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Found 21 results

  1. 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
  2. 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 particle filter it looks like the locations at the beginning (departure) and ending (arrival) of the track are missing. This seems that they were removed when I trimmed the raw data, but I double checked and this was not the case. Does anyone know how to solve this? Many thanks in advance! Camilo
  3. 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 just my best guess. Is anybody aware if this could be the problem and if it is is there anyway to correct for this problem? Thanks, Devin
  4. 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 like: > head(bank0662) Date Light 1 2013-07-05 12:37:59 64 2 2013-07-05 12:39:59 64 3 2013-07-05 12:41:59 3 4 2013-07-05 12:43:59 3 5 2013-07-05 12:45:59 5 6 2013-07-05 12:47:59 7 > head(bank066.twl) tFirst tSecond type 1 2013-07-09 22:08:07 2013-07-10 12:23:48 1 2 2013-07-10 12:23:48 2013-07-10 20:07:43 2 3 2013-07-10 20:07:43 2013-07-11 11:56:57 1 4 2013-07-11 11:56:57 2013-07-11 20:30:23 2 5 2013-07-11 20:30:23 2013-07-12 11:55:06 1 6 2013-07-12 11:55:06 2013-07-12 20:10:34 2 > th [1] 1.504077
  5. 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 two examples connect. Can someone shed some light on this?
  6. 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 attach. What are people's thoughts on such findings? Is this a common artefact of the equinox, or might this be a real shift in location? Thanks for your feedback. Louise
  7. 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 appreciated. Louise
  8. 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.ageing part from the make.calibration function: > Calibration<-make.calibration(Proc.data, Calibration.periods, model.ageing = FALSE) dusk 191 was excluded from the calibration calibration method used: parametric.slope likelihood correction switched to TRUE dusk 189 was excluded from the calibration calibration method used: parametric.slope dusk 188 was excluded from the calibration calibration method used: parametric.slope estimating correction function... There were 50 or more warnings (use warnings() to see the first 50) This resulted in loads of warnings (see below). Is this normal, do I just proceed? What do they mean? > warnings() Warning messages: 1: In is.na(First.LogIrrad) : is.na() applied to non-(list or vector) of type 'NULL' 2: In is.na(Last.LogIrrad) : is.na() applied to non-(list or vector) of type 'NULL' 3: In is.na(First.LogIrrad) : is.na() applied to non-(list or vector) of type 'NULL' 4: In is.na(Last.LogIrrad) : is.na() applied to non-(list or vector) of type 'NULL' 5: In is.na(First.LogIrrad) : is.na() applied to non-(list or vector) of type 'NULL' 6: In is.na(Last.LogIrrad) : is.na() applied to non-(list or vector) of type 'NULL' 7: In is.na(First.LogIrrad) : is.na() applied to non-(list or vector) of type 'NULL' 8: In is.na(Last.LogIrrad) : is.na() applied to non-(list or vector) of type 'NULL' 9: In is.na(First.LogIrrad) : is.na() applied to non-(list or vector) of type 'NULL' 