[R-sig-Geo] Problems with the Spatial Reference of a shapefile created with writePolyShape
Maren Huck
M.Huck at derby.ac.uk
Wed Oct 30 18:24:54 CET 2013
Hi David,
Could the problem be that the function locoh.a does not actually create a single convex hull, but a multitude. So you have to select the locoh with the percentage you want by looking at
as.data.frame(locoh)
This will give you a long list, and you select the row which comes closest to your preferred percentage value, e.g., 90% or 95%. And when you plot, you need to specify that row.
I just tried with my own data, and it worked, using spplot.
library(maptools)
library(adehabitatHS)
library(mapproj)
library(rgdal)
library(rgeos)
minX<-min(Helen_sp$X)
maxX<-max(Helen_sp$X)
minY<-min(Helen_sp$Y)
maxY<-max(Helen_sp$Y)
dista<-sqrt(((maxX-minX)^2)+((maxY-minY)^2))
dista # should be an approximation of a for LoCoH
habitat <- readShapeSpatial("clean")
proj4string(habitat) <- CRS("+proj=tmerc +lat_0=49 +lon_0=-2 +k=0.9996012717 +x_0=400000 +y_0=-100000 +ellps=airy +datum=OSGB36 +units=m +no_defs")
nn_a <- LoCoH.a(Helen_sp, a=401, unin="m", unout="ha")
plot(nn_a, border=NA)
as.data.frame(nn_a) # line 115 is the first with >90% (91.5)
# The area is given as 17204. Since unout is set to "ha" this cannot be true (should be about 1.7 ha).
# To get just the locations and the locoh:
plot(Helen_sp, pch=16, col="blue")
plot(nn_a[115,], border="red", add=T) # 91.5%
# To plot on my map
code<-c("orange", "pink", "lightblue", "blue", "green3", "green", "darkseagreen", "grey", "darkgreen") # a list of suitable colours for the map
spplot(habitat, zcol="HABITAT", col.regions=code, sp.layout=list("sp.polygons", nn_a[115,], lwd=4, col="green"))
Hope this helps,
Muchos saludos,
Maren
Maren Huck
Dep. of Biological and Forensic Sciences
University of Derby
Kedleston Road
Derby DE22 1GB
U.K.
Tel: +44-(0)1332-59 2354
-----Original Message-----
From: r-sig-geo-bounces at r-project.org [mailto:r-sig-geo-bounces at r-project.org] On Behalf Of David Villalobos
Sent: 30 October 2013 16:42
To: Manuel Spínola
Cc: r-sig-geo at r-project.org
Subject: [POSSIBLE SPAM] Re: [R-sig-Geo] Problems with the Spatial Reference of a shapefile created with writePolyShape
Hi Manuel
Thank you, I tryed your solution and it works partially
xysp <- SpatialPoints(xy)
proj4string(xysp) <- CRS("+proj=tmerc +lon_0=-84 +lat_0=0 +x_0=500000
+k=0.9999 +datum=WGS84")
> xysp
SpatialPoints:
X Y
[1,] 815196.4 1152758
[2,] 815196.0 1152759
[3,] 815055.7 1152120
[4,] 815055.7 1152120
[5,] 815056.5 1152122
[6,] 815061.6 1152131.......
Coordinate Reference System (CRS) arguments: +proj=tmerc +lon_0=-84
+lat_0=0 +x_0=500000 +k=0.9999 +datum=WGS84
> locoh<- LoCoH.a(xysp, a=657,
unin=c("m"),unout=c("ha"),duplicates=c("random"),amount=NULL)
> summary(locoh)
Object of class SpatialPolygonsDataFrame
Coordinates:
min max
x 815048.9 815365.8
y 1152113.3 1152759.5
Is projected: TRUE
proj4string :
[+proj=tmerc +lon_0=-84 +lat_0=0 +x_0=500000 +k=0.9999 +datum=WGS84] Data attributes:
area percent
Min. : 789.5 Min. : 54.17
1st Qu.: 789.5 1st Qu.: 54.17
Median : 834.9 Median : 60.83
Mean : 6311.2 Mean : 69.13
3rd Qu.: 8263.5 3rd Qu.: 85.83
Max. :31699.1 Max. :100.00
BUT, when I create the shapefile > writePolyShape(locoh, "Locohraul") the same problem appear in AarGis 10.0: "UnKnown Spatial Reference: object missing spatial reference information, this can be drawn, but can't be projected."
Then, the object is draw, but not projected. The map of my study area and the shapefile of my LoCoH.a analysis doesn't match.
Any idea? Thank you
2013/10/30 Manuel Spínola <mspinola10 at gmail.com>
> Hi David,
>
> You don´t have the CRS.
