Hi again,
I've achieved to obtain the kernel density surface but I don't really know how
I can plot these surfaces into a map using a Lambert azimuthal equal-area
projection.
Kernel1w <-kernelUD(location3a, h="href", grid=500, same4all=TRUE,
hlim=c(0.1,1.5), kern=c("bivnorm"), extent=0.5)
image(Kernel1w)
homerangew <- getverticeshr(Kernel1w, 90)
image(Kernel1w)
plot(homerangew,add=TRUE)
plot(homerangew, col=3)
Kernel2w <-getvolumeUD(Kernel1w)
image(Kernel2w)
plot(homerangew,add=TRUE)
w95 <- getverticeshr(Kernel1w, 95)
w90 <- getverticeshr(Kernel1w, 90)
w80 <- getverticeshr(Kernel1w, 80)
w70 <- getverticeshr(Kernel1w, 70)
w50 <- getverticeshr(Kernel1w, 50)
w30 <- getverticeshr(Kernel1w, 30)
w25 <- getverticeshr(Kernel1w, 25)
class(w95)
[1] "SpatialPolygonsDataFrame"
attr(,"package")
[1] "sp"
Can you recommend me some commands, please?
Laila
> From: animov-requ...@faunalia.it
> Subject: AniMov Digest, Vol 89, Issue 5
> To: animov@faunalia.it
> Date: Fri, 26 Jul 2013 00:05:32 +0200
>
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> 1. Re: AniMov Digest, Vol 89, Issue 4 (laila Aranda Romero)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 25 Jul 2013 22:05:28 +0000
> From: laila Aranda Romero <laila_...@hotmail.com>
> To: "animov@faunalia.it" <animov@faunalia.it>
> Subject: Re: [AniMov] AniMov Digest, Vol 89, Issue 4
> Message-ID: <dub116-w47a27a0bbeee54b0ab062a9e...@phx.gbl>
> Content-Type: text/plain; charset="utf-8"
>
> 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. ?
>
> 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
> > animov@faunalia.it
> >
> > To subscribe or unsubscribe via the World Wide Web, visit
> > http://lists.faunalia.it/cgi-bin/mailman/listinfo/animov
> > or, via email, send a message with subject or body 'help' to
> > animov-requ...@faunalia.it
> >
> > You can reach the person managing the list at
> > animov-ow...@faunalia.it
> >
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of AniMov digest..."
> >
> >
> > 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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