[R] Error with adehabitatHR and kernelbb
Dear all,
I'm trying to get a Brownian bridge kernel (kernelbb) for each combination of
two consecutive animal locations (see commands below) and put them, with a
loop, inside a list. It works well at the beginning but after 42 runs, it
appears the following warning :
Error in seq.default(yli[1], yli[2], by = diff(xg[1:2])) :
invalid (to - from)/by in seq(.)
I looked at the coordinates, at the id, at the time of the run 43 and it's all
good...
I looked on the net and it happened to only one person and there was no answer
to his post.
Someone could help me?
## commands
BBtraj - list()
for (i in 1:(nrow(loc@data)-1)) {
BBtraj[[i]] - kernelbb(as.ltraj(loc@coords[i:(i+1),],
date=loc@data$time[i:(i+1)], id = as.character(loc@data$id[i:(i+1)]),
typeII = TRUE), sig1=as.numeric(as.character(loc@data$sig1[i])), sig2= 5, grid
= 1000)
}
Rémi Lesmerises, biol. M.Sc.,
Candidat Ph.D. en Biologie
Université du Québec à Rimouski
remilesmeri...@yahoo.ca
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Re: [R] Error with adehabitatHR and kernelbb
On May 17, 2013, at 7:44 AM, Rémi Lesmerises wrote:
Dear all,
I'm trying to get a Brownian bridge kernel (kernelbb) for each combination of
two consecutive animal locations (see commands below) and put them, with a
loop, inside a list. It works well at the beginning but after 42 runs, it
appears the following warning :
Error in seq.default(yli[1], yli[2], by = diff(xg[1:2])) :
invalid (to - from)/by in seq(.)
I looked at the coordinates, at the id, at the time of the run 43 and it's
all good...
I looked on the net and it happened to only one person and there was no
answer to his post.
I wonder if that posting (like yours) had no data on which to display the
problem or to test potential solutions? I would think you would want to post
any setup objects and then data for items 40-45.
Someone could help me?
## commands
BBtraj - list()
for (i in 1:(nrow(loc@data)-1)) {
BBtraj[[i]] - kernelbb(as.ltraj(loc@coords[i:(i+1),],
date=loc@data$time[i:(i+1)], id = as.character(loc@data$id[i:(i+1)]),
typeII = TRUE), sig1=as.numeric(as.character(loc@data$sig1[i])), sig2= 5,
grid = 1000)
}
--
David Winsemius
Alameda, CA, USA
__
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Error with adehabitatHR and kernelbb
This is the problematic data, especially the line 43, but when I removed that
line, it bugs at line 62 and so on.
sig1 time id UTMnorthin
UTMeasting
40 4.5766 2012.05.30 08:00:00 Ade-55419576 390052
41 4.5766 2012.05.30 10:00:00 Ade-55419581 390058
42 4.5766 2012.05.30 12:00:00 Ade-55419560 390045
43 4.5766 2012.05.30 14:00:00 Ade-55419574 390051
44 4.5766 2012.05.30 16:00:00 Ade-55419490 390051
45 4.5766 2012.05.30 18:00:00 Ade-55419435 390293
46 4.5766 2012.05.30 20:00:00 Ade-55419661 390876
47 4.5766 2012.05.30 22:00:00 Ade-55419934 390673
48 4.5766 2012.05.31 02:00:00 Ade-55420636 389777
49 4.5766 2012.06.05 02:00:00 Ade-75419275 391206
50 4.5766 2012.06.05 04:00:00 Ade-75419276 391202
This is a data frame so before the loop (see commands in the previous mail
below), I transform with the following commands:
coordinates(fece)-~UTMeasting+UTMnorthin
fece@data$time - as.POSIXct(strptime(as.character(fece@data$time),%Y.%m.%d
%H:%M:%S))
Rémi Lesmerises, biol. M.Sc.,
PH.D candidate
Université du Québec à Rimouski
De : David Winsemius dwinsem...@comcast.net
À : Rémi Lesmerises remilesmeri...@yahoo.ca
Cc : r-help@r-project.org r-help@r-project.org
Envoyé le : vendredi 17 mai 2013 13h53
Objet : Re: [R] Error with adehabitatHR and kernelbb
On May 17, 2013, at 7:44 AM, Rémi Lesmerises wrote:
Dear all,
I'm trying to get a Brownian bridge kernel (kernelbb) for each combination of
two consecutive animal locations (see commands below) and put them, with a
loop, inside a list. It works well at the beginning but after 42 runs, it
appears the following warning :
Error in seq.default(yli[1], yli[2], by = diff(xg[1:2])) :
invalid (to - from)/by in seq(.)
