Converting a raster to a csv in R - r

Question

I wish to convert a raster to a csv file. I have tried to convert a raster to a dataframe on one file just to see if it works. I have tried using:
as.data.frame( rasterToPoints(species) )
but I get an error when I try to write "species" to a csv :
Error in as.data.frame.default(x[[i]], optional = TRUE) :
cannot coerce class "structure("RasterLayer", package = "raster")" to a data.frame
This is my code (I need to convert multiple rasters to csv (see the loop))
#start loop
file.names <- dir(path, pattern=".csv")
for(i in 1:length(file.names)){
file<- read.csv(file.name[i], header = TRUE, stringsAsFactors=FALSE)
#subsetting each file and renaming column header names
sub.file<-subset(file, select = c('Matched.Scientific.Name', 'Vernacular.Name...matched', 'Latitude...processed', 'Longitude...processed'))
names(sub.file) <- c('species', 'name', 'Lat','Lon')
#turn into a SpatialPointsDataFrame
coordinates(sub.file) <- ~ Lon + Lat
proj4string(sub.file) <- '+init=EPSG:4326'
plot(sub.file, axes=TRUE)
#converting to BNG
sub.file.BNG <- spTransform(sub.file, '+init=EPSG:27700')
plot(sub.file.BNG, axes=TRUE)
#creating template raster
template <- raster(xmn=400000, xmx=600000, ymn=200000, ymx=800000, res=25000, crs='+init=EPSG:27700')
#point data > presence grid
species <- rasterize(sub.file.BNG, template, field=1)
plot(species)
# UK wide
template <- raster(xmn=-200000, xmx=700000, ymn=0, ymx=1250000, res=25000, crs='+init=EPSG:27700')
# use that to turn species point data into a presence grid
species <- rasterize(sub.file, template, field=1)
plot(species)
#converting a raster>dataframe>csv?????
as.data.frame( rasterToPoints(species) )
}

Answer 1

Always provide some example data when asking a question.
library(raster)
f <- system.file("external/test.grd", package="raster")
r <- raster(f)
To get the cell values
x <- as.data.frame(r)
head(x, 2)
# test
#1 NA
#2 NA
To get the cell coordinates and values, only for cells that are not NA
x <- rasterToPoints(r)
head(x, 2)
# x y test
#[1,] 181180 333740 633.686
#[2,] 181140 333700 712.545
To get the cell coordinates and values, only for all cells (including NA)
x <- cbind(coordinates(r), v=values(r))
head(x, 2)
# x y v
#[1,] 178420 333980 NA
#[2,] 178460 333980 NA
Whichever one you choose, you can then do
write.csv(x, "test.csv")
The mistake you made is that you did not assign the result of as.data.frame to a variable, and then tried to write the RasterLayer with write.csv. That is an error, and you get
write.csv(r)
#Error in as.data.frame.default(x[[i]], optional = TRUE) :
# cannot coerce class ‘structure("RasterLayer", package = "raster")’ to a
# data.frame
By the way, if you have multiple rasters, you may want to combine them first
s <- stack(r, r, r)
x <- rasterToPoints(s)
head(x, 2)
# x y test.1 test.2 test.3
#[1,] 181180 333740 633.686 633.686 633.686
#[2,] 181140 333700 712.545 712.545 712.545
write.csv(x, "test.csv")

Answer 2

Assuming your raster is "species"
species<- raster("C:/.../species.tif")
To perform this conversion, it is necessary to take the values of each pixel: X coordinates (1), Y coordinates (2) and own values of each cell (3).
# don't run these lines
#(1) = coordinates (species) [, 1]
#(2) = coordinates (species) [, 2]
#(3) = values (species)
Having these expressions we can add them to a dataframe as follows
dat<- data.frame("X"=coordinates(species)[,1],"Y"=coordinates(species)
[,2],"Values"=values(species))