>
> Try this:
>
> proj4string(xysp) <- CRS("+proj=tmerc +lon_0=-84 +lat_0=0 +x_0=500000
> +k=0.9999 +datum=WGS84")
>
> Best,
>
> Manuel Spínola
>
>
> 2013/10/30 David Villalobos <avi3187 at gmail.com>
>
>> Dear list,
>>
>> Maybe a silly problem, but I need help to solve it.
>>
>> At this moment I am working with the R package "adehabitatHR",
>> specifically with the LoCoH.a (Adaptative LoCoh). I am calculating
>> the home range of a neotropical bat (Ectophylla alba:
>> Phyllostomidae). My commands are the followings:
>>
>> xy<-read.table("clipboard", header=T)
>>
>> head(xy)
>>
>> X Y
>>
>> 1 815802.7 1151723
>>
>> 2 815816.2 1151717
>>
>> 3 815816.1 1151811
>>
>> 4 816053.5 1151723
>>
>> 5 816027.1 1151698
>>
>> 6 816096.1 1151687
>>
>> xysp
>>
>> SpatialPoints:
>>
>> X Y
>>
>> [1,] 815802.7 1151723
>>
>> [2,] 815816.2 1151717
>>
>> [3,] 815816.1 1151811
>>
>> [4,] 816053.5 1151723
>>
>> [5,] 816027.1 1151698.........
>>
>> Coordinate Reference System (CRS) arguments: NA
>>
>>
>> locoh<- LoCoH.a(xysp, a=1419,
>> unin=c("m"),unout=c("ha"),duplicates=c("random"),amount=NULL)
>>
>> plot(locoh)
>>
>> plot(xysp,add=T)
>>
>> locohhr<- MCHu2hrsize(locoh, percent=seq(10, 100, by=5))
>>
>> locohhr
>>
>> df
>>
>> 10 2935.613
>>
>> 15 2935.613
>>
>> 20 2935.613
>>
>> 25 2935.613........
>>
>> At this point everything right, and now my purpose is to create a
>> "shapefile" using the object "locoh" (Class =
>> SpatialPolygonsDataFrame) with this command:
>>
>> writePolyShape(locohhr, "LocohI")
>>
>> Here, the real problem: I want to use the shapefile created on a map
>> of my study area (in Costa Rica). I have the map in the local
>> Projected Coordinate System:
>>
>> Projected Coordinate System: Proyeccion_CRTM05
>>
>> Projection: Transverse_Mercator
>>
>> False_Easting: 500000.00000000
>>
>> False_Northing: 0.00000000
>>
>> Central_Meridian: -84.00000000
>>
>> Scale_Factor: 0.99990000
>>
>> Latitude_Of_Origin: 0.00000000
>>
>> Linear Unit: Meter
>>
>> Geographic Coordinate System: GCS_WGS_1984
>>
>> Datum: D_WGS_1984
>>
>> Prime Meridian: Greenwich
>>
>> Angular Unit: Degree
>>
>>
>> The first step is to read the shapefile in ArcMap 10. When I try to
>> read the shapefile of my LoCoH.a analysis, I can't do it good because
>> the following message appear: "UnKnown Spatial Reference: object
>> missing spatial reference information, this can be drawn, but can't
>> be projected."
>>
>> Then, the object is draw, but not projected. The map of my study area
>> and the shapefile of my LoCoH.a analysis doesn't match.
>>
>>
>> I want to solve this problem with spatial reference information of my
>> shapefile(LoCoH.a). I suspect that the way to do it is related with
>> one part of the command writePolyShape(locoh, "LocohI"), maybe the
>> part: "proj4string=CRS(as.character(NA)".
>>
>>
>>
>> Please any help is welcome. I will be very appreciated.
>>
>>
>> Since now, THANK YOU.
>>
>>
>> --
>>
>> Saludos
>>
>> David Villalobos Chaves
>> Maestría Académica en Biología
>> Universidad de Costa Rica
>>
>> [[alternative HTML version deleted]]
>>
>>
>> _______________________________________________
>> R-sig-Geo mailing list
>> R-sig-Geo at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>
>>
>
>
> --
> *Manuel Spínola, Ph.D.*
> Instituto Internacional en Conservación y Manejo de Vida Silvestre
> Universidad Nacional Apartado 1350-3000 Heredia COSTA RICA
> mspinola at una.ac.cr mspinola10 at gmail.com
> Teléfono: (506) 2277-3598
> Fax: (506) 2237-7036
> Personal website: Lobito de
> río<https://sites.google.com/site/lobitoderio/>
> Institutional website: ICOMVIS <http://www.icomvis.una.ac.cr/>
>
--
Saludos
David Villalobos Chaves
Maestría Académica en Biología
Universidad de Costa Rica
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