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L Halpin

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  1. L Halpin

    FLightR-only one calibration period

    Try format: Calibration.periods <- data.frame(calibration.start = as.POSIXct("2014-05-05"), calibration.stop = as.POSIXct("2013-08-23"), lon = CapLocs[1], lat = CapLocs[2]) Stop date should not be before start date though.
  2. To the best of my knowledge, you can't open .trn files or other previously defined twilights, in the the various functions that define twilights. I have always had to go back in and redefine them. However, someone else may have a better response. This twilight-free method may be of interest, but I haven't tested it on any of my data yet: http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12953/abstract
  3. Hi Petra, You should be able to import .lig files using the readLig command in the package TwGeos For processing this might help: https://www.rdocumentation.org/packages/FLightR/versions/0.4.5/topics/BAStag2TAGS
  4. L Halpin

    GeoLight to FlightR workflow

    Hi there, The routine you used (i.e. in the Appendix A5) is the one that Eldar and others used in their paper to compare Geolight threshold method to FLightR template fit method of estimating positions from geolocator data and accuracy comparison to GPS tracks. If your processed twilights are in TAGS format (you can use GeoLight to do this). You can follow the FLightR algorithm in Appendix 6 from the same paper: https://github.com/eldarrak/FLightR/blob/master/examples/Black-Tailed_Godwit_JAB_example/A6_FLightR_analysis.Rmd There's also this useful workflow that details routines for several methods of light-level analysis: https://github.com/MTHallworth/LLGeo/blob/master/Light-level_geolocation_using_open_source_tools.Rmd Cheers, Luke
  5. L Halpin

    FlightR calibration error

    Try removing "NA" as follows Calibration.periods calibration.stop = as.POSIXct(c("2016-05-29"), tz="GMT"), lon=-148.80441, lat=63.6520) But your dates look wrong. Are you sure you want to add a year's worth of calibration data?
  6. 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
  7. L Halpin

    FlightR and dateline

    Hi Eldar, I think Yuhash was referring to the c(-100, 100) in the work around for the date line crossing issue that you referred to earlier in this post: A make.grid(170, -90, -170, 90, , c(-100, 100)) My understanding is that this part is not related to behavioural masks. Could you explain what the parameter “c(-100, 100)” does in order to assist with crossing the dateline issues? Thanks!
  8. Thanks for the clarification. I haven't used GLS with songbirds, nor have I used Biotrack GLS. I have used Migrate Technology tags with small seabirds and had great success using back-mounted GLS with a small light pipe/stalk. If feathers shade the light sensor you will have interference with your light data which could impact your ability to determine position estimates when you retrieve the GLS. From what I understand many folks who deploy back-mounted GLS onto songbirds tend to use devices with a light stalk. There is quite a lot of published literature on geolocators and swallows. https://scholar.google.ca/scholar?hl=en&q=swallow+AND+geolocator&btnG=&as_sdt=1%2C5&as_sdtp=
  9. Can you provide more information about the manufacturer of the tag, what your research goals are and what species you intend to put GLS tags on?
  10. L Halpin

    dealing with calibration periods

    Thanks, Jeremy. Of course, this was user error on my part. Luke
  11. L Halpin

    dealing with calibration periods

    Hi Eldar, Thanks for your response. I reran the make.calibration function as suggested. I still get the first part of the error about dawn/dusk exclusion from calibration: dusk 11 was excluded from the calibration Error in `$ replacement has 1 row, data has 0 The error is similar to the error reported in this post: http://ornithologyexchange.org/forums/topic/28569-trouble-with-calibration/ However, changing model.ageing command does not help. Luke
  12. L Halpin

    dealing with calibration periods

    Hi Hendrik, Eldar, Thank you very much for your responses. I am going to try your suggestion. I only have 6 twilight events on each calibrator tag, but I'll give it a go - hopefully it is enough calibration data. I have previously analyzed this data in GeoLight and position of birds are as expected. Unfortunately now I am experiencing errors with the make.calibration function. It may be something that I have done incorrectly, but I can't tell. First I defined twilights using GeoLight and then transform the twilights using GeoLight2TAGS function. After that my code looks like this. The error I experience is at the end. > X894.data Detected Intigeo_Mode_4 tag tag saved data every 300 seconds, and is assumed to measure data every 60 seconds, and write down max > CapLocs=c(127.9704, 50.4475) > Calibration.periods + calibration.stop = as.POSIXct(c("2016-06-28", NA)), + lon = CapLocs[1], + lat = CapLocs[2]) > Calibration.periods calibration.start calibration.stop lon lat 1 2016-06-28 127.9704 50.44757 2 2016-06-05 127.9704 50.44757 > Calibration + plot.each = FALSE, plot.final = TRUE, likelihood.correction = "auto", + suggest.irrad.borders = FALSE) dusk 21 was excluded from the calibration Error in `$ replacement has 1 row, data has 0 In addition: 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' Thanks, Luke
  13. 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
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