How can I loop through a list to create rasters and write them to .tif files?

Question

I received 3 .mat files that each contain several daily maps. I need to take them and get them into ArcMap (10.2 if that matters) as a .tif with spatial information. I have already used the R.matlab package to read the .mat files and successfully did it for one day, however I do not want to have to write hundreds of lines of code to repeat it for the remaining days. Here is my successful code:

library(R.matlab)
library(raster)
library(sp)
library(rgdal)

setwd("C:/Users/Heidi Church/Documents/Thesis/FSLE")

FSLE2006mat <- readMat("FSLEheidi2006.mat")
FSLE2007mat <- readMat("FSLEheidi2007.mat")
FSLE2008mat <- readMat("FSLEheidi2008.mat")

#Test on single day in 2006
x <- raster(FSLE2006mat$F2006812, xmn=152, xmx=155.5, ymn=47.5, ymx=50.5, crs="+proj=longlat +datum=WGS84")
plot(x, xlab="Latitude", ylab="Longitude", xlim=c(152,155.5), ylim=c(47.5,50.5), main="Submesoscale Fronts: August 12, 2006")
writeRaster(x, filename="FSLE_20060812.tif", format="GTiff", overwrite=TRUE)

I had tried doing both a for loop and lapply, however kept getting this error:

Error in .local(x, ...) : unused arguments (xmn = 152, xmx = 155.5, ymn = 47.5, ymx = 50.5, crs = "+proj=longlat +datum=WGS84")

Here are examples of each that I tried:

for (i in FSLE2006mat[1:16])
{
FSLE2006[i] <- raster(x=FSLE2006mat[i], xmn=152, xmx=155.5, ymn=47.5, ymx=50.5, crs="+proj=longlat +datum=WGS84")
}

FSLE2006 <- lapply(FSLE2006mat, (raster(x, xmn=152, xmx=155.5, ymn=47.5, ymx=50.5, crs="+proj=longlat +datum=WGS84")))
FSLE2006 <- lapply(FSLE2006mat, raster)
FSLE2006 <- lapply(FSLE2006mat[1:16], raster)

I am wondering how I can loop through all of the elements in the .mat list for each year, make them a raster with the spatial info noted, and write it to a .tif file to import into ArcGIS. I should also note that 1:16 is to only use the first 16 of 18 elements, as the last 2 are not needed.

Answer 1

Heidi's code may work, but is not very general. it still requires to copy/paste/edit the code for different years. I do not have the data, so I cannot check the below, but I would do something like this:

rasterFromMat <- function(m, crs="") {
    r <- raster(m[[1]], xmn=min(m$xvc), xmx=max(m$xvc), ymn=min(m$yvc), ymx=max(m$yvc), crs=crs)
    names(r) <- names(m[1])
    r
}

stackFromMat <- function(x, crs="+proj=longlat +datum=WGS84") {
    s <- lapply(1:(length(x)-2), function(i) rasterFromMat(x[[i]], crs=crs))
    stack(s)
}


s2006 <- stackFromMat(FSLE2006mat)
s2006 <- writeRaster(s2006, "FSLE2006.tif", overwrite=TRUE)

s2007 <- stackFromMat(FSLE2007mat)
s2007 <- writeRaster(s2007, "FSLE2007.tif", overwrite=TRUE)

Note that it might be useful not to write individual layers --- depending on your next steps, of course.

Answer 2

I have found a script that works for my question. This is the exact script that worked correctly, so please do not edit. For anyone with similar problems, here is what did work:

### Read matlab files in R
library(R.matlab)

FSLE2006mat <- readMat("FSLEheidi2006.mat")
FSLE2007mat <- readMat("FSLEheidi2007.mat")
FSLE2008mat <- readMat("FSLEheidi2008.mat")


### Make matlab files into rasters
library(raster)
library(sp)

### Script to loop through each date in 2006, make a raster, and stack them with 
### dates included in the names for each layer - THANKS TO BILL BEATTY AT USGS

r.1 <- raster(FSLE2006mat[[1]], xmn=min(FSLE2006mat$xvc), xmx=max(FSLE2006mat$xvc),
          ymn=min(FSLE2006mat$yvc), ymx=max(FSLE2006mat$yvc), 
          crs="+proj=longlat +datum=WGS84")
r.1@data@names <- names(FSLE2006mat[1])

for (i in 2:((length(FSLE2006mat))-2)) {
  r <- raster(FSLE2006mat[[i]], xmn=min(FSLE2006mat$xvc), xmx=max(FSLE2006mat$xvc),
          ymn=min(FSLE2006mat$yvc), ymx=max(FSLE2006mat$yvc), 
          crs="+proj=longlat +datum=WGS84")
  r@data@names <- names(FSLE2006mat[i])
  r.1  <- stack(r.1, r)
}

writeRaster(r.1, "FSLE2006.tif", format="GTiff", bylayer=T, suffix=names(r.1), overwrite=T)

I then was able to simply go through and use that same code for 2007 and 2008. In the end, this spat out .tif files for each date that I was able to open in R with all the specified spatial reference.