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shading events during last records


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#1 Cosme

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Posted 13 July 2017 - 11:19 AM

Hello everyone,

 

I have attached BAS geolocators (Biotrack - ML6540) on barn swallows breeding in Spain. In every light record (from July to March), I see many shading events at the end of the data (about 7-10 days). I am using the package BAStag, but I see too many shading events at this period to hand-edit these twilights. So I think the best option is to drop off this last records.

 

I think the biological meaning of these extensive shading events is the beguining of the nesting period at the breeding sites, i.e. birds spend nights at their nests.

 

However, I have some tracks in which the extensive shading events still occurr during migration (i.e. in the middle of the Sahara desert), a few days before arriving back to Spain. Thus I wonder if these shading events indicate indeed the beguining of nesting, and maybe because the tag surface become less transparent, the last estimated positions are predicted in the middle of the desert rather than in the breeding area. 

 

So I do not know what is more correct: to set "known.last=" as either TRUE or FALSE. If I set TRUE, the last location appears in Morocco (closer to Spain), but the migratory track and winter areas seem more erratic. Furthermore the "plot_lon_lat", cannot estimate confidence intervals for the last days of records.

 

I know that one option can be to do a second calibration period back in the breeding areas. However I tried this already and because of the extensive shading events in this period, the final result is completely noisy and erratic. Maybe the best would be to do a roof top post-calibration period in a know location, but I think many of my tags do not have more battery. Does anyone have a better idea? I can provide screenshots of the results if someone wants to help.

 

Thank you very much in advance,

Cosme



#2 Eldar

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Posted 17 July 2017 - 01:49 AM

  Hi Cosme,

 1. 

 

 

However, I have some tracks in which the extensive shading events still occurr during migration (i.e. in the middle of the Sahara desert), a few days before arriving back to Spain. Thus I wonder if these shading events indicate indeed the beguining of nesting, and maybe because the tag surface become less transparent, the last estimated positions are predicted in the middle of the desert rather than in the breeding area. 

How do you know that the bird was still on migration? I would say that it is likely that bird had already arrived somewhere (maybe to check other breeding grounds before breeding). If surface is becoming less transparent you will see more or less even darkness, but not several short periods.

2. 

 

 

So I do not know what is more correct: to set "known.last=" as either TRUE or FALSE. If I set TRUE, the last location appears in Morocco (closer to Spain), but the migratory track and winter areas seem more erratic. Furthermore the "plot_lon_lat", cannot estimate confidence intervals for the last days of records.

You should set known.last to TRUE only if you have the very last twilight at the breeding grounds. And you are right if confidence intervals disappear in the end known.last should be FALSE.

3. FLightR also has the find.stationary.location function, so you can try it on your tracks (but it was not tested on the mk tags as far as I know). It also works sometimes if you use calibration from a good track for other devices.

  Hope it helps



#3 Cosme

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Posted 17 July 2017 - 02:57 AM

Thank you very much for your help Eldar,

 

1. How do you know that the bird was still on migration? I would say that it is likely that bird had already arrived somewhere (maybe to check other breeding grounds before breeding). If surface is becoming less transparent you will see more or less even darkness, but not several short periods.

 

I said that the bird was still on migration because the last predicted locations of good light records are predicted in the middle of the Sahara desert (i.e. Mauritania), which is not a known breeding range for the barn swallow. It is possible that the bird had used some cavity to spend the nights at these last estimated locations. The option you say, that the bird checked other breeding sites, is not probable in this area because it is not a known breeding area. Maybe the last true positions could be in Morocco (the closest breeding area), but because the tag surface is less transparent these last positions are estimated more to the south (in Mauritania instead of Morocco)? I knew that the loss of transparency could not provoque the extensive shading events, but rather that this loss of transparency could provoque the last positions (just before the shading events) to appear southern to the true location.

 

 

2. You should set known.last to TRUE only if you have the very last twilight at the breeding grounds. And you are right if confidence intervals disappear in the end known.last should be FALSE.

 

Yes, I agree this is the most conservative. Good to know about these last confidence intervals. I supposed something was wrong.

 

3. I will check the find.stationary.location function.

 

 

Thank you very much!

Cosme



#4 Eldar

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Posted 18 July 2017 - 02:35 AM

 

 

I said that the bird was still on migration because the last predicted locations of good light records are predicted in the middle of the Sahara desert (i.e. Mauritania), which is not a known breeding range for the barn swallow. It is possible that the bird had used some cavity to spend the nights at these last estimated locations. The option you say, that the bird checked other breeding sites, is not probable in this area because it is not a known breeding area. Maybe the last true positions could be in Morocco (the closest breeding area), but because the tag surface is less transparent these last positions are estimated more to the south (in Mauritania instead of Morocco)? I knew that the loss of transparency could not provoque the extensive shading events, but rather that this loss of transparency could provoque the last positions (just before the shading events) to appear southern to the true location.

  Sure, that what I was talking about - it could be that positions are just estimated wrongly. It happens especially close to equinoxes. This is why I would say that the bird likely already arrived to the breeding grounds but the estimates you get are in Sahara. And you are right this happens when surface gets opaque. If you will get some results with find stationary location function for wintering period, you can do calibration with model.ageing=TRUE. That might help.

   Eldar



#5 Cosme

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Posted 18 July 2017 - 04:42 AM

Ok!

 

in fact, the extensive shading events are near the equinox of March (2 weeks before). So we agree that it is more probable that the shading events indicate the arrival to breeding area and the last estimated positions are wrong. In the lat_lon plot I can see a nice period during winter in which the bird was stationary (the month of october). Thus I run the find.stationary.location function for this period, including as initial coordinates these from the lat_lon plot from a given simulation.

 

I understand that this function find a location for a period in which the bird is assume to be stationary, but I do not understand the output from the function. What does it mean "stage 1..." and "stage 2..."?

First and second column from the output are longitude and latitude, but I do not know what are the rest. Should be the range of errors in slopes?

The average of coordinates from "stage 1", is very close to initial coordinates. By contrast the average of coordinates from "stage 2", is rather different and actually wrong (because this average point to the middle of the ocean).

I see that the higher the third column, the higher is the deviation from the initial coordinates. Is the third column a measure of error in the slope of the calibration? Should I take as the best estimated location, the one of lower value in the third column?

 

As well I get many warnings messages.

 

Thank you very much for your help Eldar!

Cosme






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