[AniMov] first passage time: format of coordinates

Sergio Vignali vignalisergio30 at gmail.com
Fri Feb 1 19:35:10 CET 2013


I think the problem is in the line 4 of your code. You wrote:
xy <- Xloc[,c("lat","long")]
but you have to select only the coordinates, not all the object Xloc.

What's the reference system of your coordinates? What's your area of study?
You have to use metric system if you want metric distance in the ltraj
object.
See also AdehabitatLT package and the relative documentation

https://www.google.it/url?sa=t&rct=j&q=&esrc=s&source=web&cd=2&ved=0CD4QFjAB&url=http%3A%2F%2Fcran.r-project.org%2Fweb%2Fpackages%2FadehabitatLT%2Fvignettes%2FadehabitatLT.pdf&ei=wAgMUcClKKiR4ATDxYCIBg&usg=AFQjCNEQPXZ8fO_qNTPyyR7BDnViFGbmWg&sig2=vv3VeQ-lr4Hhkiavq3Uujw&bvm=bv.41867550,d.bGE

When I opened your link I didn't see anything, it's empty, there's not your
tr1.txt file.

2013/2/1 Santiago Guallar <sguallar a yahoo.com>

> Hi Sergio,
>
> No, I don't use qgis just R.
>
> It's too bad that you can't open the link. Let me show you the head of
> object Xloc, see if you can figure out if the the format of the coordinates
> xy:
>
>        fix       date    hm     secs  trn1  trn2   lat complat  long   dist
> 1     noon 07/06/2007 13:15 39240.55 06:18 20:12 20.25   20.25 19.05
> 0.00
> 2 midnight 08/06/2007 00:59 39241.04 05:46 20:12 27.27   24.31 15.03   0.00
> 3     noon 08/06/2007 13:03 39241.54 05:46 20:20 28.81   28.02 16.00 228.65
> 4 midnight 09/06/2007 01:03 39242.04 05:46 20:20 28.76   28.76 15.98  44.41
> 5     noon 09/06/2007 12:59 39242.54 05:46 20:12 27.12   27.92 14.96  73.77
> 6 midnight 10/06/2007 00:59 39243.04 05:46 20:12 27.07   27.07 14.93  51.02
>    head veloc conf   jul                Date     ind
> 1  0.00  0.00    9 13671 2007-06-07 13:15:00 2298001
> 2  0.00  0.00    9 13672 2007-06-08 00:59:00 2298001
> 3 13.21 18.95    9 13672 2007-06-08 13:03:00 2298001
> 4 -1.36  3.70    9 13673 2007-06-09 01:03:00 2298001
> 5 46.90  6.18    9 13673 2007-06-09 12:59:00 2298001
> 6  1.79  4.25    9 13674 2007-06-10 00:59:00 2298001
> tr1 seems to be fine:
>
> *********** List of class ltraj ***********
> Type of the traject: Type II (time recorded)
> Irregular traject. Variable time lag between two locs
> Characteristics of the bursts:
>        id   burst nb.reloc NAs          date.begin            date.end
> 1 2298001 2298001      587   0 2007-06-07 15:15:00 2008-04-30 03:10:00
> But object F is full of NAs:
> List of 1
>  $ :'data.frame':       587 obs. of  30 variables:
>   ..$ r1 : num [1:587] NA NA NA NA NA NA NA NA NA NA ...
>   ..$ r2 : num [1:587] NA NA NA NA NA NA NA NA NA NA ...
>   ..$ r3 : num [1:587] NA NA NA NA NA NA NA NA NA NA ...
>   ..$ r4 : num [1:587] NA NA NA NA NA NA NA NA NA NA ...
>   ..$ r5 : num [1:587] NA NA NA NA NA NA NA NA NA NA ...
>   ..$ r6 : num [1:587] NA NA NA NA NA NA NA NA NA NA ...
>   ..$ r7 : num [1:587] NA NA NA NA NA NA NA NA NA NA ...
> .
> .
> .
> .
> Do you think coordinates format is the problem here?
>
> Thank you,
>
> Santi
>
>
>    *From:* Sergio Vignali <vignalisergio30 a gmail.com>
> *To:* Santiago Guallar <sguallar a yahoo.com>; Animal Movement <
> animov a faunalia.it>
> *Sent:* Thursday, January 31, 2013 7:41 PM
> *Subject:* Re: [AniMov] first passage time: format of coordinates
>
> Hi,
> do you usually use QGIS?
> You can convert your coordinates with qgis of course!
> PS I can't open your link.
>
> Regards
> 2013/1/31 Santiago Guallar <sguallar a yahoo.com>
>
>
>  Hello,
>
>  I am trying to create a ltraj object to obtain first passage times (with
> the aim to reveal stopover sites of migratory seabirds) using package
> adehabitat, My code is:
>
>  require(adehabitat)
> Xloc$Date <- paste( Xloc$date, Xloc$hm)
> Xloc$Date <- as.POSIXct( Xloc$Date, format = "%d/%m/%Y %H:%M", tz = "GMT"
> )
> xy <- Xloc[,c("lat","long")]
> id= Xloc$ind
> tr1 <- as.ltraj( xy, Xloc$Date, id )
> F <- fpt(tr1, seq(300,1000, length=30))
> plot(F, scale = 500, warn = FALSE)
>
> However, I only obtain NAs. I think the problem lies in the format of the
> coordinates. I'm using a decimal format but function fpt() apparently works
> with UTM coordinates. How can I convert them into this format?
> Here is a link to a dput() to file tr1.txt:
>  http://file-manager.000webhost.com/file-manager/index.php
>
> Thank you for your help!
>
> Santi
>
>
>
>
> _______________________________________________
> AniMov mailing list
> AniMov a faunalia.it
> http://lists.faunalia.it/cgi-bin/mailman/listinfo/animov
>
>
>
>
> --
> Sergio Vignali
> CERM Centro Rapaci Minacciati
> (Endangered Raptors Centre)
>
>
>
>
>


-- 
Sergio Vignali
CERM Centro Rapaci Minacciati
(Endangered Raptors Centre)
-------------- parte successiva --------------
Un allegato HTML ? stato rimosso...
URL: <http://lists.faunalia.it/pipermail/animov/attachments/20130201/9719b57f/attachment.html>


More information about the AniMov mailing list