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

[Edzer Pebesma]

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
> 
> _______________________________________________
> R-sig-Geo mailing list
> R-sig-Geo at r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-geo

-- 
Edzer Pebesma
Institute for Geoinformatics (ifgi),  University of Münster,
Heisenbergstraße 2, 48149 Münster, Germany; +49 251 83 33081
Journal of Statistical Software:   http://www.jstatsoft.org/
Computers & Geosciences:   http://elsevier.com/locate/cageo/
Spatial Statistics Society http://www.spatialstatistics.info

-------------- next part --------------
A non-text attachment was scrubbed...
Name: signature.asc
Type: application/pgp-signature
Size: 490 bytes
Desc: OpenPGP digital signature
URL: <https://stat.ethz.ch/pipermail/r-sig-geo/attachments/20151119/8b95be7f/attachment.bin>