Great, it works now, thanks a lot.
This is how I do it:
#Using a raster map to stratify a sample
#Non-interesting classes set as "NA"
> library(rgdal)
> library(sp)
> x <- GDAL.open("C:/ALOBO/dipu2006/STLL_VEG2006/ESTRAT3_OBAC.tif")
> ESTRAT3OBAC <- asSGDF_GROD(x, output.dim=c(118,189))
> GDAL.close(x)
Closing GDAL dataset handle 0x0171c668... destroyed ... done.
> [EMAIL PROTECTED]@data==55537]<- NA
> X <- ESTRAT3OBAC[seq(1,118,by=10),seq(1,189,by=10)] #small example
> class(X)
[1] "SpatialGridDataFrame"
attr(,"package")
[1] "sp"
> fullgrid(X)=F
> class(X)
[1] "SpatialPixelsDataFrame"
attr(,"package")
[1] "sp"
> test.stsamp <- spsample(X, n = 10, "stratified")
> test.stsamp
SpatialPoints:
x1 x2
[1,] 411328.3 4608544
[2,] 412220.4 4608288
[3,] 412856.2 4608528
[4,] 413195.9 4608455
[5,] 414354.4 4608723
[6,] 414804.9 4608653
[7,] 412880.7 4609431
[8,] 413441.1 4608874
[9,] 414629.3 4609258
[10,] 414903.8 4609542
[11,] 412511.0 4609699
[12,] 413290.9 4610094
Coordinate Reference System (CRS) arguments: +proj=utm +zone=31
+ellps=intl +units=m +no_defs
> o <- overlay(X, test.stsamp)
> o
[1] 71 89 77 79 67 85 26 64 41 31 18 14
Agus
Edzer J. Pebesma escribió:
> additional to the
>
> X = as(X, "SpatialPixelsDataFrame")
>
> etc. there's a helper function that toggles between them; try:
>
> fullgrid(X) = TRUE
> class(X)
> fullgrid(X) = FALSE
> class(X)
> --
> Edzer
>
> Agustin Lobo wrote:
>> I understand, but how do I convert between one type and the other?
>> I've tried:
>>
>> x <- GDAL.open("C:/ALOBO/dipu2006/STLL_VEG2006/ESTRAT3_OBAC.tif")
>> ESTRAT3OBAC <- asSGDF_GROD(x, output.dim=c(118,189))
>> GDAL.close(x)
>> [EMAIL PROTECTED]@data==55537]<- NA
>> X <- ESTRAT3OBAC[seq(1,118,by=10),seq(1,189,by=10)] #small example
>> > summary(X)
>> Object of class SpatialGridDataFrame
>> Coordinates:
>> min max
>> x 410649.7 415399.7
>> y 4607910.5 4610910.5
>> Is projected: TRUE
>> proj4string : [ +proj=utm +zone=31 +ellps=intl +units=m +no_defs]
>> Number of points: 2
>> Grid attributes:
>> cellcentre.offset cellsize cells.dim
>> x 410774.7 250 19
>> y 4608035.5 250 12
>> Data attributes:
>> band1
>> Min. : 4.0
>> 1st Qu.: 67.0
>> Median :156.0
>> Mean :125.8
>> 3rd Qu.:163.0
>> Max. :237.0
>> NA's :119.0
>>
>> > Y <- SpatialPixels(X)
>> > summary(Y)
>> Object of class SpatialPixels
>> Coordinates:
>> min max
>> x 410649.7 415399.7
>> y 4607910.5 4610910.5
>> Is projected: TRUE
>> proj4string : [ +proj=utm +zone=31 +ellps=intl +units=m +no_defs]
>> Number of points: 2
>>
>> So X and Y are not the same at all.
>>
>> Thanks for your help.
>>
>> Agus
>>
>>
>> Edzer J. Pebesma escribió:
>>> Not only to avoid NAs, but also to get approximately right sample size.
>>>
>>> Stratified sampling does not take place based on strata defined by
>>> attributes (map layers), but rather by dividing the area into square
>>> blocks (strata) and randomly sample (n=1) from each block. That is
>>> why the resulting sample doesn't have exactly the
>>> prescribed/requested size (although one could iterate). See also
>>> Ripley 1981 Spatial Statistics for explanation.
