WindowSweep: Perform window sweep for BCPA

In bcpa: Behavioral Change Point Analysis of Animal Movement

Perform window sweep for BCPA

Description

This is the workhorse function of the BCPA. It performs a sweep of the time series, searching for most significant change points and identifying the parsimonious model according to an adjusted BIC.

Usage

WindowSweep(
  data,
  variable,
  time.var = "T.mid",
  windowsize = 50,
  windowstep = 1,
  units = "hours",
  K = 2,
  tau = TRUE,
  range = 0.6,
  progress = TRUE,
  plotme = FALSE,
  ...
)

Arguments

data	the data to be analyzed. Generically, the output of the GetVT function containing step lengths, absolute and turning angles, etc, but can be any data frame with a column representing times and any column (or set of columns) that can be converted to a time series for change point analysis.
variable	a character string representing the response variable to apply the BCPA to. For example "V*cos(theta)" for persistence velocity, "log(V)" for log of velocity if the data are outputs of 'codeGetVT'. Otherwise, any column (e.g. "Depth") in the data.
time.var	character string for the time variable. The default is T.mid from the output of the 'codeGetVT'.
windowsize	integer size of the analysis window as a number of data points (not time units). Should probably be no smaller than 20.
windowstep	integer step size of analysis. Values greater than 1 speed the analysis up.
units	if the times are POSIX, units (one of "secs", "mins", "hours", "days", "weeks") determine the unit of the windowstep.
K	sensitivity parameter for the adjusted BIC. Smaller values make for a less sensitive model selection, i.e. more likely that the null model of no significant changes will be selected.
tau	a logical indicating whether the autocorrelation "rho" or the characteristic time "tau" should be estimated.
range	a number between 0 and 1 that determines the extent of each window that is scanned for changepoints. I.e., if the window is 100 datapoints long, at the default range=0.6, changepoints will be scanned between 20 and 80.
progress	logical - whether or not to output a progress bar as the analysis is being performed.
plotme	logical - whether or not to plot the analysis as it is happening. This slows the analysis considerably, especially in non-dynamic graphic environments like RStudio.
...	additional parameters to be passed to the PartitionParameters function.

Value

an object of class windowsweep, which is a list containing:

ws	a data frame containing the change point, selected model, and parameter estimates
x	the response variable
t	the time variable - in the units specified in the data object
t.POSIX	the time variable as a POSIX object (containing Y-M-D H:S)
windowsize	the window size
windowstep	the window step size

Author(s)

Eliezer Gurarie

See Also

for internal functions: GetModels, GetBestBreak, GetDoubleL; for summarizing output: ChangePointSummary; for plotting output: plot.bcpa

Examples

# Using the included simulated  movement data
require(bcpa)
data(Simp)
plot(Simp)
Simp.VT <- GetVT(Simp)
## note: column names of Simp.VT include:
###  "S" - step length
### "Theta" - turning angle
###  T.start" "T.end"   "T.mid"  "T.POSIX" - time variables

if(interactive())
  Simp.ws <- WindowSweep(Simp.VT, "V*cos(Theta)", windowsize = 50, 
                         windowstep = 1, progress=TRUE) else
  Simp.ws <- WindowSweep(Simp.VT, "V*cos(Theta)", windowsize = 50, 
                         windowstep = 1, progress=FALSE)

plot(Simp.ws, threshold = 7)
plot(Simp.ws, type = "flat", clusterwidth = 3)
PathPlot(Simp, Simp.ws)
PathPlot(Simp, Simp.ws, type="flat")
DiagPlot(Simp.ws)

# Example of application on one dimensional data (e.g. depth)

# simulate some data with three change points: surface, medium, deep, surface

## random times within 100 hours of now
n.obs <- 100
time = sort(Sys.time() - runif(n.obs, 0, n.obs) * 60 * 60)

d1 <- 50; d2 <- 100
t1 <- 25; t2 <- 65; t3 <- 85
sd1 <- 1; sd2 <- 5; sd3 <- 10

dtime <- as.numeric(difftime(time, min(time), units="hours"))
phases <- cut(dtime, c(-1, t1, t2, t3, 200), labels = c("P1","P2","P3","P4")) 
means <- c(0,d1,d2,0)[phases]
sds <- c(sd1,sd2,sd3,sd1)[phases]
depth <- rnorm(n.obs,means, sds)
# make all depths positive!
depth <- abs(depth)
mydata <- data.frame(time, depth)

# perform windowsweep
ws <- WindowSweep(mydata, "depth", time.var = "time", windowsize = 30, 
                  windowstep = 1, progress=interactive())
plot(ws)
plot(ws, type = "flat", cluster = 6)
ChangePointSummary(ws, cluster = 6)

bcpa documentation built on May 30, 2022, 5:07 p.m.