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Found 6 results

  1. 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
  2. Bonjour, I am working with geolocators data collected with Intigeo C65 devices on seabirds breeding in the Arctic (higher red dot on map1) and migrating in southern Atlantic in winter. Parts of the migration occurs during spring and fall equinoxes. I used a rooftop cablibration made in southern Quebec (lower red dot on map1) for about 14 days and I used the findHEZenith function to calculate a new zenith angle on the wintering area. Then I set a list of Zenith changing depending on the period of the year. All my script is running, but for some birds, I have a strange movement up-north after a first staging period. When I create the initial path (thresholdPath function), everything seems to be okay, but when I run the estelleMetropolis function in 3 steps (burn-in, tuning, final runs), no matter how many iterations I do and no matter how many chains I set, the up-north movement appears. On the path on map2, the blue part is ± 10 days around equinoxes, gray is ± 15 days and black ± 20 days. I tried changing all the parameters one by one, but the problem persists. Any idea what could cause this issue? Merci, Yannick
  3. Hello everyone, I have recently begun trying to process a .lig file using TwGeos( although I also have .lux files as well) and i have been having some general problems most likely due to my lack of experience with this software, so I apologize if i'm asking introductory level questions. The code that I have been using is: palette=c(5,2, 9, 3, 4, 1, 13) Twl<-preprocessLight(Bird, threshold = 1.5, offset = 17, lmax = 64, zlim = c(0,64), extend = 0, dark.min = 0, twilights = NULL, stage = 1, point.cex = 0.8, width = 12, height = 4, palette = palette ,gr.Device = "default") Stage 1: Is the point of the subset function to remove the twilights that occured before and after the geo was attached? Stage 2: I don't think I have been performing this stage right, I'm not exactly even sure what i'm supposed to be doing.. Stage 3: I believe that this step is dependent on the previous one, but regardless I'm not sure how to identify whether a twilight is missing or if one has to be added. Stage 4: My light profiles do not show sunrise and sunset in one screen, is there a mistake in my code that would fix this? I'm also not sure what a bad twilight looks like and which ones should be marked for deletion. I have gone through this process several times trying different methods and settings to familiarize myself with it but have been unsuccessful. After accepting the twilights that I believed were acceptable i saved my edits and exited out of the window, this provided me with a subset of data and 8 warning messages that are as follow: Warning messages: 1: In structure(xx, class = c("POSIXct", "POSIXt"), tzone = tz) : Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead. 2: In structure(xx, class = c("POSIXct", "POSIXt"), tzone = tz) : Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead. 3: In structure(xx, class = c("POSIXct", "POSIXt"), tzone = tz) : Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead. 4: In structure(xx, class = c("POSIXct", "POSIXt"), tzone = tz) : Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead. 5: In structure(xx, class = c("POSIXct", "POSIXt"), tzone = tz) : Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead. 6: In structure(xx, class = c("POSIXct", "POSIXt"), tzone = tz) : Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead. 7: In structure(xx, class = c("POSIXct", "POSIXt"), tzone = tz) : Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead. 8: In structure(xx, class = c("POSIXct", "POSIXt"), tzone = tz) : Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead. I'm not sure if these warnings are due to me performing one of the previous stages wrong or are normal errors associated with the package. Any help relating to these problems would be greatly appreciated. Thank you, Devin
  4. While using FLightR I am still having a few points fall over the Ocean. I thought that establishing the grid within FLightR and setting the “distance.from.land.to.use=c(-Inf, Inf)” would prevent any points from falling into the Ocean? This is only occurring for a few of the geolocators that I have analyzed although I am still baffled to why this is occurring on the select few. Any advice on why this is happening and/or how to correct this problem would be greatly appreciated. Cheers, Devin
  5. I'm using FLightR to process my geolocator data. After performing the run.particle. filter I am able to plot it successfully using map.FLightR.ggmap, my issue comes after that, I would like to be able to plot those points in ArcMap. Is there a way in which I can export the Lat/Long data and its associated dates from the run.particle.filter to either a .csv or a shapefile? I'm aware that a previous post mentioned it being easy using the ("add xy data") but i couldn't figure it out. Any advice would be greatly appreciated. Thank you, Devin
  6. I would like to estimate (with uncertainty) the cumulative distance traveled by an organism between two specific time periods. Let's say that I used the find.times.distribution function to identify that a tagged bird most likely commenced spring migration on 1 April 2016 and most likely reached its breeding grounds on 23 April 2016. I would like to sum the distance traveled by that bird between every consecutive twilight from 1 April to 23 April. The ideal final result would be something like, "The cumulative spring distance traveled between 1 April and 23 April was median=1034.2 km (95% credible interval: 650.2 to 1840.2 km). Getting the median cumulative distance is easy: migration.longitude.values migration.latitude.values library(sp) sum(spDists(cbind(migration.longitude.values, migration.latitude.values),segments=TRUE,longlat=TRUE)) But I cannot figure out a 'good' way to estimate the uncertainty component. One (non-parsimonious) solution would be: 1) generate 95% isopleths (with the plot_util_distr function) for every twilight [or perhaps just every day] between 1 April and 23 April, 2) generate 1000 random points (assuming a uniform distribution) within the confines of each 95% isopleth, 3) create 1000 paths/polylines that run between all 23 isopleths (using a single point in each isopleth), 4) and finally measure the length of those 1000 paths and create summary statistics (median, mean, 0.25 and 0.975 percentile values). I had been trying to modify the get_ZI_distances function in FlightR to avoid my non-parsimonious solution, but I have so far failed miserably. Hopefully a better programmer than myself can provide some help. Thank you and cheers, Jason Hill
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