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

  1. What's new in this group
  2. Hi Jenny, 1. You could try increasing the distance they are allowed to fly. The maximum distance can be fixed in particle.filter and the mean and sd in make.prerun.object. 2. Try running first without any spatial constrains. It sometimes happen that particle filter just cannot find a proper solution if bir migrated to far every day for a long period. Hope this helps, Eldar
  3. Hi, all I'm using FLightR 0.4.9 to track migration of shorebirds. Tags were deployed in Alaska and recovered at the same site a year later. FLightR gives me nice-looking tracks for the breeding season in Alaska, fall migration to Chile, and the non-breeding season in Chile. But the track for spring migration is consistently problematic -- instead of returning north to Alaska, it heads south toward Antarctica. Has anyone experienced something similar? Any ideas for what I can do? Calibration periods are from the study site (lon = -150.725, lat = 61.272): one from the beginning of the study (shortly after tag deployment) and another from the end (shortly before tag recovery). Both verified by plot_slopes_by_location. > Calibration.periods <- data.frame(calibration.start=as.POSIXct(c("2009-05-17", "2010-05-10")), calibration.stop=as.POSIXct(c("2009-06-15", NA)),lon=-150.725, lat=61.272) > print(Calibration.periods) calibration.start calibration.stop lon lat 1 2009-05-17 2009-06-15 -150.725 61.272 2 2010-05-10 <NA> -150.725 61.272 Calibrating from pre-deployment data instead yields similar results. For the particle filter run I've tried known.last=TRUE and known.last=FALSE. Changing behavioral masks, outlier check, nParticles, etc. also do not seem to help. > all.in <- make.prerun.object(Proc.data, Grid, start=c(-150.725, 61.272), Calibration=Calibration) > nParticles=1e6 > Result <- run.particle.filter(all.in, threads=-1, nParticles=nParticles, known.last=TRUE, check.outliers=TRUE) Since I'm using the correct lon/lat at the end of the track to calibrate, why might the output show my end coordinates so far away from there? Jenny
  4. Hi Diane, have you plotted your light data to make sure that the threshold is within the range of measured light. And have you got any NA's in your time column (check for sum(is.na(raw$Date))). Simeon
  5. Hi I'm working on my thesis playing with the GCSP tag data sets, trying to process them with GeoLocTools and FLightR. I am coming up on an error message when I selecting my twilight threshold. I have tried changing the threshold a variety of different times and still receive the same error message. > threshold <- 0.6 > twl <- preprocessLight(raw, + threshold = threshold, + offset = offset, + lmax = 20, # max. light value (adjust if contrast between night and day is weak) + gr.Device = "x11") Waiting for input Error in class(xx) <- cl : attempt to set an attribute on NULL Any thoughts or suggestion would be greatly appreciated. Thank you so much Diane Nelson
  6. That is correct, median deviation for thresholdPath, since it ignores the error structure and zero devotion for the Estelle model. Running calibration during the equinox ist actually a good thing, if you have enough time around the equinox. Given the structure of errors around the equinox, estimates of latitude are very sensitive to zenith angles (sun elevation angles). Hope that helps, Simeon
  7. Hi! I am running my data with SGAT, but I am not sure which zenith should I use in the thresholdPath and which in the Estelle model. I think I should use the median deviation zenith in the thresholdPath and the zero deviation in the Estelle? Also, which could it be the effect of running my calibration during the spring equinox? Thank you in advance!!! Melina
  8. 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
  9. 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?
  10. 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
  11. 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
  12. 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!
  13. The move is done now. Let me know if you have any questions about how this new Groups feature works.
  14. 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:
  15. 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.
  16. 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
  17. 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
  18. 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
  19. 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
  20. Hi Don-Jean, Looks like a bug... Could you please send me the RData and the script? I will have a look. Eldar
  21. 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
  22. 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
  23. 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.
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