percent drop if the first results in the first circle being the only non-identified site

Value

Plot of the bar chart of residence times and site positions

Details

The first subplot (plot_bar_chart) shows the residence times of circles that are left after overlapping ones are removed and identifies where the maximum percent drop occurs by a change in the colour of bars.

The second subplot (plot.hoops) includes the animal's trajectory as well as the three different types of circles overlaid (sites, non-overlapping circles and removed circles). The colour and thickness of these circles can be changed.

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 to find the residence times. Sites can be used to find the coordinates of the centres of the sites and non-overlapping circles from the csv files produced by Alt_Alg. See plot_bar_chart and plot.hoops for how to plot each separately and also the different presentation options.

Examples

# NOT RUN {
##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"])

class(X) <- "bars_and_hoops"
class(Y) <- "bars_and_hoops"

##Calculate the residence time with a radius of 0.3 and not including the first circle
Alt_Alg("OU_14",t,X,Y,0.3,first='y',save='y')

##Plot the bar chart of ranked non-overlapping residence times and the plot showing
##the positions of these circles
plot_bars_and_hoops(X,Y,"OU_14",0.3,first='y')

##Reset the original working directory
setwd(wd)
# }