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Found 11 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 Departure.Q.50 25.595678 2.4360796 -12.919237 1.0270114 453.1756 2019-09-28 07:40:58 2019-10-11 20:53:39 19.598708 2.1146732 -3.262447 0.6437934 1310.7202 2019-10-12 00:57:31 2020-03-16 08:01:10
  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 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
  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 48.57245 > 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 `$<-.data.frame`(`*tmp*`, "Dusk", value = c(FALSE, TRUE, FALSE, : replacement has 772 rows, data has 735 Is there a solution that would allow me to use the real coordinates of my study site as the start location? or at least to avoid using the coordinates of the calibration site? Advice would be much appreciated! Don-Jean
  4. Hello, I am using Lotek Lat2800 geolocators to track the year-round movements of thick-billed murres. This tag type is not recognized in FLightR. How can I determine the 'log.light.borders' and 'log.irrad.borders' for my tags? So far I have tried inserting different values until I am able to successfully create a calibration object, which works, but is probably not the best solution. Thank you, Allison Patterson
  5. Hi I'm using FLightR to analyse data from Migrate Technology devices, but the function 'make.prerun.object' is returning the following error on two of them (the number of rows is different for each device): Error in `$<-.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 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
  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 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
  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 two examples connect. Can someone shed some light on this?
  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 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
  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 appreciated. Louise
  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.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
  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) # 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
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