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This group provides support for those using geolocator technology to study animal movement and behavior.

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  2. This is strange. I have just tried installing from GitHub and got the 0.4.9... It is not on CRAN yet, so do not try there. Eldar
  3. Hi Eldar, I just tried updating to FLightR version 0.4.9 but can only get 0.4.8 to install via GitHub and CRAN. Any ideas about what might be happening?
  4. Please note that there was a bug in FLightR 0.4.8 that creared weird resuls with point jumping all over the place - Please update FLightR to 0.4.9: devtools::install_github('eldarrak/FLightR') Eldar
  5. Hi Dan, I have discovered a bug in FLightR 0.4.8. Please reinstall from Grithub with devtools::install_github('eldarrak/FLightR') and report whether you still have problems. Sorry for the inconvenience. Eldar
  6. I am part of a long-term study monitoring Cerulean Warbler populations using point counts, a geolocator study, and nest monitoring. For the past 10 or so years, we have been using mini Radioshack amplifiers connected to an mp3 player with an auxiliary cable for our playback surveys and target netting. Since the start of the study, Radioshack has gone out of business, and we are unable to purchase replacements of the amplifiers when they break. I am asking for recommendations of speakers/amplifiers that others have field-tested with success. The speaker/amplifier must be able to project sound for a minimum of 100 m, be easily transported in the field, and have an auxiliary cable port. Thank you!
  7. The move is done now. Let me know if you have any questions about how this new Groups feature works.
  8. Hi- I am usingTwGeos (findTwilights and twilightEdit) to determine twlights. I define my capture locations and define those for the start and end period calibrations. CapLocs=c(-73.091342, 42.680602); FLightR generates start and end locations that are not even close to the capture locations. Also, the locations zigzag all over during periods I think should be stationary. Any ideas where I should start looking? Thanks, Dan FlightR output:
  9. Recently we started using a new application on OE called Groups. As a result, you now see a Groups tab on the navigation menu above. With this application, users can start their own sub-communities on OE, like this Geolocator Discussion & Support group. Several new groups have already been created, and more are on the way. I a now beginning to transition our existing groups to this new app. On Friday February 15 I will pull the trigger and have this forum moved over to the Groups app. Here is what to expect: The forum will be moved from the Forums page to the Groups page. When you click on Groups in the navigation menu, you will see a list of groups, including the new Geolocator Discussion & Support group. When you click on the group, there will be a home page, a members page, and a forum page. The forum page will look just like the current one does. All the past forum topics will be there too. Anybody who is signed up for notifications on the current forum will be added to the new group and your personal notification settings for the forum will be maintained as they currently are. Eli Bridge will be the owner of the group, and the moderator. If anybody else wants to help moderate, talk to Eli. If anybody has any questions or concerns, please reply to this message or contact me directly. And if anybody has an I can use as either a logo or a banner for the new group, please send it to me.
  10. Thanks, Eldar! I installed Rtools from the website you sent. Then, per the subsequent error messages trying to install TwGeos, I also had to run: install.packages("SGAT"); install.packages("zoo"); devtools::install_github("SLisovski/TwGeos"); It looks like Twgeos is successfully loaded. > search() [1] ".GlobalEnv" "package:SGAT" "package:zoo" [4] "package:TwGeos" "package:stats" "package:graphics" [7] "package:grDevices" "package:utils" "package:datasets" [10] "package:methods" "Autoloads" "package:base" Now I just have to figure out how to use it! thanks! Dan
  11. Hi Dan, rtools is not a package, so you should download it from here https://cran.r-project.org/bin/windows/Rtools/ and install manually. Hope this helps, Cheers, Eldar
  12. I'm just starting with handling the .lux files. I want to bring them into TwGeos in order generate the TAGS files for FlightR. I am following the directions from slisovski's GitHub for TwGeos. I'm running R version 3.5.2. I installed devtools package. When try to install TwGeos it fails. > devtools::install_github("SLisovski/TwGeos") Downloading GitHub repo SLisovski/TwGeos@master WARNING: Rtools is required to build R packages, but is not currently installed. Please download and install Rtools 3.5 from http://cran.r-project.org/bin/windows/Rtools/. checking for file 'C:\Users\a30014061\AppData\Local\Temp\RtmpqyjgQG\remotesa347e027eb5\slisovski-TwGeos-32fdd54/DESCRIPTION' ... checking for file 'C:\Users\a30014061\AppData\Local\Temp\RtmpqyjgQG\remotesa347e027eb5\slisovski-TwGeos-32fdd54/DESCRIPTION' ... √ checking for file 'C:\Users\a30014061\AppData\Local\Temp\RtmpqyjgQG\remotesa347e027eb5\slisovski-TwGeos-32fdd54/DESCRIPTION' checking DESCRIPTION meta-information ... checking DESCRIPTION meta-information ... √ checking DESCRIPTION meta-information - checking for LF line-endings in source and make files and shell scripts - checking for empty or unneeded directories - building 'TwGeos_0.0-1.tar.gz' Installing package into ‘C:/Users/a30014061/Documents/R/win-library/3.5’ (as ‘lib’ is unspecified) * installing *source* package 'TwGeos' ... ** R ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : there is no package called 'SGAT' ERROR: lazy loading failed for package 'TwGeos' * removing 'C:/Users/a30014061/Documents/R/win-library/3.5/TwGeos' In R CMD INSTALL Error in i.p(...) : (converted from warning) installation of package ‘C:/Users/A30014~1/AppData/Local/Temp/RtmpqyjgQG/filea3441a7f6f/TwGeos_0.0-1.tar.gz’ had non-zero exit status In addition: Warning messages: 1: In untar2(tarfile, files, list, exdir) : skipping pax global extended headers 2: In untar2(tarfile, files, list, exdir) : skipping pax global extended headers I tried installing Rtools, but that is not available. > install.packages("Rtools"); Installing package into ‘C:/Users/a30014061/Documents/R/win-library/3.5’ (as ‘lib’ is unspecified) Warning message: package ‘Rtools’ is not available (for R version 3.5.2) Any help and suggestions would be appreciated! Thanks, Dan
