How to use data in a text file? - r

Question

Given three rasters, I need to extract values corresponding to u (row) = 5 and c (column) from a text file smoke.
smoke <- matrix(c(5, 4, 2, 9, 2, 2), ncol=2, byrow=TRUE)
The function I'm using is:
library(raster)
r <- raster(nrows=10, ncols=10)
r <- setValues(r, 1:ncell(r))
func <- function(c, u, sit){
rasters <- mget(c('r', paste0('r', 1:2)))
x <- sapply(rasters, function(x) getValues(x, c)[u])
y <- sapply(rasters, function(x) getValues(x, u)[c])
g <- data.frame(y, x)
write.table(g, paste0("res_", sit, u, "_", c, ".txt"))
}
Here's how I use the function to extract values that correspond to c and u in smoke:
res <- lapply(split(smoke[,c('c', 'u', 'sit')], 1:nrow(smoke)),
FUN=function(x) func(c=x[1], u=x[2], sit=x[3]))
I get this error: error: value for ‘r’ not found

Answer 1

By default, mget only looks for the objects r, r1, and r2 in the environment in which it's called, but in your case, those objects are in the global environment. You can either add inherits=TRUE to the mget call, which will force it to keep looking in parent environments, or else specify the environment to look in with envir=.GlobalEnv.
You have a couple of other problems, though.
First, r1 and r2 don't exist in your example.
Second, the list arising from split is a list of data frames, and you need to index them accordingly in your function. This means either using $ notation (e.g. x$c), double brackets (e.g. x[[1]]), or use a comma (e.g. x[, 1]).
Implementing all of this, you should have something like:
func <- function(c, u, sit) {
rasters <- mget(c('r', paste0('r', 1:2)), envir=.GlobalEnv)
x <- sapply(rasters, function(x) getValues(x, c)[u])
y <- sapply(rasters, function(x) getValues(x, u)[c])
g <- data.frame(y, x)
write.table(g, paste0("res_", sit, u, "_", c, ".txt"))
}
library(raster)
res <- lapply(split(smoke[, c('c', 'u', 'sit')], 1:nrow(smoke)),
function(x) func(c=x[[1]], u=x[[2]], sit=x[[3]]))
Finally, res will just be a list of NULL values, since your function returns the value of write.table, which is NULL. If you want func to return g, then add a final line to the function that simply reads g (or, explicitly, return(g)).
I'm not sure how closely your small example reflects your true data, but you could probably approach this more efficiently - see ?extract, ?cellFromRowCol, and ?stack, for example.