[R-sig-Geo] Match polygon and dataframe IDs after raster::extract

[Loïc Dutrieux]

Thanks Edzer,

But then, how safe is it to match attributes and geometries based on the 
record order? Is there any chance that records get shuffled during the 
dataframe manipulation steps, or the raster::extract?

Also one note, SpatialPointsDataFrame() gives a warning, but 
SpatialPolygonsDataFrame() doesn't. (I made a mistake in my initial 
example, I want to create a SpatialPolygonsDataFrame, not a 
SpatialPointsDataFrame).

Cheers,
Loïc


On 11/19/2015 03:08 PM, Edzer Pebesma wrote:
>
>
> On 19/11/15 14:37, Loïc Dutrieux wrote:
>> Hi all,
>>
>> I'm trying to look at correlation between two raster layers, for
>> different polygons. So I use raster::extract to get all the raster
>> values for every polygon, do the calculation and feed the output back to
>> a SpatialPolygonDataFrame.
>> I got it working, but I have a doubt regarding the order of the rows;
>> and it doesn't look like I can use match.ID = TRUE.
>>
>> See the example below.
>>
>> library(raster)
>> library(dplyr)
>>
>> # Create brick with 2 layers
>> b <- brick(ncol=36, nrow=18, nl=2)
>> b[[1]] <- rnorm(ncell(b))
>> b[[2]] <- rnorm(ncell(b))
>>
>> # Create sp
>> cds1 <- rbind(c(-180,-20), c(-160,5), c(-60, 0), c(-160,-60), c(-180,-20))
>> cds2 <- rbind(c(80,0), c(100,60), c(120,0), c(120,-55), c(80,0))
>> cds3 <- rbind(c(-10,20), c(50,60), c(70,-10))
>> polys <- spPolygons(cds1, cds2, cds3)
>>
>> # Extract all values
>> df0 <- extract(b, polys, df = TRUE)
>>
>> # Compute correlation betwen the two layers for every polygons (sorry
>> for the pipe)
>> df1 <- group_by(df0, ID) %>%
>>    summarise(cor = cor(layer.1, layer.2)) %>%
>>    data.frame()
>>
>> # Attach to df to spdf
>> spdf <- SpatialPointsDataFrame(polys, df1)
>>
>>
>>
>> How do I know for sure that the order of the rows in the dataframe did
>> not get mixed up? Can I just assume that they will remain in the same
>> order?
>
> If it does reshuffle and you didn't specify match.ID, it will warn you:
>
>> pts = matrix(1:4,2,2,dimnames=list(c("a", "b"), NULL))
>> pts
>    [,1] [,2]
> a    1    3
> b    2    4
>> df = data.frame(a = 2:3, row.names = c("b", "a"))
>> df
>    a
> b 2
> a 3
>> SpatialPointsDataFrame(pts, df)
>    coordinates a
> a      (1, 3) 3
> b      (2, 4) 2
> Warning message:
> In SpatialPointsDataFrame(pts, df) :
>    forming a SpatialPointsDataFrame based on maching IDs, not on record
> order. Use match.ID = FALSE to match on record order
>> SpatialPointsDataFrame(pts, df, match.ID = FALSE)
>    coordinates a
> b      (1, 3) 2
> a      (2, 4) 3
>
> Using match.ID = FALSE ensures the input order of coordinates and points
> is kept.
>
>>
>> The dataframe returned by extract has an ID column, but the IDs do not
>> correspond to the polygons IDs. For instance if I remove the second
>> polygon (which has the ID "2"), the IDs in the df extracted are still 1
>> and 2 (instead of 1 and 3).
>>
>> # Quick function to get polygons IDs
>> getPolyID <- function(x) {
>>    sapply(x at polygons, function(x) {x at ID} )
>> }
>>
>>
>> getPolyID(polys)
>> # [1] "1" "2" "3"
>> getPolyID(polys[-2])
>> # [1] "1" "3"
>>
>> unique(extract(b, polys[-2], df = TRUE)$ID)
>> # [1] 1 2
>>
>>
>> Any suggestions?
>>
>> Thanks,
>> Loïc
>>
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>
>
>
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