> Can I ask you some doubts about the adehabitat packages and its commands?
As far as I understand, it is prefereable to use the adehabitatHR package,
because adehabitat is no longer maintained. I believe the methods are the
same between adehabitat and adehabitatHR, with the exception of the
underlaying data structure. adehabitatHR makes use of sp object. But also
see: vignette("adehabitatHR") for more informaiton.
Best
Johannes
On Fri, Jul 26, 2013 at 12:05 AM, laila Aranda Romero <laila_...@hotmail.com
> wrote:
> Thank very much!!!!!!
>
> I want to use the adehabitat but as you realised I mixed up both packages
> thinking their command were the same. I got almost crazy to understand why
> this error happened. [image: Emoji]
>
> Can I ask you some doubts about the adehabitat packages and its commands?
>
> Laila
>
> > From: animov-requ...@faunalia.it
> > Subject: AniMov Digest, Vol 89, Issue 4
> > To: animov@faunalia.it
> > Date: Thu, 25 Jul 2013 23:45:52 +0200
> >
> > Send AniMov mailing list submissions to
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> >
> > Today's Topics:
> >
> > 1. Kernel density surfaces (laila Aranda Romero)
> > 2. Re: Kernel density surfaces (Johannes Signer)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Thu, 25 Jul 2013 21:07:53 +0000
> > From: laila Aranda Romero <laila_...@hotmail.com>
> > To: "animov@faunalia.it" <animov@faunalia.it>
> > Subject: [AniMov] Kernel density surfaces
> > Message-ID: <dub116-w35ce0e71e75e84184256929e...@phx.gbl>
> > Content-Type: text/plain; charset="iso-8859-1"
> >
> > He everybody,
> >
> > I'm studying the migration pattern and wintering distribution of the
> Great shearwater using geolocation data. For this, I want to work out the
> kernel density surfaces using the package adehabitat of R. However, I've
> some problems when I'm trying to run my script.
> >
> > Original data:
> > head(Geo7)
> > lon latcom
> > 27 30.73 -41.08
> > 30 37.44 -40.66
> > 31 37.59 -40.54
> > 33 46.27 -43.86
> > 35 49.94 -43.25
> > 38 53.52 -40.07
> > > class(Geo7)
> > [1] "data.frame"
> > > str(Geo7)
> > 'data.frame': 160 obs. of 2 variables:
> > $ lon : num 30.7 37.4 37.6 46.3 49.9 ...
> > $ latcom: num -41.1 -40.7 -40.5 -43.9 -43.2 ..
> > Script:
> > Geo7 <- subset(Geo6b, select=c (lon, latcom)) ########## cambiar latitud
> y longitud de orden
> > location<-project(Geo7,list(proj="laea", lat_O=1,lon_0=2, x_0=6,
> y_0=7),inverse=FALSE, degrees=TRUE, silent=FALSE) #### we use Lambert
> azimuthal equal-area projection
> > location1a <- data.frame(location) #### It's necessary to convert the
> list into dataframe
> > xy= location1a[c("x", "y")]
> > class(location1a)
> > coordinates(location1a) <- ~x+y ###### To convert mapping coordinates to
> Spatial points
> > class(location1a)
> >
> > ################KERNEL
> > Kernel1<-kernelUD(location1a, h="href",grid=40,same4all=F,
> hlim=c(0.1,1.5),kern=c("bivnorm"),extent=0.5) ###
> > image(Kernel1, axes=FALSE, mar=c(0,0,2,0), addcontour=TRUE,
> addpoints=TRUE)
> > kernel2 <-getvolumeUD(Kernel1)
> > Kernel3 <- kernel.area(kernel2, id=NULL, h="href", grid=40,
> same4all=FALSE, hlim=c(0.1,1.5), kern="bivnorm", levels=seq(25,95,by=10),
> unin=c("m"), unout=c("m2"), extent=0.5) ###### same problem I need two
> columns instead of oneele
> > Kernel6<-getverticeshr(Kernel1,lev=40)
> > image(Kernel1) ### problemas con la paleta por eso he eliminado
> col=rainbow(4)
> > plot(Kernel6, add=TRUE)
> > Kernel7 <- getverticeshr(kernel1,lev=90)
> > image(Kernel1)
> > plot(Kernel6, add=TRUE)
> >
> > When a run it:
> > location<-project(Geo7,list(proj="laea", lat_O=1,lon_0=2, x_0=6,
> y_0=7),inverse=FALSE, degrees=TRUE, silent=FALSE) #### we use Lambert
> azimuthal equal-area projection
> > > class(location)
> > [1] "list"
> > > str(location)
> > List of 2
> > $ x: num [1:160] 2533084 3115667 3132780 3682706 3994351 ...
