Reconstruct Animal Paths from Solar Geolocation Loggers Data

Spatio-temporal locations of an animal are computed from annotated data with a hidden Markov model via particle filter algorithm. The package is relatively robust to varying degrees of shading. The hidden Markov model is described in Movement Ecology (Rakhimberdiev et al., 2015) , general package description is in the Methods in Ecology and Evolution (Rakhimberdiev et al., 2017) and package accuracy assessed in the Journal of Avian Biology (Rakhimberdiev et al. 2016) .

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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.

FLightR is on CRAN now, so


I will try to update CRAN version several times a year, but to get the latest version from GitHub try:


Version 0.4.4 All function names started from plot. are replaced wit plot_, e.g. 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 (>=0.4.7) workflow for red-backed shrike example with Intigeo tag
  2. new (>=0.3.9) workflow for black-tailed godwit example with Intigeo tag
  3. old (<0.3.9) workflow for tree swallow example with BAS tag
  4. 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 available here


  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. (2017). FLightR: An R package for reconstructing animal paths from solar geolocation loggers. Methods in Ecology and evolution. Check it

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.


Reference manual

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0.5.1 by Eldar Rakhimberdiev, 5 months ago

Report a bug at

Browse source code at

Authors: Eldar Rakhimberdiev [aut, cre] , Anatoly Saveliev [aut] , Julia Karagicheva [aut] , Simeon Lisovski [ctb]

Documentation:   PDF Manual  

Task views:

GPL-3 license

Imports bit, ggsn, ggmap, ggplot2, CircStats, circular, GeoLight, fields, maptools, methods, mgcv, nlme, parallel, RcppArmadillo, rgdal, rgeos, sp, truncnorm

Suggests covr, testthat, knitr, rmarkdown

See at CRAN