Navigating an Object of class 'SpatialPolygonsDataFrame' to filter on Polygon Area

Question

I have an Object of class 'SpatialPolygonsDataFrame' with the structure shown below.

What's the secret to getting to the @area slot? Ultimately, I'm trying to filter this file so that I'm only left with polygons >= 64m^2. The resultant shapefile will be imported to OCAD (orienteering mapping software), in an attempt to semi-automatically map a class of vegetation.

I thought I had some understanding of S4 classes, but clearly I have a gap.

among many similar failed attempts:

> xfile@polygons$Polygons@Polygons$Polygon
Error: trying to get slot "Polygons" from an object of a basic class ("NULL") with no slots
> xfile@polygons$Polygons@Polygons
Error: trying to get slot "Polygons" from an object of a basic class ("NULL") with no slots
> xfile@polygons@Polygons
Error: trying to get slot "Polygons" from an object of a basic class ("list") with no slots
> xfile@polygons$Polygons
NULL
> xfile@polygons$'Polygons'@Polygons$'Polygon'@area
Error: trying to get slot "Polygons" from an object of a basic class ("NULL") with no slots
> xfile@polygons$'Polygons'@Polygons
Error: trying to get slot "Polygons" from an object of a basic class ("NULL") with no slots
> xfile@polygons$'Polygons'
NULL
> xfile@polygons$area
NULL
> xfile$polygons
NULL
> xfile@polygons
( the whole file )

Formal class 'SpatialPolygonsDataFrame' [package "sp"] with 5 slots
  ..@ data       :'data.frame': 1 obs. of  1 variable:
  .. ..$ layer: num 1
  ..@ polygons   :List of 1
  .. ..$ :Formal class 'Polygons' [package "sp"] with 5 slots
  .. .. .. ..@ Polygons :List of 191
  .. .. .. .. ..$ :Formal class 'Polygon' [package "sp"] with 5 slots
  .. .. .. .. .. .. ..@ labpt  : num [1:2] 513021 4319805
  .. .. .. .. .. .. ..@ area   : num 9.64
  .. .. .. .. .. .. ..@ hole   : logi FALSE
  .. .. .. .. .. .. ..@ ringDir: int 1
  .. .. .. .. .. .. ..@ coords : num [1:19, 1:2] 513018 513025 513025 513024 513024 ...
  .. .. .. .. ..$ :Formal class 'Polygon' [package "sp"] with 5 slots
  .. .. .. .. .. .. ..@ labpt  : num [1:2] 513053 4319805
  .. .. .. .. .. .. ..@ area   : num 1.85
  .. .. .. .. .. .. ..@ hole   : logi FALSE
  .. .. .. .. .. .. ..@ ringDir: int 1
  .. .. .. .. .. .. ..@ coords : num [1:5, 1:2] 513051 513054 513054 513051 513051 ...

......

.. .. .. .. .. [list output truncated]
  .. .. .. ..@ plotOrder: int [1:191] 18 118 101 168 110 148 61 135 166 90 ...
  .. .. .. ..@ labpt    : num [1:2] 513181 4319787
  .. .. .. ..@ ID       : chr "0"
  .. .. .. ..@ area     : num 38206
  ..@ plotOrder  : int 1
  ..@ bbox       : num [1:2, 1:2] 512793 4319369 513380 4319807
  .. ..- attr(*, "dimnames")=List of 2
  .. .. ..$ : chr [1:2] "x" "y"
  .. .. ..$ : chr [1:2] "min" "max"
  ..@ proj4string:Formal class 'CRS' [package "sp"] with 1 slot
  .. .. ..@ projargs: chr "+proj=utm +zone=13 +datum=WGS84 +units=m +no_defs"

Answer 1

Ref Hong Ooi's answer in https://stackoverflow.com/questions/42059378/cant-use-operator-on-s4-objects-stored-in-a-list-in-r, I've worked out that the area value for individual Polygons in this object can be accessed via:

> xfile@polygons[[1]]@Polygons[[1]]@area
[1] 9.642906
> xfile@polygons[[1]]@Polygons[[2]]@area
[1] 1.854405

Now I just need to figure out how to filter on area. I think I see a lapply() fcn in my future.

Instead of lapply(), I found my way to purrr::keep():

("mba" = "minimum blob area")

smthd.filt@polygons <- smthd@polygons %>% purrr::keep(~min(.@area) >= mba)

Answer 2

Rather than working through the headache of accessing slots using sapply, I would recommend just using rgeos::gArea (or it's sf analog sf::st_area) and filter using the vector. In R ordering is your friend. In this case, the resulting vector from rgeos::gArea will match the SpatialPolygonsDataFrame so, you can just pull indices from the vector to operate on the polygons.

Add packages (note; adding sf for the nc polygon data). Need to reproject the polygons so they are in a planar coordinate space. We are wrapping st_read in as to coerce to a sp class object. This is a good thing to know when working with sp objects as, st_read is much faster than rgdal:readOGR and allow for queries.

library(sf)
library(sp)
library(rgeos)

nc = as(st_read(system.file("shape/nc.shp", 
        package="sf")), "Spatial")
  nc <- spTransform(nc, CRS("ESRI:102003"))

We can now get the area of each polygon and subset based on the area. We use which to return an index of our query [area < 1270326706] which is the mean of the polygon areas. Using a standard bracket index (operating on rows) and a minus sign, we can remove the polygons from our which index.

( a <- gArea(nc, byid=TRUE) )
nc.sub <- nc[-which(a < 1270326706),]

plot(nc)
  plot(nc.sub, col="blue", add=TRUE)