I looked at the coordinates, at the id, at the time of the run 43 and it's
all good...
I looked on the net and it happened to only one person and there was no
answer to his post.
I wonder if that posting (like yours) had no data on which to display the
problem or to test potential solutions? I would think you would want to post
any setup objects and then data for items 40-45.
Someone could help me?
## commands
BBtraj - list()
for (i in 1:(nrow(loc@data)-1)) {
BBtraj[[i]] - kernelbb(as.ltraj(loc@coords[i:(i+1),],
date=loc@data$time[i:(i+1)], id = as.character(loc@data$id[i:(i+1)]),
typeII = TRUE), sig1=as.numeric(as.character(loc@data$sig1[i])), sig2= 5,
grid = 1000)
}
--
David Winsemius
Alameda, CA, USA
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Error with adehabitatHR and kernelbb
There was some mistakes in my previous sending. The following are correct.
This is the problematic data, especially the line 43, but when I removed that
line, it bugs at line 62 and so on.
sig1 time id
UTMnorthin UTMeasting
40 4.5766 2012.05.30 08:00:00 Ade-5 5419576 390052
41 4.5766 2012.05.30 10:00:00 Ade-5 5419581 390058
42 4.5766 2012.05.30 12:00:00 Ade-5 5419560 390045
43 4.5766 2012.05.30 14:00:00 Ade-5 5419574 390051
44 4.5766 2012.05.30 16:00:00 Ade-5 5419490 390051
45 4.5766 2012.05.30 18:00:00 Ade-5 5419435 390293
46 4.5766 2012.05.30 20:00:00 Ade-5 5419661 390876
47 4.5766 2012.05.30 22:00:00 Ade-5 5419934 390673
48 4.5766 2012.05.31 02:00:00 Ade-5 5420636 389777
49 4.5766 2012.06.05 02:00:00 Ade-7 5419275 391206
50 4.5766 2012.06.05 04:00:00 Ade-7 5419276 391202
This is a data frame so before the loop (see commands in the previous mail
below), I transform with the following commands:
coordinates(fece)-~UTMeasting+UTMnorthin
loc@data$time - as.POSIXct(strptime(as.character(loc@data$time),%Y.%m.%d
%H:%M:%S))
Rémi Lesmerises, biol. M.Sc.,
PH.D candidate
Université du Québec à Rimouski
De : David Winsemius dwinsem...@comcast.net
À : Rémi Lesmerises remilesmeri...@yahoo.ca
Cc : r-help@r-project.org r-help@r-project.org
Envoyé le : vendredi 17 mai 2013 13h53
Objet : Re: [R] Error with adehabitatHR and kernelbb
On May 17, 2013, at 7:44 AM, Rémi Lesmerises wrote:
Dear all,
I'm trying to get a Brownian bridge kernel (kernelbb) for each combination of
two consecutive animal locations (see commands below) and put them, with a
loop, inside a list. It works well at the beginning but after 42 runs, it
appears the following warning :
Error in seq.default(yli[1], yli[2], by = diff(xg[1:2])) :
invalid (to - from)/by in seq(.)
I looked at the coordinates, at the id, at the time of the run 43 and it's
all good...
I looked on the net and it happened to only one person and there was no
answer to his post.
I wonder if that posting (like yours) had no data on which to display the
problem or to test potential solutions? I would think you would want to post
any setup objects and then data for items 40-45.
Someone could help me?
