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Found 8 results

  1. 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
  2. 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
  3. 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
  4. 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
  5. AmelieRobertoCharron

    Plotting FLightR Results

    Hello! I am currently using FLightR to analyze some geolocator data, and am trying to visualize the error around the migration route that is estimated by the package. I am attempting to plot the mean latitude and longitude from the results with both the 1st and 3rd quartiles and the 95% confidence interval (CI). Essentially, I am trying to merge the figures produced by the map.FLightR.ggmap() function and the plot_lon_lat() function. I have tried plotting the migration route with error bars, as well as plotting the quartiles and confidence intervals as lines in ggplot2. Unfortunately I have found the error bars to be very messy, making it difficult to discern where the mean coordinates are and where the quartiles and CI differ. Additionally, the plotting of the quartiles and CI values as lines is a confusing representation of the uncertainty in the location estimates as they often cross the mean coordinates when the bird switches direction. To attempt to create a range around the migration route that shows the error I also ran an if else function that switched the upper and lower latitude ranges when the bird changes direction to keep the CI or quartile line from crossing the route. Unfortunately, this solution seemed a bit too sensitive and caused more jogs in the upper and lower CI and quantiles than I started with! Would anyone have any recommendations on how to plot the 1st and 3rd quartiles and upper and lower confidence intervals on a migration route? Any recommendations would be appreciated! Thank you, Amélie
  6. I am analyzing data from a couple of light-level geologgers that were attached to Western Bluebirds; I have been going back and forth between analyzing the data with the FLightR and Geolight R packages. Now I'm having trouble picking the tag-specific parameters for the FLightR get.tags.data function. These tags are the sort that record light intensity as values between 0 and 127; they take a light-level reading every minute and average the readings over each 10-minute period. So, I used the log.light.borders and log.irrad.borders as for the Intigeo tags here: https://github.com/eldarrak/FLightR/wiki/setting-up-tag-specific-boundaries. My code: tag.612.FLightR.data <- get.tags.data("tag_612_twilights_TAGS_threshold_5.csv", log.light.borders = log(c(1, 127)), log.irrad.borders = c(-3, 3), saves = c("mean"), measurement.period = 60, impute.on.boundaries = FALSE) Is this correct? And can somebody explain the difference between the log.light.borders and log.irrad.borders parameters?
  7. 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
  8. 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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