FLightR v0.5.0

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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) <doi:10.1186/s40462-015-0062-5>, general package description is in the Methods in Ecology and Evolution (Rakhimberdiev et al., 2017) <doi:10.1111/2041-210X.12765> and package accuracy assessed in the Journal of Avian Biology (Rakhimberdiev et al. 2016) <doi:10.1111/jav.00891>.

Readme

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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. 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.

Functions in FLightR

Name Description
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 Creates a calibration object, further used for calculation of coordinates in the run.particle.filter.
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Vignettes of FLightR

Name
FLightR_with_black-tailed_godwit_vignette_from_MEE_2017.Rmd
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Details

Type Package
Date 2020-05-11
URL https://CRAN.R-project.org/package=FLightR
BugReports http://github.com/eldarrak/FLightR/issues
License GPL-3
ByteCompile true
RoxygenNote 7.1.0
VignetteBuilder knitr
NeedsCompilation no
Packaged 2020-05-13 08:00:51 UTC; eldar
Repository CRAN
Date/Publication 2020-05-15 06:00:02 UTC

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