Raster of multiple polygon associating values in R?

Question

I am new to R-Gis.

Here is what I need to do, I need to make a raster inside the larger polygon (image above) each cell has to be 10x10 m, mask it to cut cells outside the the larger polygon and then assign a different value for each cell in the smaller polygons. Furthermore, I'd like to have a list (dataframe) with the coordinate of the center of each cell and the value associated to it.

And here is my code (not much):

library(tidyverse)
library(sp)
library(raster)
coords <-structure(list(id = structure(c(1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 
                                        3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L), .Label = c("1.1", "2.1", "3.1", 
                                                                                    "3.2"), class = "factor"), lon = c(-47.720315, -47.7135780555556, 
                                                                                                                       -47.7122261111111, -47.7175261111111, -47.7187488888889, -47.715595, 
                                                                                                                       -47.7135130555556, -47.7166461111111, -47.7181161111111, -47.7169469444444, 
                                                                                                                       -47.71553, -47.716925, -47.7161630555556, -47.71552, -47.7139961111111, 
                                                                                                                       -47.7148438888889), lat = c(-22.5507461111111, -22.5456230555556, 
                                                                                                                                                   -22.549705, -22.5537280555556, -22.550825, -22.5479419444444, 
                                                                                                                                                   -22.5494280555556, -22.5521630555556, -22.5507561111111, -22.549725, 
                                                                                                                                                   -22.5507461111111, -22.5515380555556, -22.54924, -22.5486061111111, 
                                                                                                                                                   -22.5494769444444, -22.55026)), class = "data.frame", .Names = c("id", 
                                                                                                                                                                                                                    "lon", "lat"), row.names = c(NA, -16L))

coord.poly <- coords %>%
  nest(-id) %>%
  mutate(Poly = purrr::map(data, ~dplyr::select(., lon, lat) %>% Polygon()),
         polys = map2(Poly, id, ~Polygons(list(.x),.y))
  ) %>%
  {SpatialPolygons(.$polys)}

proj4string(coord.poly) <- CRS("+proj=utm +zone=23 +south +ellps=WGS84 +towgs84=0,0,0,0,0,0,0 +units=m +no_defs") 

r <- raster(coord.poly, ncol = 100, nrow = 100) #don't know how to set cell size in meters :/
r[] <- 1:length(r)

plot(mask(r, coord.poly), axes = TRUE)

EDIT: forgot to include the libraries

Answer 1

First, you cannot arbitrary assign a desired projection, you need to actually transform the data into a different projection.

Here we assign the correct projection and then transform the data into a UTM projection. It will also be easier to work with a SpatialPolygonsDataFrame so, we will coerce into this class as well.

utm = "+proj=utm +zone=23 +south +ellps=WGS84 +towgs84=0,0,0,0,0,0,0 +units=m +no_defs"

proj4string(coord.poly) <-"+proj=longlat +ellps=WGS84 +datum=WGS84" 

polys <- spTransform(coord.poly, utm)

polys <- SpatialPolygonsDataFrame(polys, 
             data.frame(ID=1:length(polys)),
                        match.ID = FALSE)

Now, we can create an empty raster to use in rasterizing your polygons. The result will be a unique raster value for each polygon.

r <- raster(extent(polys), crs=proj4string(polys),
            resolution=10)
r <- rasterize(polys, r, field=polys@data[,"ID"])

# if you just want the encompassing polygon you could use a 
#   bracket index to subset it:
#   r <- rasterize(polys[1,], r, field=polys@data[,"ID"][1])

plot(r)
  plot(polys, add=TRUE)

It is not clear exactly what you are after in manipulating your resulting raster but, here is an example where we assign random values to the raster values corresponding to polygon 4

r[r == 4] <- runif(length(r[r == 4]))   

plot(r)
  plot(polys, add=TRUE)

To get at the coordinates of the raster cells you can just coerce to a SpatialPointsDataFrame. The coordinates slot corresponds to each row in the @data slot containing a data.frame of the attributes.

r.pts <- as(r, "SpatialPointsDataFrame")
  head( coordinates(r.pts) )

It is redundant but you can add the coordinates to the data.frame using

r.pts@data <- data.frame(r.pts@data, coordinates(r.pts))
  head(r.pts@data)