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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

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

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