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 packageImportant 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) |
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 |
|
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 LtdII. 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 ) |
<b><code>R</code></b> Packages for Further Spatial Ananlyses
spatstat
adehabitat
gstat
trip
tripEstimation
move
...Acknowledgements
Steffen Hahn, Felix Liechti, Fraenzi Korner-Nievergelt, Andrea Koelzsch, Eldar Rakhimberdiev, Erich Baechler, Eli Bridge, Andrew Parnell, Richard IngerAuthors
Simeon Lisovski, Simon Wotherspoon, Michael Sumner, Silke Bauer, Tamara Emmenegger
Maintainer: Simeon Lisovski 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.