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>.
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
Version 0.3.9 has got two major changes:
- Workflow was completely rewritten 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 (>=0.4.7) workflow for red-backed shrike example with Intigeo tag
- 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 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
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. (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
|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.|
Vignettes of FLightR
Last month downloads
|Packaged||2020-05-13 08:00:51 UTC; eldar|
|Date/Publication||2020-05-15 06:00:02 UTC|
|imports||bit , CircStats , circular , fields , GeoLight , ggmap , ggplot2 , ggsn , maptools , methods , mgcv , nlme , parallel , raster , RcppArmadillo , rgdal , rgeos , sp , truncnorm|
|suggests||covr , knitr , rmarkdown , testthat|
|depends||R (>= 3.0.2)|
|Contributors||Simeon Lisovski, Anatoly Saveliev, Julia Karagicheva|
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