10: In is.na(Last.LogIrrad) : is.na() applied to non-(list or vector) of type 'NULL' 11: In is.na(First.LogIrrad) : is.na() applied to non-(list or vector) of type 'NULL' 12: In is.na(Last.LogIrrad) : is.na() applied to non-(list or vector) of type 'NULL' 13: In is.na(First.LogIrrad) : is.na() applied to non-(list or vector) of type 'NULL' 14: In is.na(Last.LogIrrad) : is.na() applied to non-(list or vector) of type 'NULL' 15: In is.na(First.LogIrrad) : is.na() applied to non-(list or vector) of type 'NULL' 16: In is.na(Last.LogIrrad) : is.na() applied to non-(list or vector) of type 'NULL' 17: In is.na(First.LogIrrad) : is.na() applied to non-(list or vector) of type 'NULL' 18: In is.na(Last.LogIrrad) : is.na() applied to non-(list or vector) of type 'NULL' 19: In is.na(First.LogIrrad) : is.na() applied to non-(list or vector) of type 'NULL' 20: In is.na(Last.LogIrrad) : is.na() applied to non-(list or vector) of type 'NULL' 21: In log(cur.slope$slope) : NaNs produced 22: In log(All.slopes$Slopes$Slope) : NaNs produced 23: In is.na(First.LogIrrad) : is.na() applied to non-(list or vector) of type 'NULL' 24: In is.na(Last.LogIrrad) : is.na() applied to non-(list or vector) of type 'NULL' 25: In is.na(First.LogIrrad) : is.na() applied to non-(list or vector) of type 'NULL' 26: In is.na(Last.LogIrrad) : is.na() applied to non-(list or vector) of type 'NULL' 27: In is.na(First.LogIrrad) : is.na() applied to non-(list or vector) of type 'NULL' 28: In is.na(Last.LogIrrad) : is.na() applied to non-(list or vector) of type 'NULL' 29: In is.na(First.LogIrrad) : is.na() applied to non-(list or vector) of type 'NULL' 30: In is.na(Last.LogIrrad) : is.na() applied to non-(list or vector) of type 'NULL' 31: In is.na(First.LogIrrad) : is.na() applied to non-(list or vector) of type 'NULL' 32: In is.na(Last.LogIrrad) : is.na() applied to non-(list or vector) of type 'NULL' 33: In is.na(First.LogIrrad) : is.na() applied to non-(list or vector) of type 'NULL' 34: In is.na(Last.LogIrrad) : is.na() applied to non-(list or vector) of type 'NULL' 35: In is.na(First.LogIrrad) : is.na() applied to non-(list or vector) of type 'NULL' 36: In is.na(Last.LogIrrad) : is.na() applied to non-(list or vector) of type 'NULL' 37: In is.na(First.LogIrrad) : is.na() applied to non-(list or vector) of type 'NULL' 38: In is.na(Last.LogIrrad) : is.na() applied to non-(list or vector) of type 'NULL' 39: In is.na(First.LogIrrad) : is.na() applied to non-(list or vector) of type 'NULL' 40: In is.na(Last.LogIrrad) : is.na() applied to non-(list or vector) of type 'NULL' 41: In is.na(First.LogIrrad) : is.na() applied to non-(list or vector) of type 'NULL' 42: In is.na(Last.LogIrrad) : is.na() applied to non-(list or vector) of type 'NULL' 43: In log(cur.slope$slope) : NaNs produced 44: In log(All.slopes$Slopes$Slope) : NaNs produced 45: In log(all.slopes$Slopes$Slope) : NaNs produced 46: In log(Slope) : NaNs produced 47: In log(Slope) : NaNs produced 48: In log(Slope) : NaNs produced 49: In log(Slope) : NaNs produced 50: In is.na(First.LogIrrad) : is.na() applied to non-(list or vector) of type 'NULL' Thanks Louise
  9. Louise de Raad

