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FlightR - calibration location assigned as start of migration

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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

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  Hi Don-Jean,

I would suggest you reread the  original file starting from the deployment date and plug the already created calibration into it.

 Hope this helps!

  Eldar

PS Note that in many cases you get too clean results in case of rooftop calibration, so you might want to find the wintering site and recalibrate there to get reasonable uncertainty estimates. 

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Dear Eldar,

Thank you for your answer. Sadly, it didn't solve the problem.

However, I tried to change the coordinates in start=c(lon, lat) in the make.prerun.object function. Using the real longitude works fine (long=-79.88566) but I get the same error message when I try the real latitude (lat=72.89986). Any values below 65.6 of latitude works, though. Could there be a constraint in the maximum latitude we can use with this function?

I then tried to extend the grid to up to lat=90, but the prerun function still didn't work with latitudes above 65.

Grid<-make.grid(left=-83, bottom=3, right=8, top=90,
                distance.from.land.allowed.to.use=c(-Inf, Inf),
                distance.from.land.allowed.to.stay=c(-500, 0),
                plot=TRUE,
                probability.of.staying=0.5)

P.S. Thanks for the tip about the rooftop calibration!

Don-Jean

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  Hi Don-Jean,

Looks like a bug...

Could you please send me the RData and the script? I will have a look.

     Eldar

 

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Thanks a lot! I'll send it to you in a private message.

Don-Jean

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This problem is solved in FLightR >=0.4.8 .

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