Extract Values from Multiple Raster to CSV Using R – Guide

csvextractgeotiff-tiffrraster

I have multiple raster TIF files. I'm using R and want to extract a cell's attribute value from all rasters based on an latitude and longitude input, and saved in a single CSV file. The output should be formatted as follows:

      Lat          Long       Value*       Value**
     20.15        77.12        12            20

* denotes attribute values from raster 1.
** denotes attribute values from raster 2.

Can anyone help me in this?

Best Answer

EDIT 2: I provide a shorter version based on extract function from the raster package.

library(raster)
library(sp) # used to create a SpatialPoint object

# LOAD RASTERS INTO A LIST OBJECT. 
tmp <- lapply(list.files("D:/rasters", pattern = ".tif$", full.names = TRUE), raster)

# A DATA FRAME WITH THE FOLLOWING STRUCTURE IS REQUIRED
coords <- data.frame("lat" = c(-2.2, -13.76, 4.47), "lon" = c(5.97, 10.57, 8.7))

# NEW CODE STARTS HERE
pts <- SpatialPoints(coords = coords, 
              proj4string = CRS("+proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs "))

# THE NEXT LINE PROVIDES THE SAME OUTPUT AS THE FOLLOWING LONG CODE
as.data.frame(cbind(coords, do.call("rbind", lapply(tmp, extract, pts))))

I provide a generalized answer by making usage of a raster library functionality. It can be used to process multiple raster files and multiple lat-lon pairs.

The main idea is to use cellFromXY to get the cell index for a specific lat-lon pair. Then just extract the value using r[cellIndex], when r is a raster object.

This is given for a data frame with one row - i.e. only one pair of lat-lon, but you can easily wrap it with another lapply combined with rbind to iterate it over multiple lat-lon pairs.

EDIT: now you can run the code using multiple lat-lon points. Note that the input data.frame structure should be kept. 

library(magrittr) # I used piping in my answer (%>%)
library(raster)   # raster functionality in r

# Assuming my .tif files are in this path: "D:/rasters"    

# LOAD RASTERS INTO A LIST OBJECT. 
tmp <- lapply(list.files("D:/rasters", pattern = ".tif$", full.names = TRUE), raster)

# A DATA FRAME WITH THE FOLLOWING STRUCTURE IS REQUIRED
coords <- data.frame("lat" = c(-2.2, -13.76, 4.47), "lon" = c(5.97, 10.57, 8.7))

# RUN THE FOLLOWING TO GET A MATRIX WITH VALUES
cellData <- lapply(tmp, function(r) {
  apply(coords, MARGIN = 1, FUN = function(row) {
    # as.matrix(coords[row, c("lat", "lon")]) # print(row)
    cellIndex <- cellFromXY(r, row) # gives cell Index for lat/lon pair
    r[cellIndex]
  })
}) %>% do.call("cbind", .)

# BIND MATRIX AS A DATA FRAME
output <- as.data.frame(cbind(coords, cellData))

Finally my result for 3 rasters and 3 points looks like this:

results

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