## commands
BBtraj - list()
for (i in 1:(nrow(loc@data)-1)) {
BBtraj[[i]] - kernelbb(as.ltraj(loc@coords[i:(i+1),],
date=loc@data$time[i:(i+1)], id = as.character(loc@data$id[i:(i+1)]),
typeII = TRUE), sig1=as.numeric(as.character(loc@data$sig1[i])), sig2= 5,
grid = 1000)
}
--
David Winsemius
Alameda, CA, USA
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Error with adehabitatHR and kernelbb
I presume it's related to the fact that the X coordinate is duplciated
in the two records, and the grid generated by adehabitatHR is a single
column,
Here's a test:
require(adehabitatHR)
m - matrix(c(5419574 ,390051, 5419490 , 390051), ncol = 2,
byrow = TRUE)
tt - as.POSIXct(c(2012-05-30 14:00:00, 2012-05-30 16:00:00))
id - c(Ade=5, Ade-5)
x - kernelbb(as.ltraj(m, date = tt, id = id, typeII=TRUE), sig1 =
4.5766, sig2 = 5, grid = 1000)
This degenerate Y dimension affects downstream methods (like image),
and I'd say this is worth reporting to the package author as an issue:
dim(x[[1]])
[1] 10001
dim(x[[2]])
[1] 10001
The clue comes from points2grid in sp:
Warning messages:
1: In points2grid(points, tolerance, round) :
cell size from constant coordinate 2 possibly taken from other coordinate
You could override the auto-generated grid by passing in your own,
probably something you will want anyway so that your collection share
the same extent and resolution. See ?kernelbb, the grid argument can
be a Spatial object rather than a pixel size.
I would really wonder about what is the point in generating summaries
from single line-segments, but that is off-topic I guess.
Cheers, Mike.
On Sat, May 18, 2013 at 4:47 AM, Rémi Lesmerises
remilesmeri...@yahoo.ca wrote:
There was some mistakes in my previous sending. The following are correct.
This is the problematic data, especially the line 43, but when I removed that
line, it bugs at line 62 and so on.
sig1timeid
UTMnorthin UTMeasting
40 4.5766 2012.05.30 08:00:00 Ade-5 5419576 390052
41 4.5766 2012.05.30 10:00:00 Ade-5 5419581 390058
42 4.5766 2012.05.30 12:00:00 Ade-5 5419560 390045
43 4.5766 2012.05.30 14:00:00 Ade-5 5419574 390051
44 4.5766 2012.05.30 16:00:00 Ade-5 5419490 390051
45 4.5766 2012.05.30 18:00:00 Ade-5 5419435 390293
46 4.5766 2012.05.30 20:00:00 Ade-5 5419661 390876
47 4.5766 2012.05.30 22:00:00 Ade-5 5419934 390673
48 4.5766 2012.05.31 02:00:00 Ade-5 5420636 389777
49 4.5766 2012.06.05 02:00:00 Ade-7 5419275 391206
50 4.5766 2012.06.05 04:00:00 Ade-7 5419276 391202
This is a data frame so before the loop (see commands in the previous mail
below), I transform with the following commands:
coordinates(fece)-~UTMeasting+UTMnorthin
loc@data$time - as.POSIXct(strptime(as.character(loc@data$time),%Y.%m.%d
%H:%M:%S))
Rémi Lesmerises, biol. M.Sc.,
PH.D candidate
Université du Québec à Rimouski
De : David Winsemius dwinsem...@comcast.net
À : Rémi Lesmerises remilesmeri...@yahoo.ca
Cc : r-help@r-project.org r-help@r-project.org
Envoyé le : vendredi 17 mai 2013 13h53
Objet : Re: [R] Error with adehabitatHR and kernelbb
On May 17, 2013, at 7:44 AM, Rémi Lesmerises wrote:
Dear all,
I'm trying to get a Brownian bridge kernel (kernelbb) for each combination
of two consecutive animal locations (see commands below) and put them, with
a loop, inside a list. It works well at the beginning but after 42 runs, it
appears the following warning :
Error in seq.default(yli[1], yli[2], by = diff(xg[1:2])) :
invalid (to - from)/by in seq(.)
I looked at the coordinates, at the id, at the time of the run 43 and it's
all good...
I looked on the net and it happened to only one person and there was no
answer to his post.
I wonder if that posting (like yours) had no data on which to display the
problem or to test potential solutions? I would think you would want to post
any setup objects and then data for items 40-45.
Someone could help me?
## commands
BBtraj - list()
for (i in 1:(nrow(loc@data)-1)) {
BBtraj[[i]] - kernelbb(as.ltraj(loc@coords[i:(i+1),],
date=loc@data$time[i:(i+1)], id = as.character(loc@data$id[i:(i+1)]),
typeII = TRUE), sig1=as.numeric(as.character(loc@data$sig1[i])), sig2= 5,
grid = 1000)
}
--
David Winsemius
Alameda, CA, USA
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Michael Sumner
Hobart, Australia
e-mail: mdsum...@gmail.com
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