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FLightR

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

    install.packages("FLightR")

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

    devtools::install_github("eldarrak/FLightR")
   library(FLightR)

NB

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 rewritten 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 initially 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


References

  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.

  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.

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Version

Install

install.packages('FLightR')

Monthly Downloads

314

Version

0.5.0

License

GPL-3

Maintainer

Eldar Rakhimberdiev

Last Published

May 15th, 2020

Functions in FLightR (0.5.0)

map.FLightR.ggmap

plots result over map
plot_lon_lat

plots result by longitude and latitude
plot_util_distr

plots resulting track over map with uncertainty shown by space utilisation distribution
run.particle.filter

Run Particle Filter
plot_likelihood

plot likelihood surface over map
plot_slopes_by_location

plots log of observed versus expected slope by time for a known location
stationary.migration.summary

find potential stationary periods and estimates their location and movement schedule
find.stationary.location

find unknown calibration location
twGeos2TAGS

Function to write down twilights annotated in twGeos package data in so-called TAGS format
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
FLightR2Movebank

Summary of estimated locations for Movebank
find.times.distribution

extracts times of arrival and departure to/from spatial extent
get.tags.data

read TAGS formatted data
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