> > $ y: num [1:160] -4593850 -4615167 -4603968 -5069889 -5060989 ...
> > > location1a <- data.frame(location) #### It's necessary to convert the
> list into dataframe
> > > xy= location1a[c("x", "y")]
> > > class(location1a)
> > [1] "data.frame"
> > > coordinates(location1a) <- ~x+y ###### To convert mapping coordinates
> to Spatial points
> > > class(location1a)
> > [1] "SpatialPoints"
> > attr(,"package")
> > [1] "sp" Kernel1<-kernelUD(location1a, h="href",grid=40,same4all=F,
> hlim=c(0.1,1.5),kern=c("bivnorm"),extent=0.5) ###
> > Error en if (ncol(xy) != 2) stop("xy should have 2 columns") :
> > argumento tiene longitud cero I would appreciate a lot if someone can
> help me to find a solution to this error. Laila
> > -------------- next part --------------
> > An HTML attachment was scrubbed...
> > URL: <
> http://lists.faunalia.it/pipermail/animov/attachments/20130725/53483280/attachment-0001.html
> >
> >
> > ------------------------------
> >
> > Message: 2
> > Date: Thu, 25 Jul 2013 23:45:48 +0200
> > From: Johannes Signer <j.m.sig...@gmail.com>
> > To: Animal Movement <animov@faunalia.it>
> > Subject: Re: [AniMov] Kernel density surfaces
> > Message-ID:
> > <CAC8qavs_gJNVT_27R3Fp2BfCRgm6jg7oBk5eL8x=gbg+s+m...@mail.gmail.com>
> > Content-Type: text/plain; charset="iso-8859-1"
> >
> > Hello Laila,
> >
> > do you possibly mix adehabitat and adehabitatHR? See code below.
> >
> > Hope this helps,
> > Johannes
> >
> >
> > library(adehabitat)
> > library(adehabitatHR)
> > library(proj4)
> >
> > ## Original data:
> >
> > Geo7 <- read.table(textConnection("
> > lon latcom
> > 27 30.73 -41.08
> > 30 37.44 -40.66
> > 31 37.59 -40.54
> > 33 46.27 -43.86
> > 35 49.94 -43.25
> > 38 53.52 -40.07"), header=TRUE)
> >
> >
> >
> > location <- proj4::project(Geo7,list(proj="laea", lat_O=1,lon_0=2, x_0=6,
> > y_0=7),inverse=FALSE, degrees=TRUE, silent=FALSE) #### we use Lambert
> > azimuthal equal-area projection
> >
> > location1a <- data.frame(location) #### It's necessary to convert the
> > list into dataframe
> > xy= location1a[c("x", "y")]
> > class(location1a)
> > coordinates(location1a) <- ~x+y ###### To convert mapping coordinates
> > to Spatial points
> > class(location1a)
> >
> > ################ KERNEL
> > ## Do you load adehabitat or adehabitatHR?
> >
> > ## This fails, because adehabitat::kernelUD requires coordinates as a
> data
> > frame
> > Kernel1 <- adehabitat::kernelUD(location1a, h="href",grid=40,same4all=F,
> > hlim=c(0.1,1.5),kern=c("bivnorm"),extent=0.5) ###
> > ## Error in if (ncol(xy) != 2) stop("xy should have 2 columns") :
> > ## argument is of length zero
> >
> > ## Works
> > Kernel1 <- adehabitat::kernelUD(data.frame(location),
> > h="href",grid=40,same4all=F,
> > hlim=c(0.1,1.5),kern=c("bivnorm"),extent=0.5) ###
> >
> >
> > ## Works as expected
> > Kernel1 <- adehabitatHR::kernelUD(location1a,
> h="href",grid=40,same4all=F,
> > hlim=c(0.1,1.5),kern=c("bivnorm"),extent=0.5) ###
> >
> >
> >
> > On Thu, Jul 25, 2013 at 11:07 PM, laila Aranda Romero <
> laila_...@hotmail.com
> > > wrote:
> >
> > > He everybody,
> > >
> > > I'm studying the migration pattern and wintering distribution of the
> > > Great shearwater using geolocation data. For this, I want to work out
> the
> > > kernel density surfaces using the package adehabitat of R. However,
> I've
> > > some problems when I'm trying to run my script.
