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Found 23 results

  1. Hi, I am performing gls analysis of Intigeo devices in FlightR. When I use stationary.migration.summary function I get overlapping dates for stationary period. So I decided to use find.times.distribution to find arrival/departure dates to/from stationary periods calculated by stationary.migration.summary. Now I am wondering what key should I use to unify this approach across all my birds? Any advise? Here is a piece of my results of two stationary periods. Meanlat SDlat Meanlon SDlon Dist2 Arrival.Q.50
  2. Hi all, I have a few geolocator files that I have not been able to process ( The location estimates are scattered all across the specified grid) and I believe it has something to do with the plot_slopes_by_location function. I know that this function is just to determine whenever the bird leaves the study site, however, in the graph it revealed that there are no dusk estimates after September (see attached picture). All of the geolocators that I have been unable to analyze have this similar problem. I'm not sure if that's actually the root of my problems or if its something else, this is
  3. Hi, I’m using FlightR 0.4.7 to analyse geolocation from Arctic-nesting birds. Because my study site is located above the Arctic circle, I did a rooftop calibration in the “south” prior to the field season. This works well and the make.calibration function gives good estimates. > Calibration.periods<-data.frame( + calibration.start=as.POSIXct("2016-05-07"), + calibration.stop=as.POSIXct("2016-05-17"), + lon=-68.21627, lat=48.57245) > print(Calibration.periods) calibration.start calibration.stop lon lat 1 2016-05-07 2016-05-17 -68.21627 48.
  4. Hello, I am using Lotek Lat2800 geolocators to track the year-round movements of thick-billed murres. This tag type is not recognized in FLightR. How can I determine the 'log.light.borders' and 'log.irrad.borders' for my tags? So far I have tried inserting different values until I am able to successfully create a calibration object, which works, but is probably not the best solution. Thank you, Allison Patterson
  5. Hi I'm using FLightR to analyse data from Migrate Technology devices, but the function 'make.prerun.object' is returning the following error on two of them (the number of rows is different for each device): Error in `$<-.data.frame`(`*tmp*`, "Dusk", value = c(FALSE, TRUE, FALSE, : replacement has 740 rows, data has 707 Although I don't know where this error arises within the function, I tried to cut out the rows before tag deployment and after tag retrieval from the raw data (I'm calibrating at a stationary location). This made the function work, but after running the part
  6. I've used twilightCalc in GeoLight to identify sunrise and sunsets, but now I can't seem to get the data into a format for FlightR. I've tried the following (with and without all the arguments): TAGSbank066 But I consistently get the following error: Error in GeoLight2TAGS(raw = bank0662, gl_twl = bank066.twl, threshold = th, : unused arguments (raw = bank0662, gl_twl = bank066.twl, threshold = th, filename = NULL) Can someone help me figure this error our of show me what has worked for them? I'm using R version 3.4.2 on Mac OS Sierra 10.12.6 Here's what my data looks li
  7. I am new to working in R, but have been trying my hand at FlightR for analyzing Geolocator data. I have been using a csv that has the following format: tFirst, tSecond, type, movement_cat In this case, tFirst and tSecond are timestamps, type is either a 1 or a 2, and movement_cat is a 1 or 0. With this data, I have been able to work through the excellent example here: https://github.com/eldarrak/FLightR/blob/master/examples/Black-Tailed_Godwit_JAB_example/A5_GeoLight_analysis.Rmd At the end of that example, it states that I can proceed to the FlightR workflow. I am unsure how the tw
  8. Hi, I'm at the stage of interpreting my results (after now having produced the beautiful maps). One thing that slightly troubles me is that, for most birds, the locations in Africa either side of the autumn equinox differ. I am wondering if this is real, or an artefact of the equinox. Most of the locations after the equinox are further S, but a couple are N. There is a similar effect for some birds in spring. I tried to insert some examples (lat-lon plot & map), but seem unable to insert pictures (unless they have a URL?) and I am unsure how to upload files (to my "media library") to attac
  9. I have recently been getting an error when trying to map the FlightR results. I have re-installed and loaded the latest versions of packages: ggmap, ggplot2, RgoogMaps, maptools and grid (just in case this had anything to do with it). I even installed the latest version of ggmap from GitHub > install_github("dkahle/ggmap") as I read in some forum that the error would be resolved with version 2.7 .. but not so). > map.FLightR.ggmap(Result) Error in mapproj::mapproject(x, y, projection = coord$projection, parameters = coord$params, : object 'C_setproj' not found Any thoughts much
  10. I have a number of tags that stopped working (at an unknown location) at some point, before the bird returned and the tag was retrieved. I have changed the Calibration.periods as follows: > Calibration.periods<-data.frame( + calibration.start=as.POSIXct(NA), # start of the second calibration period + calibration.stop=as.POSIXct(c("2013-08-05", NA)), # end of the first calibration period + lon=-4.37, lat=58.38) > print(Calibration.periods) calibration.start calibration.stop lon lat 1 <NA> 2013-08-05 -4.37 58.38 2 <NA> <NA> -4.37 58.38 and removed the model
  11. I have run the LightImage function as part of the FLightR script many times without any issues, but recently it "stopped working". I have updated various packages, R studio and R versions, but I don't see why I'm now getting the error I do. > d.lux$Light<- log(d.lux$Light) > head(d.lux) Date Light 1 2013-04-20 15:14:01 6.302619 2 2013-04-20 15:19:01 5.159055 3 2013-04-20 15:24:01 5.257495 4 2013-04-20 15:29:01 5.594711 5 2013-04-20 15:34:01 5.181784 6 2013-04-20 15:39:01 4.663439 > lightImage(tagdata = d.lux, + offset = offset, + zlim = c(0, 12), # y axis + dt = 300) # re
