Using the GRASS command g.list in R

Running grass commands within R is easy using either the system function or the spgrass6 package. But sometimes the GRASS outputs are not easy to read into a data frame or vector. For example, what if you want a vector with all raster data layers in mapset ‘species’.

EDIT: There is a much easier solution, see my next post. Read on if you want to see a much more cumbersome solution using gsub and strsplit to convert the output in a vector.

In GRASS you would use the function

g.list type=rast mapset=species

The output is not very easy to handle though, it looks e.g., like:

raster files available in mapset <species>:
Acacia_seyal              Warburgia_ugandensisv2
Acacia_seyalv2            Zanthoxylum_chalybeum
Albizia_gummifera         Zanthoxylum_chalybeumv2
(Tue Feb 22 23:15:17 2011) Command finished (0 sec)

In R (which should be run within GRASS), you can run one of the two lines below:

system("g.list type=rast mapset=species", intern=TRUE)
execGRASS("g.list", parameters=list(type="rast", mapset="species"), intern=TRUE)

However, the output is not easy to use in R without some further processing:

[1] "----------------------------------------------"
[2] "raster files available in mapset <species>:"
[3] "Acacia_seyal              Warburgia_ugandensisv2"
[4] "Acacia_seyalv2            Zanthoxylum_chalybeum"
[5] "Albizia_gummifera         Zanthoxylum_chalybeumv2"
[6] ""
[7] "----------------------------------------------"

The first and last two rows are easy to remove:

a <- execGRASS("g.list", parameters=list(type="rast", mapset="species"), intern=TRUE)

a <- a[-c(1,2,length(a)-1,length(a))]

The next two lines of code will replace the white spaces by a comma, split the vector elements using the comma as separator and combine all in one vector:

b <- as.vector(gsub('[[:space:]]+', ',', a))
c <- unlist(strsplit(b,","))

There you go, a nice vector with one layer name per vector element.

Thinks are getting a little bit more complicated if you want to list raster and vector layers or layers from more than one mapset. But that is for later.


One thought on “Using the GRASS command g.list in R

  1. Pingback: Using the GRASS command g.mlist in R | Ecostudies

Leave a Reply

Fill in your details below or click an icon to log in: Logo

You are commenting using your account. Log Out /  Change )

Google+ photo

You are commenting using your Google+ account. Log Out /  Change )

Twitter picture

You are commenting using your Twitter account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )


Connecting to %s