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Cosme

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    University of Seville
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    Spain
  1. Hi Eldar, thank you very much. I have been correcting these points by hand, it is possible but very time-consuming if I want to pool together in the same map many different tracks. Best wishes, Cosme
  2. Dear all, I am trying to geographically illustrate the 95% Credible Intervals of the estimated positions along the track. My goal is to obtain a polygon defined as the "concave minimum polygon" of positions UCI and LCI, which indicate the upper and lower limits of the 95% credible intervals (or confidence intervals). The depiction of this error is nicely illustrated by the lat/long plots, but I wanted to show them geographically explicit within a map. My problem is: the line defined by UCI crosses the line defined by LCI during first October. Interestingly, lines cross each other close to the Greenwhich Meridian. So I wonder if the CI limits are inverted when the bird travel through the Greenwhich Meridian, because the longitude changes from positive to negative, or vice-versa. I also wonder if the equinox may be involved in this. In summary, UCI and LCI positions build up a polygon with the shape of a sandglass. How are the UCI and LCI positions calculated in FLightR? Best whises, Cosme sandglass
  3. Hello, thank you for our answer Simeon. Since I posted this issue two monts ago I could finally sort this out and realized that. Thank you anyway for your kindness. Cosme.
  4. Hello, thank you for your answer Simeon. You were right! if I use a bigger window, the error dissapear and the result is fine. However now I see that I do not understand what the parameter "windows" means ("the number of neighboring twilights"). Depending of this number the function deletes or not specific twilights. Kind regards, Cosme
  5. Dear all, after spending so many time hand-editing the twilights with preprocessLight from package BAStag, I have just realized that the new inserted twilights had never been saved. I know how the interactive windows work, I have done it many times; but I DO NOT KNOW why in the output, the columns "Twilight" and "Twilight3" are the same. In other words, the new inserted twlights are not saved. Here it is an example: Twilight Rise Deleted Marker Inserted Twilight3 Marker3 387 25/06/2016 20:11 FALSE FALSE 9 TRUE 25/06/2016 20:11 9 388 26/06/2016 4:45 TRUE FALSE 5 TRUE 26/06/2016 4:45 5 389 29/06/2016 20:11 FALSE FALSE 9 TRUE 29/06/2016 20:11 9 390 30/06/2016 4:48 TRUE FALSE 5 TRUE 30/06/2016 4:48 5 391 30/06/2016 20:11 FALSE FALSE 5 TRUE 30/06/2016 20:11 5 392 01/07/2016 4:45 TRUE FALSE 5 TRUE 01/07/2016 4:45 5 See that "Twilight3" is the same than "Twilight" for twilights that have been edited (inserted=TRUE). Is it necessary to do some editions at stage four of preprocessLight? Kind regards, Cosme
  6. Hello everyone! I am trying to use the function twilightEdit from TwGeos, which is supposed to edit and delete twilight outliers automatically. I do not know why I get this error: "Error in x[(window/2) + 1, 2] : subindex out of limits" My code is: readLig <- function(file,skip=0) { ## Read csv file and add column names d <- read.csv(file,header=FALSE,skip=skip, col.names=c("Valid","Date","Julian","Light"), colClasses=c("character","character","numeric","integer")) ## Parse date d$Date <- as.POSIXct(strptime(d$Date,"%d/%m/%y %H:%M:%S",tz="GMT")) d } lig.raw<-readLig("V4221 023_cal.lig") head(lig.raw, n=10) ###Search for twilight times twilights<-findTwilights(lig.raw, threshold=16, include = c(c("2016-06-21","2017-03-15"), c("2017-07-20", "2017-07-27")), exclude = NULL, extend = 0, dark.min = 300) head(twilights, n=10) ###Automated (Objective) editing and deletion of twilight times (experimental) twilightEdit(twilights, offset = 17, window = 4, outlier.mins = 45, stationary.mins = 15, zlim = c(0, 64), plot = T) In addition, I do not know how to use the result object from twilightEdit and work with FlightR. Does anyone know something about it? Thank you very much in advance, Cosme
  7. 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
  8. 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
  9. 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
  10. Thank you stormpetrel, I know that it is recommended to use a light stalk when attaching as leg-loop. However, there are already studies that have tried a leg-loop position without any light stalk: https://www.researchgate.net/profile/Malcolm_Burgess2/publication/288038790_An_experimental_evaluation_of_the_effects_of_geolocator_design_and_attachment_method_on_between-year_survival_on_Whinchats_Saxicola_rubetra/links/56f12ad608ae6cccf439dad7.pdf I put on the last year 64 tags with a small light stalk and I obtained nice results. However, I noticed a significant reduced survival rate of tagged compared to control birds. This year I wanted to test if I could increase the survival rate by eliminating the light stalk. This is because the body of the barn swallow is very aerodinamic. I also made a trial at my office: I put a rectrix on the light sensor and I analyzed the data. The tag recorded light values normally, as the light sensor was saturated even under the feather. However I wonder if this could be extrapolated to a real migrating bird. Thank you again
  11. Yes, sorry! the model of my tag is ML650 (Biotrack). My study species is the barn swallow, and my purpose is to determine the migratory routes and winter areas, as well as testing the effects of the tag on survival and posterior reproduction. Thank you
  12. Hello everyone! I wonder if the quality of light data obtained by a geolocator tagged like in this picture, is good enough: http://blog.une.edu/perlutlab/files/2013/03/Martin-with-geolocator-reduced.jpg It is a tag without stalk, attached as leg-loop position. Thank you very much in advance! Cosme
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