Extract values from raster matching csv and raster filenames

Question

I have a folder with many csv files. Each file has several columns as well as lat and long columns. Another folder have many rasters in tif format. The .csv files are named based on Julian date (e.g. 251.csv), and so the rasters (e.g. 251.tif). I would like to be able to add the raster value to the csv with matching name and save to a new csv in R. What I want to achieve is this:

raster<-raster("c:/temp/TIFF/2001/273.tif")
points<-read.csv("c:/temp/csv/2001/273.csv")
coordinates(points)=~long+lat
rasValue=extract(raster,points)
combinePointValue <- cbind(points,rasValue)
head(combinePointValue)
library(spdplyr)
combinePointValue <- combinePointValue %>% 
  rename(chloro = 10)
write.table(combinePointValue,file="c:/temp/2001/chloro/273_chloro.csv",append=FALSE, 
sep=",",row.names=FALSE, col.names=TRUE)

Considering the many csv and many tif files, I would prefer avoiding having to type this over and over.

Anyone able to help?

Answer 1

Here's a function (untested) that takes a number and makes the paths and does the work:

process_one = function(d){

folder = "c:/temp/TIFF/2001"
rasterinput = file.path(folder, paste0(d,".tif"))
pointsinput = file.path(folder, paste0(d,".csv"))

output = file.path("C:/temp/2001/chloro/", paste0(d,"_chloro.csv"))

message("Reading from ",rasterinput, " and ",pointsinput)
message("Writing to ",output)

raster<-raster(rasterinput)
points<-read.csv(pointinput)
coordinates(points)=~long+lat
rasValue=extract(raster,points)
combinePointValue <- cbind(points,rasValue)

## is this what that mutate pipeline is doing? 
combinePointValue$chloro = 10

write.table(combinePointValue,file=output,append=FALSE, 
sep=",",row.names=FALSE, col.names=TRUE)

message("...done")

}

Then you loop:

for(dd in 200:250){
 process_one(dd)
}

which will say stuff like this (I don't actually have these files, so this is a smaller function that just prints the names):

Reading from c:/temp/TIFF/2001/200.tif and c:/temp/TIFF/2001/200.csv
Writing to C:/temp/2001/chloro//200_chloro.csv
Reading from c:/temp/TIFF/2001/201.tif and c:/temp/TIFF/2001/201.csv
Writing to C:/temp/2001/chloro//201_chloro.csv