  12. Hello! I am currently using FLightR to analyze geolocator data for migration routes and timing events, but I have been having issues specifically with loading the package geosphere (sometimes the package MASS is an issue too, but geosphere only works less than half the time for the past month I'd say). I am using geosphere to produce final FLightR maps showing migration results and movements represented by a calendar year legend. I am working on two monitors, one computer, where very often I have two different RStudios running and when installing geosphere it continually says geosphere
  13. Hi, I am using FlightR on geolocator data from common sandpiper. I have pre-processed my .lux files using TwGeos package and manage to subsequently run the FlightR script without problems. I do have some questions about the results it produces and some bits of the script: Do I understand correctly that a location is calculated by the slope of a twilight and that thus, in contrast to geolight, you obtain a location per sunrise and another location per sunset (rather than getting one location for each sunrise and sunset 'pair')? And that as such, excluding / deleting twilights does not mean
  14. Hi Folks, Can anyone describe how outlier detection works in FLightR? How does it determine which points are outliers and what are the criteria for outlier detection? check.outliers=TRUE is part of the run.particle.filter function. Thanks, Luke
  15. Hello all, I am having an issue generating the prerun object for FlightR analyses. The first signs of trouble occur when running "make.calibration", I get the following warnings: [68] WARNING: Warning in log(cur.slope$slope) : NaNs produced Warning in log(All.slopes$Slopes$Slope) : NaNs produced Then, when attempting to generate the prerun object, I get: [69] ERROR: invalid subscript type 'list' Given the error, I assume this is something silly, but I would greatly appreciate any help that anyone could provide. Here is the last line of code: all.in Thank you! Andy Boyce
  16. I'm using FLightR to process my geolocator data. After performing the run.particle. filter I am able to plot it successfully using map.FLightR.ggmap, my issue comes after that, I would like to be able to plot those points in ArcMap. Is there a way in which I can export the Lat/Long data and its associated dates from the run.particle.filter to either a .csv or a shapefile? I'm aware that a previous post mentioned it being easy using the ("add xy data") but i couldn't figure it out. Any advice would be greatly appreciated. Thank you, Devin
  17. I am using FLightR (ver.0.4.5) to process light-level data from Migrate Technology GLS deployed on burrow nesting seabirds. Most GLS were deployed directly on the birds with no calibration period on the island where they nest. However, I kept a subset of different GLS near to the location where GLS were deployed on birds (i.e. within 20 km) in an open location, without artificial light and without any foliage shading, for 1 week. Of course, we know the location of the burrows, and those coordinates could be used as a calibration location, but the problem is that these birds go long dis
  18. I would like to estimate (with uncertainty) the cumulative distance traveled by an organism between two specific time periods. Let's say that I used the find.times.distribution function to identify that a tagged bird most likely commenced spring migration on 1 April 2016 and most likely reached its breeding grounds on 23 April 2016. I would like to sum the distance traveled by that bird between every consecutive twilight from 1 April to 23 April. The ideal final result would be something like, "The cumulative spring distance traveled between 1 April and 23 April was median=1034.2 km (95%
  19. FLightR is on CRAN now, so install.packages('FLightR') library(FLightR) should work on any system.
  20. #Package FLightR version 0.4.6 I have been using FlightR to analyze geolocator data for Grasshopper Sparrows, and I have been really pleased. I am wondering, however, if there is a way to export the kernel density results from the plot_util_distr command into ArcGIS. Exporting the median (w/ 95% CRI) lat/long values for use in ArcGIS (via "add XY data") is easy enough: write.csv(run.particle.filter.Results$Results$Quantiles,"GIS_import.csv") But what about exporting the utilization distributions to ArcGIS for replotting and further manipulation? plot_util_distr(particle.
  21. Hello! I am interested in plotting the results from the Estelle Model in SGAT as graphs of latitude and longitude over time while showing the error (similarly to the 'plot.lat.lon()' function in FLightR). Would anyone have any recommendations on how to do so? Any help would be appreciated! Thanks, Amélie
  22. Hello! I was trying to run FLightR and when trying to run the 'all.in' function I got the following message: Error in create.proposal(Processed.light, start = start, Grid = Grid) : object 'start_no_polar' not found I ran this function: all.in113 I'm not surprised that the function was unable to find 'start_no_polar' as I haven't defined it. I haven't found 'start_no_polar' defined in any examples of FLightR analysis that I have come across, and I don't know what I should be defining it as. Would anyone have any recommendations on how to proceed? Any help would be appreciated!
  23. Hello! I would like to try FLightR (i.e. template fit) method on some of my Intigeo data. I have previously analyzed these tags with GeoLight. I am following the example posted on GitHub for the Godwits but I run into a problem getting the 'twilight events' file. This actually uses the BAStag package not the FLightR package, but I don't know another way to have my data formatted properly for FLightR. It seems to be an issue with the interactive plots called by the 'twl' function. Here is the code from the Godwit example as well as the error. > twl Error in setGraphicsEve
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