This is a summary of all features of GeoLight, a R-package for
analyzing light based geolocator data
Details
GeoLight is a package to derive geographical positions from daily light intensity pattern.
Positioning and calibration methods are based on the threshold-method (Ekstrom 2004, Lisovski et al. 2012).
A changepoint model from the R package changepoint is implemented to distinguish between periods of
residency and movement based on the sunrise and sunset times. Mapping functions are implemented
using the R package maps.
Getting Started
We refrain from giving detailed background on the (several steps of)
analysis of light-based geolocator data here but strongly recommend the key-publications below.
Updates
We advise all users to update their installation of GeoLight regularly.
Type news(package="GeoLight") to read news documentation about changes to the recent and all previous version of the package
Important notes
Most functions in GeoLight require the same initial units and mostly the format and object type is mandatory:
tFirst
yyyy-mm-dd hh:mm "UTC" (see: as.POSIXct, time zones)
tSecond
as tFirst (e.g. 2008-12-01 17:30)
type
either 1 or 2 depending on wheter tFirst is sunrise (1) or sunset (2)
coord
SpatialPoints or a matrix, containing x and y coordinates (in that order)
degElevation
a vector or a single value of sun elevation angle(s) in degrees (e.g. -6)
FUNCTIONS AND DATASETS
In the following, we give a summary of the main functions and sample datasets in the GeoLight package.
Alternatively a list of all functions and datasets in alphabetical order is available by typing library(help=GeoLight).
For further information on any of these functions, type help(function name).
CONTENTS
I.
Determination of sunset and sunrise
II.
Residency analysis
III.
Calibration
IV.
Positioning
V.
Data visualisation
VI.
Examples
I. Determination of sunset and sunrise
gleTrans
transformation of already defined twilight events*
glfTrans
transformation of light intensity measurements over time*
luxTrans
transformation of light intensity measurements over time**
lightFilter
filter to remove noise in light intensity measurements during the night
twilightCalc
definition of twilight events (sunrise, sunset) from light intensity measurements
* written for data recorded by geolocator devices from the Swiss Ornithological Institute
** written for data recorded by geolocator devices from Migrate Technology Ltd
II. Residency Analysis
changeLight
function to distinguish between residency and movement periods
schedule
function to produce a data frame summerizing the residency and movement pattern
III. Calibration
See Lisovski et al. 2012 for all implemented calibration methods.
getElevation
function to calculate the sun elevation angle for data with known position
HillEkstromCalib
Hill-Ekstrom calibration for one or more defined stationary periods
IV. Positioning
coord
main function to derive a matrix of spatial coordinates
distanceFilter
filter function to reduce unrealistic positions (not recommended, since the filtering ignore positioning error)
loessFilter
filter function to define outliers in sunrise and sunset times (defined twilight events)
V. Data visualisation
tripMap
function to map the derived positions and combine the coordinates in time order
siteMap
function to show the results of the residency analysis on a map
IV. Examples
calib1
data for calibration: light intensities
calib2
data for calibration: Calculated twilight events (from calib1 by twilightCalc)
hoopoe1
light intensity measurements over time recorded on a migratory bird
hoopoe2
sunrise and sunset times: From light intensity measurement (from hoopoe1)
Steffen Hahn, Felix Liechti, Fraenzi Korner-Nievergelt, Andrea Koelzsch, Eldar Rakhimberdiev, Erich Baechler, Eli Bridge, Andrew Parnell, Richard Inger
Authors
Simeon Lisovski, Simon Wotherspoon, Michael Sumner, Silke Bauer, Tamara Emmenegger
Maintainer: Simeon Lisovski <simeon.lisovski(at)gmail.com>
References
Ekstrom, P.A. (2004) An advance in geolocation by light. Memoirs of the National Institute of Polar Research, Special Issue, 58, 210-226.
Fudickar, A.M., Wikelski, M., Partecke, J. (2011) Tracking migratory songbirds: accuracy of light-level loggers (geolocators) in forest habitats. Methods in Ecology and Evolution, DOI: 10.1111/j.2041-210X.2011.00136.x.
Hill, C. & Braun, M.J. (2001) Geolocation by light level - the next step: Latitude. Electronic Tagging and Tracking in Marine Fisheries (eds J.R. Sibert & J. Nielsen), pp. 315-330. Kluwer Academic Publishers, The Netherlands.
Hill, R.D. (1994) Theory of geolocation by light levels. Elephant Seals: Population Ecology, Behavior, and Physiology (eds L. Boeuf, J. Burney & R.M. Laws), pp. 228-237. University of California Press, Berkeley.
Lisovski, S. and Hahn, S. (2012) GeoLight - processing and analysing light-based geolocator data in R. Methods in Ecology and Evolution, doi: 10.1111/j.2041-210X.2012.00248.x
Lisovski, S., Hewson, C.M, Klaassen, R.H.G., Korner-Nievergelt, F., Kristensen, M.W & Hahn, S. (2012) Geolocation by light: Accuracy and precision affected by environmental factors. Methods in Ecology and Evolution, doi: 10.1111/j.2041-210X.2012.00185.x
Wilson, R.P., Ducamp, J.J., Rees, G., Culik, B.M. & Niekamp, K. (1992) Estimation of location: global coverage using light intensity. Wildlife telemetry: remote monitoring and tracking of animals (eds I.M. Priede & S.M. Swift), pp. 131-134. Ellis Horward, Chichester.