    LightImage function error

    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) # recording interval in seconds (300 if every 5min) Error in if (as.numeric(tmax) < as.numeric(date[length(date)])) tmax <- tmax + : missing value where TRUE/FALSE needed > sessionInfo() R version 3.4.2 (2017-09-28) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows >= 8 x64 (build 9200) Matrix products: default locale: [1] LC_COLLATE=English_United Kingdom.1252 [2] LC_CTYPE=English_United Kingdom.1252 [3] LC_MONETARY=English_United Kingdom.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United Kingdom.1252 attached base packages: [1] grid stats graphics grDevices utils datasets methods [8] base other attached packages: [1] maptools_0.9-2 sp_1.2-5 MASS_7.3-47 SGAT_0.1.3 [5] TwGeos_0.0-1 GeoLight_2.0.0 maps_3.2.0 FLightR_0.4.6 [9] BAStag_0.1.3 loaded via a namespace (and not attached): [1] Rcpp_0.12.13 lattice_0.20-35 changepoint_2.2.2 zoo_1.8-0 [5] spam_2.1-1 coda_0.19-1 raster_2.5-8 tools_3.4.2 [9] foreign_0.8-69 fields_9.0 compiler_3.4.2 dotCall64_0.9-04 > Any thought? Many thanks, Louise
  10. 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 was successfully unpacked in both R sessions, but then only one or none of the maps will load after running the following line, "map.FLightR.ggmap(Result163, seasonal.donut.location=NULL, save=TRUE)" I am currently running version 3.4.1 "Single Candle", and I have also used/run version 3.3.2 "Sincere Pumpkin Patch" where geosphere also used to only work occasionally. Geosphere does not appear to be on the update packages list, therefore any recommendations on how to get geosphere to consistently work? Thank you so much for your time and help in advance! Sabina
  11. 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 the twilights (locations) before and after the deleted twilight are also lost? In Eldar's (2015) paper (page 6 of 15) it states that for all their models, they assumed that the truncation points were a = 45 and b = 1000km. "That is, when birds initiated a movement, they could not fly less than 45km or more than 1500km in a single between-twilight interval." This seems to me that 'b' should have thus been 1500. What is actually being used in the script 1000 or 1500km? I take it that this means that a bird is classified as being in a movement state if it moves >= 45km from one estimated location to the next, but are geolocator data derived locations not more imprecise than that (so that the bird could be classified as in a movement state whereas the "movement" is actually due to inaccurately calculated positions)? Should this threshold therefore not be higher, e.g. >= 300km (see e.g. paper Fudickar et al 2011, but even Eldar's 2016 paper showed a 43.3 +/- 51.5km deviation from the true position) A question about identifying staging areas using this bit of script stationary.migration.summary(Result, prob.cutoff = 0.1, min.stay = 3) min.stay is presumably the number of twilights, but what happens if twilights have been excluded from what could potentially be a staging area? So for example you say min.stay= 3 (which normally could mean a sunrise, sunset and another sunrise (e.g. approximately 24 hours minimum stay) but the sunset was excluded - does it then become sunrise, sunrise, sunset (i.e. approximately 36 hours minimum stay)? Then a couple of questions about the outputs of the script: In the plot of the locations (map.FLightR.ggmap(Result)), it doesn't look like all locations are plotted (I have 521 coordinates in the coords.csv file, but the map seems to only show around 70 points). What locations are plotted? Which coordinates from the coords.csv file are plotted (Medianlat/Medianlons or Meanlat/Meanlons)? In the coords.csv file what is the difference between Medianlat and MedianlatJ (and the same for long)? In the plots of lat and long, what do the dark grey and pale grey limits show (are these first and third percentiles respectively?) Sorry, a lot of questions (I saved them all up!!), I hope you can help me with. Thanks Louise
  12. 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
  13. 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
  14. 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
  15. 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 distances (up to several hundred km) between attending their burrow and they only come and go from their burrows during dark hours of the night. The birds are long distance travelers and can be a long way from the colony by the time the sun rises. Therefore, as I see it, light-levels of the device would not correspond well with the actual light levels at the calibration location if I used the colony site as the calibration location. I would appreciate any advice on how best to deal with calibration in FLightR based on this scenario. Cheers, Luke
  16. 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% credible interval: 650.2 to 1840.2 km). Getting the median cumulative distance is easy: migration.longitude.values migration.latitude.values library(sp) sum(spDists(cbind(migration.longitude.values, migration.latitude.values),segments=TRUE,longlat=TRUE)) But I cannot figure out a 'good' way to estimate the uncertainty component. One (non-parsimonious) solution would be: 1) generate 95% isopleths (with the plot_util_distr function) for every twilight [or perhaps just every day] between 1 April and 23 April, 2) generate 1000 random points (assuming a uniform distribution) within the confines of each 95% isopleth, 3) create 1000 paths/polylines that run between all 23 isopleths (using a single point in each isopleth), 4) and finally measure the length of those 1000 paths and create summary statistics (median, mean, 0.25 and 0.975 percentile values). I had been trying to modify the get_ZI_distances function in FlightR to avoid my non-parsimonious solution, but I have so far failed miserably. Hopefully a better programmer than myself can provide some help. Thank you and cheers, Jason Hill
  17. FLightR is on CRAN now, so install.packages('FLightR') library(FLightR) should work on any system.
  18. #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.filter.results, dates=data.frame(as.POSIXct('2015-12-01'), as.POSIXct('2016-02-01')), percentiles=c(0.5,0.9), save.options = list(filename="winter.pdf")) I've tried saving or converting the plot object to a SpatialPolygonsDataFrame but I don't know of a way to coerce a 'list' into a SpatialPolygonsDataFrame. I suppose that I could draw the winter.pdf file with a blank background (then geo-reference the winter.pdf file) and bring that file into ArcGIS with the georeference toolbar. That would not be a parsimonious option for my 30+ birds and I still couldn't manipulate the results in ArcGIS (I could only view them). Thanks for your help and suggestions everyone, Jason
  19. AmelieRobertoCharron

    plot.lon.lat() in SGAT.

    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
  20. AmelieRobertoCharron

    FLightR Error Message.

    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! Thanks, Amélie
  21. 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 setGraphicsEventEnv(which, as.environment(list(...))) : this graphics device does not support event handling I am using Mac OS X 10.11.3 El Capitan, R version 3.2.4 Very Secure Dishes I have not had any trouble looking at the transitions with GeoLight but it doesn't seem to produce files in the correct format for FlightR. Thanks for any help! Emily
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