Package: FLightR 0.5.6.900

FLightR: 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>.

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

FLightR_0.5.6.900.tar.gz
FLightR_0.5.6.900.zip(r-4.7)FLightR_0.5.6.900.zip(r-4.6)FLightR_0.5.6.900.zip(r-4.5)
FLightR_0.5.6.900.tgz(r-4.6-any)FLightR_0.5.6.900.tgz(r-4.5-any)
FLightR_0.5.6.900.tar.gz(r-4.7-any)FLightR_0.5.6.900.tar.gz(r-4.6-any)
FLightR_0.5.6.900.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
FLightR/json (API)

# Install 'FLightR' in R:

install.packages('FLightR', repos = c('https://eldarrak.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/eldarrak/flightr/issues

On CRAN:

movement-ecology solar-geolocation-loggers solar-geolocator

7.20 score 23 stars 115 scripts 445 downloads 18 exports 71 dependencies

Last updated from:83c77ec9a5. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	238
source / vignettes	OK	389
linux-release-x86_64	OK	246
macos-release-arm64	OK	144
macos-oldrel-arm64	OK	163
windows-devel	OK	320
windows-release	OK	230
windows-oldrel	OK	216
wasm-release	OK	136

Exports:BAStag2TAGS find.stationary.location find.times.distribution FLightR2Movebank GeoLight2TAGS get_ZI_distances get.tags.data make.calibration make.grid make.prerun.object map.FLightR.ggmap plot_likelihood plot_lon_lat plot_slopes_by_location plot_util_distr run.particle.filter stationary.migration.summary twGeos2TAGS

Dependencies:askpass bit bitops boot CircStats circular class classInt cli cpp11 curl DBI digest dotCall64 dplyr e1071 farver fields generics geosphere ggmap ggplot2 glue gtable httr isoband jpeg jsonlite KernSmooth labeling lattice lifecycle magrittr maps MASS Matrix mgcv mime mvtnorm nlme openssl pillar pkgconfig plyr png proxy purrr R6 RColorBrewer Rcpp RcppArmadillo rlang s2 S7 scales sf spam stringi stringr suntools sys tibble tidyr tidyselect truncnorm units utf8 vctrs viridisLite withr wk

FLightR with black-tailed godwit vignette from MEE 2017

Rendered fromFLightR_with_black-tailed_godwit_vignette_from_MEE_2017.Rmdusingknitr::rmarkdown

Last update: 2021-07-02
Started: 2017-03-09

Help page	Topics
Function to write down twilights annotated in BAStag package data in so-called TAGS format	BAStag2TAGS
find unknown calibration location	find.stationary.location
extracts times of arrival and departure to/from spatial extent	find.times.distribution
Summary of estimated locations for Movebank	FLightR2Movebank
Function to write down twilights annotated in GeoLight package data in so-called TAGS format	GeoLight2TAGS
Estimate distances moved between twilights	get_ZI_distances
read TAGS formatted data	get.tags.data
Creates a calibration object, further used for calculation of coordinates in the 'run.particle.filter'.	make.calibration
makes spatial grid	make.grid
combines data, calibration and sets up priors	make.prerun.object
plots result over map	map.FLightR.ggmap
Match GPS fixes to FLightR twilight times	match_gps_to_twilights
plot likelihood surface over map	plot_likelihood
plots result by longitude and latitude	plot_lon_lat
plots log of observed versus expected slope by time for a known location	plot_slopes_by_location
plots resulting track over map with uncertainty shown by space utilisation distribution	plot_util_distr
Extract posterior point distribution for one twilight	posterior_point_distribution
Read a GPS track for validation	read_gps_track
Read local validation configuration	read_validation_config
Run Particle Filter	run.particle.filter
find potential stationary periods and estimates their location and movement schedule	stationary.migration.summary
Function to write down twilights annotated in twGeos package data in so-called TAGS format	twGeos2TAGS
Summarize validation against matched GPS fixes	validation_summary

Package: FLightR 0.5.6.900

FLightR: Reconstruct Animal Paths from Solar Geolocation Loggers Data

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