Dear all,
I have some bird movement data which I'm trying to analyse through the
package adehabitatLT.
It is collected by GPS with a location fix every 30 minutes. It has to be
manually downloaded in the field etc., as a result it contains many gaps (half
a day, a day, a couple of days...)
I know it is an irregular trajectory and perhaps I shouldn't be analysing it
through adehabitatLT.
Although it seems to work fine so far and I regularized the trajectory
through the steps outlined in the package, I now get the error : Error in
1:indiceNA[lalo[i]] : NA/NaN argument.
This is at the point where I'm trying to partition the trajectory. (code
provided below)
Regularized trajectory (Breg) in R (has a lot of NA values -> came from
irregular.
Breg:
head(Breg)
*********** List of class ltraj ***********
Type of the traject: Type II (time recorded)
* Time zone: UTC *
Regular traject. Time lag between two locs: 900 seconds
Characteristics of the bursts:
id burst nb.reloc NAs date.begin
date.end
1 2172 2172 4449 1683 2015-08-07 00:22:00 2015-09-22
08:22:00
infolocs provided. The following variables are available:
[1] "pkey"
> head(Breg[[1]])
x y date dx
dy dist dt R2n abs.angle rel.angle
1 409662.0 6448915 2015-08-07 00:22:00 NA NA NA 900 0.000000
NA NA
2 NA NA 2015-08-07 00:37:00 NA NA NA 900 NA
NA NA
3 409663.9 6448913 2015-08-07 00:52:00 NA NA NA 900 9.245614
NA NA
4 NA NA 2015-08-07 01:07:00 NA NA NA 900 NA
NA NA
5 409633.7 6448906 2015-08-07 01:22:00 NA NA NA 900 885.556316
NA NA
6 NA NA 2015-08-07 01:37:00 NA NA NA 900 NA
NA NA
List of 1
$ :'data.frame': 4449 obs. of 10 variables:
..$ x : num [1:4449] 409662 NA 409664 NA 409634 ...
..$ y : num [1:4449] 6448915 NA 6448913 NA 6448906 ...
..$ date : POSIXct[1:4449], format: "2015-08-07 00:22:00" "2015-08-07
00:37:00" "2015-08-07 00:52:00" "2015-08-07 01:07:00" ...
..$ dx : num [1:4449] NA NA NA NA NA NA NA NA NA NA ...
..$ dy : num [1:4449] NA NA NA NA NA NA NA NA NA NA ...
..$ dist : num [1:4449] NA NA NA NA NA NA NA NA NA NA ...
..$ dt : num [1:4449] 900 900 900 900 900 900 900 900 900 900 ...
..$ R2n : num [1:4449] 0 NA 9.25 NA 885.56 ...
..$ abs.angle: num [1:4449] NA NA NA NA NA NA NA NA NA NA ...
..$ rel.angle: num [1:4449] NA NA NA NA NA NA NA NA NA NA ...
..- attr(*, "id")= chr "2172"
..- attr(*, "burst")= chr "2172"
..- attr(*, "infolocs")='data.frame': 4449 obs. of 1 variable:
.. ..$ pkey: int [1:4449] 1 NA 2 NA 3 NA 4 NA NA NA ...
- attr(*, "class")= chr [1:2] "ltraj" "list"
- attr(*, "typeII")= logi TRUE
- attr(*, "regular")= logi TRUE
- attr(*, "proj4string")=Formal class 'CRS' [package "sp"] with 1 slot
.. ..@ projargs: chr NA
I'm following the Gueguen method for segmenting my trajectory, explained in
the adehabitatlt pdf: Analysis of Animal Movements in R.
I have created the models based on my
tested means, got the probability densities for each model and estimated the
number of segments:
(limod <- as.list(paste("dnorm(dist, mean =", tested.means,",sd = 5000)")))
mod <- modpartltraj(Breg, limod)
bestpartmod(mod)
Maximum likelihood for K = 4
But when i try to partition the trajectory into the 4 segments i get this error:
> pm <- partmod.ltraj(Breg, 4, mod)
Error in 1:indiceNA[lalo[i]] : NA/NaN argument
I'm not quite sure what it means, it looks like R is having problems finding
the exact place to cut off between segments because of my NA values? Not sure
how to get around it or if I'm in the wrong for even trying it at all.
Kind regards,
Sam Rycken
Sam Rycken MSc
PhD Candidate
School of Veterinary and Life Sciences
Murdoch University
South St, Murdoch 6150 WA
Mobile: 0497530868
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