Hidden Markov Model for Solar Geolocation Archival Tags
Estimate positions of animal from data collected by solar geolocation archival tags.
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:
require("devtools") install_github("eldarrak/FLightR") library(FLightR)
Version 0.4.4 All function names started from
plot. are replaced wit
Version 0.3.9 has got two major changes:
- Workflow was completely rewtitten and simplified. Updated workflow is here
- 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:
- new (>=0.3.9) workflow for black-tailed godwit example with Intigeo tag
- old (<0.3.9) workflow for tree swallow example with BAS tag
- 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)
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
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
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
|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|
Last month downloads
|Packaged||2016-12-15 11:48:23 UTC; Eldar|
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