FLightR (version 0.4.5)

plot_likelihood: plot likelihood surface over map

Description

plots specific likelihood surface over map

Usage

plot_likelihood(object, date = NULL, twilight.index = NULL)

Arguments

object

either output from make.prerun.object or run.particle.filter

date

either NULL or a date (possibly with time) closest to the twilight you wan tto be plotted

twilight.index

number of likelohood surface to be plotted

Details

function plots likelihoods before particle filter run, so these are pure results of calibrations without any movement model

Examples

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('2013-07-02', 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=2)
plot_likelihood(all.in, twilight.index=10)