>>>
>>> Best wishes,
>>> --
>>> Edzer
>>>
>>> Roger Bivand wrote:
>>>> There are two forms of sp objects for grids, SpatialPixelsDataFrame
>>>> and SpatialGridDataFrame, and you need the former to avoid NAs. I am
>>>> not sure how to proceed without access to a copz of zour data to see
>>>> whz spsample is including the NA cells.
>>>>
>>>> Roger
>>>>
>>>> --- Roger Bivand, NHH, Helleveien 30, N-5045 Bergen,
>>>> [EMAIL PROTECTED]
>>>>
>>>> ________________________________
>>>>
>>>> Od: Agustin Lobo w imieniu Agustin Lobo
>>>> Wys³ano: Cz 21.06.2007 09:41
>>>> Do: Roger Bivand
>>>> DW: R-sig-Geo@stat.math.ethz.ch
>>>> Temat: Re: ODP: [R-sig-Geo] spsample and NA
>>>>
>>>>
>>>>
>>>> The test with meuse.grid works:
>>>>
>>>> #copied from file:SpatialGridDataFrame-class.html
>>>> coordinates(meuse.grid) = c("x", "y") # promote
>>>> toSpatialPointsDataFrame
>>>> gridded(meuse.grid) <- TRUE # promote to SpatialPixelsDataFrame
>>>> x = as(meuse.grid, "SpatialGridDataFrame") # creates the full grid
>>>> #Now me:
>>>> > unique([EMAIL PROTECTED])
>>>> [1] NA 1 2 3
>>>>
>>>> > table([EMAIL PROTECTED])
>>>> 1 2 3
>>>> 1665 1084 354
>>>>
>>>> test.stsamp <- spsample(x, n = 10, "stratified")
>>>> o <- overlay(x, test.stsamp)
>>>> > o
>>>> coordinates part.a part.b dist soil ffreq
>>>> 5556 (179156, 330917) 0 1 0.1030270 1 1
>>>> 6670 (180039, 330336) 0 1 0.0703333 1 2
>>>> 2240 (180677, 332606) 1 0 0.0975136 1 1
>>>>
>>>>
>>>> But don't know how to make that my raster behave in the same way. What
>>>> does it mean "cast to SpatialPixels first"? I thought that as
>>>> X comes from an imported raster it was an sp object already.
>>>>
>>>> Also, there are several components in the x coming from meuse.grid:
>>>> str(x)
>>>> Formal class 'SpatialGridDataFrame' [package "sp"] with 6 slots
>>>> ..@ data :'data.frame': 8112 obs. of 5 variables:
>>>> .. ..$ part.a: num [1:8112] NA NA NA NA NA NA NA NA NA NA ...
>>>> .. ..$ part.b: num [1:8112] NA NA NA NA NA NA NA NA NA NA ...
>>>> .. ..$ dist : num [1:8112] NA NA NA NA NA NA NA NA NA NA ...
>>>> .. ..$ soil : num [1:8112] NA NA NA NA NA NA NA NA NA NA ...
>>>> .. ..$ ffreq : Factor w/ 3 levels "1","2","3": NA NA NA NA NA NA NA
>>>> NA NA NA ...
>>>>
>>>> how does spsample know which layer has to be used for the
>>>> stratification?
>>>>
>>>> Thanks!
>>>>
>>>> Agus
>>>>
>>>> Roger Bivand escribió:
>>>>
>>>>> I think that if you cast to SpatialPixels first, the problem will
>>>>> go away, because the all-NA cases are dropped with their
>>>>> coordinates. Could you try the same example with meuse.grid and see
>>>>> how it goes?
>>>>>
>>>>> Roger
>>>>>
>>>>> ---
>>>>> Roger Bivand, NHH, Helleveien 30, N-5045 Bergen, [EMAIL PROTECTED]
>>>>>
>>>>> ________________________________
>>>>>
>>>>> Od: [EMAIL PROTECTED] w imieniu Agustin Lobo
>>>>> Wys³ano: ¦r 20.06.2007 10:11
>>>>> Do: R-sig-Geo@stat.math.ethz.ch
>>>>> Temat: [R-sig-Geo] spsample and NA
>>>>>
>>>>>
>>>>>
>>>>> It is often the case, at least with raster (grid) objects,
>>>>> that you are not interested on a part of the raster.
>>>>> For example because it's outside a non.rectangular region of study
>>>>> and/or because some types of terrain (some classes) are outside
>>>>> the scope of the study. In any case, those parts can be
>>>>> represented by NA.
