Hi, I am using FlightR on geolocator data from common sandpiper. I have pre-processed my .lux files using TwGeos package and manage to subsequently run the FlightR script without problems. I do have some questions about the results it produces and some bits of the script:
Do I understand correctly that a location is calculated by the slope of a twilight and that thus, in contrast to geolight, you obtain a location per sunrise and another location per sunset (rather than getting one location for each sunrise and sunset 'pair')? And that as such, excluding / deleting twilights does not mean the twilights (locations) before and after the deleted twilight are also lost?
In Eldar's (2015) paper (page 6 of 15) it states that for all their models, they assumed that the truncation points were a = 45 and b = 1000km. "That is, when birds initiated a movement, they could not fly less than 45km or more than 1500km in a single between-twilight interval."
- This seems to me that 'b' should have thus been 1500. What is actually being used in the script 1000 or 1500km?
- I take it that this means that a bird is classified as being in a movement state if it moves >= 45km from one estimated location to the next, but are geolocator data derived locations not more imprecise than that (so that the bird could be classified as in a movement state whereas the "movement" is actually due to inaccurately calculated positions)? Should this threshold therefore not be higher, e.g. >= 300km (see e.g. paper Fudickar et al 2011, but even Eldar's 2016 paper showed a 43.3 +/- 51.5km deviation from the true position)
A question about identifying staging areas using this bit of script
stationary.migration.summary(Result, prob.cutoff = 0.1, min.stay = 3)
min.stay is presumably the number of twilights, but what happens if twilights have been excluded from what could potentially be a staging area? So for example you say min.stay= 3 (which normally could mean a sunrise, sunset and another sunrise (e.g. approximately 24 hours minimum stay) but the sunset was excluded - does it then become sunrise, sunrise, sunset (i.e. approximately 36 hours minimum stay)?
Then a couple of questions about the outputs of the script:
- In the plot of the locations (map.FLightR.ggmap(Result)), it doesn't look like all locations are plotted (I have 521 coordinates in the coords.csv file, but the map seems to only show around 70 points). What locations are plotted?
- Which coordinates from the coords.csv file are plotted (Medianlat/Medianlons or Meanlat/Meanlons)?
- In the coords.csv file what is the difference between Medianlat and MedianlatJ (and the same for long)?
- In the plots of lat and long, what do the dark grey and pale grey limits show (are these first and third percentiles respectively?)
Sorry, a lot of questions (I saved them all up!!), I hope you can help me with.