FLightR v0.4.5


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Hidden Markov Model for Solar Geolocation Archival Tags

Estimate positions of animal from data collected by solar geolocation archival tags.


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Welcome to FLightR, an R package that deals with solar geolocation data. The scope of the package is to position animal using data from solar geolocation archival tags the package is in the active development.

to install the package try:



Version 0.4.4 All function names started from plot. are replaced wit plot_, e.g. plot.lon.lat() became plot_lon_lat() Version 0.3.9 has got two major changes:

  1. Workflow was completely rewtitten and simplified. Updated workflow is here
  2. New version does not require lots of RAM, but it became slower.

Very important changes were made for version 0.3.6 Just contact me if results come out strange.

##Examples of packages use:

  1. new (>=0.3.9) workflow for black-tailed godwit example with Intigeo tag
  2. old (<0.3.9) workflow for tree swallow example with BAS tag
  3. old (<0.3.9) workflow for black-tailed godwit example with Intigeo tag

Do not know what the difference between BAS and Intigeo is? In short intigeo are being currently produced by Migrate Technology Ltd, and measure data up to very high sun elevation angles, BAS tags are the old ones produced inititally by British Antarctic Survey, then by Migrate Technology (till ~2013) and Lotek (still available) and measured data at the low sun angles (with maximum written at 64). More on the tag specific differences can be found here.

Vignette for the package is coming very soon,

I am also developing [wiki pages for the package] (https://github.com/eldarrak/FLightR/wiki)


  1. Rakhimberdiev, E., Winkler, D.W., Bridge, E., Seavy, N.E., Sheldon, D., Piersma, T. & Saveliev, A. (2015). A hidden Markov model for reconstructing animal paths from solar geolocation loggers using templates for light intensity. Movement Ecology, 3, 25. Check it

  2. Rakhimberdiev, E., Senner, N.R., Verhoeven, M.A., Winkler, D.W., Bouten, W. & Piersma, T. (2016). Comparing inferences of solar geolocation data against high-precision GPS data: annual movements of a double-tagged black-tailed godwit. Journal of Avian Biology, 47, 589–596. Check it

  3. Rakhimberdiev, E. (2016). Ornithology by light levels today: dealing with a developing teenager. Wader Study, 123, 1–3. DOI

  4. Rakhimberdiev, E.Saveliev A., Piersma, T. & Karagicheva, J. FLightR: An R package for reconstructing animal paths from solar geolocation loggers - submitted

Discussion web forum for solar geolocation is available at ornithologyexchange. Ask there if you need help with the FLightR per se or with solar geolocation in general.

Functions in FLightR

Name Description
map.FLightR.ggmap plots result over map
make.grid makes spatial grid
make.prerun.object combines data, calibration and sets up priors
BAStag2TAGS Function to write down twilights annotated in BAStag package data in so-called TAGS format
find.stationary.location find undknown calibration location
get.tags.data #@title FLightR #@import ggplot2 #@description With a hidden Markov model package estimates postions of animal from data collected by solar geolocation archival tags.
GeoLight2TAGS Function to write down twilights annotated in GeoLight package data in so-called TAGS format
get_ZI_distances Estimate distances moved between twilights
make.calibration Creates a calibration object, further used for calculation of coordinates in the run.particle.filter.
find.times.distribution extracts times of arrival and departure to/from spatial extent
plot_lon_lat plots result by longitude and latitude
plot_slopes_by_location plots log of observed vesus expected slope by time for a known location
plot_likelihood plot likelihood surface over map
stationary.migration.summary find potential stationary periods and estimates their location and movement schedule
run.particle.filter Run Particle Filter
plot_util_distr plots resulting track over map with uncertainty shown by spave utilisation distribution
twGeos2TAGS Function to write down twilights annotated in twGeos package data in so-called TAGS format
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Type Package
Date 2016-12-07
URL http://github.com/eldarrak/FLightR
BugReports http://github.com/eldarrak/FLightR/issues
License GPL-3
ByteCompile true
RoxygenNote 5.0.1
NeedsCompilation no
Packaged 2016-12-15 11:48:23 UTC; Eldar
Repository CRAN
Date/Publication 2016-12-15 13:52:54

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