>>>>>
>>>>> Unfortunately, while some functions like table() would not
>>>>> include the NA in the statistics, spsample includes
>>>>> the NA as just another class, which implies that a fraction
>>>>> of the resulting coordinates will lay on the NA
>>>>> part of the raster. This makes it difficult, to get N valid (i.e., not
>>>>> on NA parts) points using spsample. Is there any way around this?
>>>>> For example, if I want 10 points on non-NA cells of
>>>>> raster X, I would like
>>>>>
>>>>> spsample(X, 10, "stratified")
>>>>>
>>>>> to provide 10 positions on non-NA cells.
>>>>>
>>>>> At the moment, I get:
>>>>>
>>>>> x <- GDAL.open("C:/ALOBO/dipu2006/STLL_VEG2006/ESTRAT3_OBAC.tif")
>>>>> ESTRAT3OBAC <- asSGDF_GROD(x, output.dim=c(100,100))
>>>>> GDAL.close(x)
>>>>>
>>>>> [EMAIL PROTECTED]@data==55537]<- NA
>>>>>
>>>>> X <- ESTRAT3OBAC
>>>>> X$cut <- as.ordered(cut(X$band1, c(0,10,100),include.lowest=TRUE))
>>>>> table(X$cut)
>>>>>
>>>>> [0,10] (10,100]
>>>>> 83 1961
>>>>>
>>>>> summary(X$cut)
>>>>> [0,10] (10,100] NA's
>>>>> 83 1961 7956
>>>>> table(X$cut)
>>>>>
>>>>> [0,10] (10,100]
>>>>> 83 1961
>>>>>
>>>>> Xspsample <- spsample(X,10,"stratified")
>>>>> Xo <- overlay(X,Xspsample)
>>>>> summary(Xo)
>>>>> Object of class SpatialPointsDataFrame
>>>>> Coordinates:
>>>>> min max
>>>>> x1 410995.6 414954.4
>>>>> x2 4608002.1 4610566.0
>>>>> Is projected: TRUE
>>>>> proj4string : [ +proj=utm +zone=31 +ellps=intl +units=m +no_defs]
>>>>> Number of points: 9
>>>>> Data attributes:
>>>>> band1 cut
>>>>> Min. : 67 [0,10] :0
>>>>> 1st Qu.: 97 (10,100]:3
>>>>> Median : 159 NA's :6
>>>>> Mean :24745
>>>>> 3rd Qu.:55537
>>>>> Max. :55537
>>>>>
>>>>> That is, I get 6 positions on NA values of X
>>>>>
>>>>> Thanks!
>>>>>
>>>>> Agus
>>>>>
>>>>> --
>>>>> Dr. Agustin Lobo
>>>>> Institut de Ciencies de la Terra "Jaume Almera" (CSIC)
>>>>> LLuis Sole Sabaris s/n
>>>>> 08028 Barcelona
>>>>> Spain
>>>>> Tel. 34 934095410
>>>>> Fax. 34 934110012
>>>>> email: [EMAIL PROTECTED]
>>>>> http://www.ija.csic.es/gt/obster
>>>>>
>>>>> _______________________________________________
>>>>> R-sig-Geo mailing list
>>>>> R-sig-Geo@stat.math.ethz.ch
>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>>> --
>>>> Dr. Agustin Lobo
>>>> Institut de Ciencies de la Terra "Jaume Almera" (CSIC)
>>>> LLuis Sole Sabaris s/n
>>>> 08028 Barcelona
>>>> Spain
>>>> Tel. 34 934095410
>>>> Fax. 34 934110012
>>>> email: [EMAIL PROTECTED]
>>>> http://www.ija.csic.es/gt/obster
>>>>
>>>>
>>>>
>>>> [[alternative HTML version deleted]]
>>>>
>>>>
>>>> ------------------------------------------------------------------------
>>>>
>>>>
>>>> _______________________________________________
>>>> R-sig-Geo mailing list
>>>> R-sig-Geo@stat.math.ethz.ch
>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>>>
>>>
>>>
>>
>
>
--
Dr. Agustin Lobo
Institut de Ciencies de la Terra "Jaume Almera" (CSIC)
LLuis Sole Sabaris s/n
08028 Barcelona
Spain
Tel. 34 934095410
Fax. 34 934110012
email: [EMAIL PROTECTED]
http://www.ija.csic.es/gt/obster
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