  13. Hi Leah, I also have been experiencing the same error when I use the mergeSites function. I have tried with multiple different geolocator tags and keep getting the same error. Were you able to get past this error? If anyone is able to provide any suggestions on how to overcome this error that would be greatly appreciated. Thanks, Kristen
  14. Hi Don-Jean, Looks like a bug... Could you please send me the RData and the script? I will have a look. Eldar
  15. Dear Eldar, Thank you for your answer. Sadly, it didn't solve the problem. However, I tried to change the coordinates in start=c(lon, lat) in the make.prerun.object function. Using the real longitude works fine (long=-79.88566) but I get the same error message when I try the real latitude (lat=72.89986). Any values below 65.6 of latitude works, though. Could there be a constraint in the maximum latitude we can use with this function? I then tried to extend the grid to up to lat=90, but the prerun function still didn't work with latitudes above 65. Grid<-make.grid(left=-83, bottom=3, right=8, top=90, distance.from.land.allowed.to.use=c(-Inf, Inf), distance.from.land.allowed.to.stay=c(-500, 0), plot=TRUE, probability.of.staying=0.5) P.S. Thanks for the tip about the rooftop calibration! Don-Jean
  16. Hello, I encountered the same error in one of my geolocator files. What worked for me was to subset the raw data to make sure the dates don't span more than 1 year. My original data file spanned from 6/15/16 to 8/5/17, and I think having >1 year of raw data is what causes that error to pop up. I subsetted my raw data so it only went from 6/15/16 to 6/14/17 and then the preprocessLight function worked. In my case I only needed the 1 year, so I didn't lose data that I wanted. I suppose if you wanted to cover the whole span that you have and it's more than 1 year, you might have to do it in two chunks (separate your raw data into two dataframes). I realize this reply is a year after your original post, but I hope this helps in case this has still been a problem. Or at least it can help other folks looking this error up as I did at first just recently. Best, Evelien
  17. Hi Don-Jean, I would suggest you reread the original file starting from the deployment date and plug the already created calibration into it. Hope this helps! Eldar PS Note that in many cases you get too clean results in case of rooftop calibration, so you might want to find the wintering site and recalibrate there to get reasonable uncertainty estimates.
  18. 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 48.57245 > Calibration<-make.calibration(Proc.data, Calibration.periods) checking dusk 10 calibration method used: parametric.slope likelihood correction switched to TRUE estimating correction function... Further on, the make.prerun.object function works fine if I keep the same geographic coordinates in start=c(lat, lon) than the coordinates I used for the calibration. But the calibration site is then considered to be the location where the birds were released (i.e. the start of the migration). And when I change the coordinates in start=c(lat, lon) for the real location of the study site I get this error: > #Pre-run# > all.in<-make.prerun.object(Proc.data, Grid, start=c(-79.88566, 72.89986), Calibration=Calibration) Error in `$<-.data.frame`(`*tmp*`, "Dusk", value = c(FALSE, TRUE, FALSE, : replacement has 772 rows, data has 735 Is there a solution that would allow me to use the real coordinates of my study site as the start location? or at least to avoid using the coordinates of the calibration site? Advice would be much appreciated! Don-Jean
  19. Hi Eldar, thanks a lot for your comments. I will keep the on bird calibration in mind for future analysis! It improved things a lot with this data set! Again, many thanks and have a nice Sunday! Hendrik
  20. Hi Hendrik, Yes, we had this issue already with some other roof top calibrations. I must admit that on bird works better. The calibration consists of the two main parameters - slope (mean+- sd) of measured irradiance vs expected irradiance. Mean should be the same, but the sd differs between the roof top and the on bird. Hope this helps, Eldar
  21. Hi Eldar, I am currently helping a friend to analyse data from mottled petrels breeding on Codfish Island, South of New Zealand. She used migrate technology tags, the same model (C-250) as I used on skua. Her light data looks very clean and she has a few days of 'rooftop' callibration from the study site. When running the model, it always comes out with a track that makes sense given what is known from previous tracking of the species. However, there are no confidence areas displayed on the lat lon graph (looking at the data, Min.lat, Max.lat and Medianlat/Lon values are all the same for each location). Switching "known last" to False makes them appear in the very end of the track, but they are still missing for the rest. We have tried different individuals, but the problem persists. I also tried using a calibration from my skua data (Chatham Islands), but the same problem occurs. Have you had a similar problem before, and do you think it could be due to issues with the callibration? I would be very thankful for any suggestions. Thanks a lot in advance! All the best, Hendrik UPDATE: I have tried doing the calibration from onbird data as estimated by the 'plot_slopes_by_location' function. This now results in confidence intervals on the tracks throughout. Could it be that the onbird data is simply better suited in this case? Many thanks in advance! Hendrik
  22. Hi Eldar, That's great, thank you so much. I do have on bird calibration data. I will send you some example files in a direct message. Allison
  23. Hi Allison, I can add a tag to FLightR to make it processing yur tags automatically. DO you have on bird calibration data from several tags? If so, sould you sent me those together with the calibration coordinates? I will try to have a look. Cheers, Eldar
  24. 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


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