Read binary raster files in R - r

Question

I want to read binary integers in R and convert them into raster grids.
The files have the following charterers:
NCols= 4320
NRows= 2160
pixel-size: 1/12=0.833 degrees
upper-left-lat: 90.0-1/24
upper-left-lon: -180.0+1/24
lower-right-lat: -90.0+1/24
lower-right-lon: 180.0
nodata= -5000
scale-factor= 10000
datatype: 16-bit signed integer
byte-order: big endian
Here is what I do:
file <-"http://nasanex.s3.amazonaws.com/AVHRR/GIMMS/3G/1980s/geo81aug15a.n07-VI3g"
dat <- readBin(file,what="integer", size=4, signed = TRUE, n = NRows * NCols, endian = "big")
r <- raster(nrow=2160, ncol=4320)
r[] <- dat
But this doesn't seem to be right, I appreciate any suggestions.
.

Answer 1

I built greenbrown from source (based on the files staged on GitHub) and found that it took considerably long to process one single file.
system.time(
r1 <- ReadVI3g("http://nasanex.s3.amazonaws.com/AVHRR/GIMMS/3G/1980s/geo81aug15a.n07-VI3g")
)
# user system elapsed
# 3.252 0.973 143.846
Therefore, I suggest to have a look at the gimms package which has been designed for this particular kind of data and, moreover, is available from CRAN. Note that in contrast to ReadVI3g, it does not offer automated quality control yet, but this feature is scheduled for the next version update. In the meantime, overlay from the raster package should be employed to discard low-quality values.
# install.packages("gimms")
library(gimms)
system.time({
## download file, see ?downloadGimms for further options
f <- updateInventory()
f <- downloadGimms(f[3], overwrite = TRUE) # download 3rd file in 'f', viz. geo81aug15a.n07-VI3g
## rasterize ndvi and flags
ndvi <- rasterizeGimms(f)
flag <- rasterizeGimms(f, flag = TRUE)
## perform quality control
r2 <- overlay(ndvi, flag, fun = function(x, y) {
x[y[] > 1] <- NA
return(x)
})
})
# user system elapsed
# 4.538 3.894 26.781
The two resulting images are obviously identical
> unique(r1 - r2, na.rm = TRUE)
[1] 0
but as you can see, the gimms-based code performs much faster. Moreover, it offers parallel functionality (via doParallel) in case you would like to download and process multiple files at once.

Answer 2

You can read such files with the greenbrown R package.
Install it in R with
install.packages("greenbrown", repos="http://R-Forge.R-project.org")
If that fails because the package needs to be rebuilt by its authors, an alternative is to first download the sources directly from the repo, and then install them manually, as explained in the greenbrown installation instructions. In the latter case you may also have to manually install a couple of packages that greenbrown depends on first: install.packages on Kendall, bfast, strucchange.
After installation, reading the raster from a URL is as easy as:
library(greenbrown)
r <- ReadVI3g("http://nasanex.s3.amazonaws.com/AVHRR/GIMMS/3G/1980s/geo81aug15a.n07-VI3g")
The object returned by greenbrown::ReadVI3g is a RasterLayer. We can display it with
plot(r)
which gives