FLightR (version 0.5.0)

stationary.migration.summary: find potential stationary periods and estimates their location and movement schedule

Description

This function will find any sites where birds stayed longer than min.stay. Potential movement is detected by the minimum probability of movement prob.cutoff.

Usage

stationary.migration.summary(Result, prob.cutoff = 0.1, min.stay = 3)

Arguments

Result

FLightR result object obtained from run.particle.filter

prob.cutoff

Minimum probability that defines movement

min.stay

Minimum duration of stationary period (in twilights)

Value

list with stationary and movement statistics

Examples

# NOT RUN {
File<-system.file("extdata", "Godwit_TAGS_format.csv", package = "FLightR")
# to run example fast we will cut the real data file by 2013 Aug 20
Proc.data<-get.tags.data(File, end.date=as.POSIXct('2013-06-25', tz='GMT'))
Calibration.periods<-data.frame(
       calibration.start=as.POSIXct(c(NA, "2014-05-05")),
       calibration.stop=as.POSIXct(c("2013-08-20", NA)),
       lon=5.43, lat=52.93) 
       #use c() also for the geographic coordinates, if you have more than one calibration location
       # (e. g.,  lon=c(5.43, 6.00), lat=c(52.93,52.94))

# NB Below likelihood.correction is set to FALSE for fast run! 
# Leave it as default TRUE for real examples
Calibration<-make.calibration(Proc.data, Calibration.periods, likelihood.correction=FALSE)

Grid<-make.grid(left=0, bottom=50, right=10, top=56,
  distance.from.land.allowed.to.use=c(-Inf, Inf),
  distance.from.land.allowed.to.stay=c(-Inf, Inf))

all.in<-make.prerun.object(Proc.data, Grid, start=c(5.43, 52.93),
                             Calibration=Calibration, threads=1)
# here we will run only 1e4 partilces for a very short track.
# One should use 1e6 particles for the full run.
Result<-run.particle.filter(all.in, threads=1,
           nParticles=1e3, known.last=TRUE,
           precision.sd=25, check.outliers=FALSE)

Summary<-stationary.migration.summary(Result, prob.cutoff=1)
# Use lower cut offs for real runs!
# }

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