> > >
> > > Original data:
> > >
> > > head(Geo7) lon latcom
> > > 27 30.73 -41.08
> > > 30 37.44 -40.6631 37.59 -40.54
> > > 33 46.27 -43.86
> > > 35 49.94 -43.25
> > > 38 53.52 -40.07> class(Geo7)[1] "data.frame"> str(Geo7)'data.frame':
> 160 obs. of 2 variables:
> > > $ lon : num 30.7 37.4 37.6 46.3 49.9 ...
> > > $ latcom: num -41.1 -40.7 -40.5 -43.9 -43.2 ..
> > >
> > >
> > > Script:
> > > Geo7 <- subset(Geo6b, select=c (lon, latcom)) ########## cambiar
> latitud y
> > > longitud de orden
> > > location<-project(Geo7,list(proj="laea", lat_O=1,lon_0=2, x_0=6,
> > > y_0=7),inverse=FALSE, degrees=TRUE, silent=FALSE) #### we use Lambert
> > > azimuthal equal-area projection
> > > location1a <- data.frame(location) #### It's necessary to convert the
> > > list into dataframe
> > > xy= location1a[c("x", "y")]
> > > class(location1a)
> > > coordinates(location1a) <- ~x+y ###### To convert mapping coordinates
> > > to Spatial points
> > > class(location1a)
> > >
> > > ################KERNEL
> > > Kernel1<-kernelUD(location1a, h="href",grid=40,same4all=F,
> > > hlim=c(0.1,1.5),kern=c("bivnorm"),extent=0.5) ###
> > > image(Kernel1, axes=FALSE, mar=c(0,0,2,0), addcontour=TRUE,
> addpoints=TRUE)
> > > kernel2 <-getvolumeUD(Kernel1)
> > > Kernel3 <- kernel.area(kernel2, id=NULL, h="href", grid=40,
> > > same4all=FALSE, hlim=c(0.1,1.5), kern="bivnorm",
> levels=seq(25,95,by=10),
> > > unin=c("m"), unout=c("m2"), extent=0.5) ###### same problem I need two
> > > columns instead of oneele
> > > Kernel6<-getverticeshr(Kernel1,lev=40)
> > > image(Kernel1) ### problemas con la paleta por eso he eliminado
> > > col=rainbow(4)
> > > plot(Kernel6, add=TRUE)
> > > Kernel7 <- getverticeshr(kernel1,lev=90)
> > > image(Kernel1)
> > > plot(Kernel6, add=TRUE)
> > >
> > > When a run it:
> > >
> > > location<-project(Geo7,list(proj="laea", lat_O=1,lon_0=2, x_0=6,
> y_0=7),inverse=FALSE, degrees=TRUE, silent=FALSE) #### we use Lambert
> azimuthal equal-area projection> class(location)[1] "list">
> str(location)List of 2
> > > $ x: num [1:160] 2533084 3115667 3132780 3682706 3994351 ...
> > > $ y: num [1:160] -4593850 -4615167 -4603968 -5069889 -5060989 ...>
> location1a <- data.frame(location) #### It's necessary to convert the list
> into dataframe> xy= location1a[c("x", "y")]> class(location1a)[1]
> "data.frame"> coordinates(location1a) <- ~x+y ###### To convert mapping
> coordinates to Spatial points> class(location1a)[1] "SpatialPoints"
> > > attr(,"package")
> > > [1] "sp"
> > >
> > >
> > >
> > >
> > >
> > > Kernel1<-kernelUD(location1a, h="href",grid=40,same4all=F,
> hlim=c(0.1,1.5),kern=c("bivnorm"),extent=0.5) ###Error en if (ncol(xy) !=
> 2) stop("xy should have 2 columns") :
> > > argumento tiene longitud cero
> > >
> > >
> > >
> > > I would appreciate a lot if someone can help me to find a solution to
> this error.
> > >
> > >
> > >
> > > Laila
> > >
> > >
> > > _______________________________________________
> > > AniMov mailing list
> > > AniMov@faunalia.it
> > > http://lists.faunalia.it/cgi-bin/mailman/listinfo/animov
> > >
> > >
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--
## ## Contact:
## Johannes Signer, MSc
## PhD-Candidate -- Wildlife Management
## Dept. of Forest Zoology & Forest Conservation
## University of Goettingen
## Buesgenweg 3 (room 85)
## 37077 Goettingen, Germany
## e: jmsig...@gmail.com
## skype: j.m.signer
## ##
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