Aster Analysis User Group

If you're having code problems, please provide a reproducible example script (example.R) and any necessary data files (example_data.csv) so we can help you as quickly as possible!  If you don't want to post your data publicly, then you don't have to.  You can start the discussion without an example script.  But you will get help faster, and -- what is more important -- other people can see what the issue was -- if you do post an example script with data.  It is simplest if you save an RData object (using the R function save) and then load that in your example (using the R function load) and the RData object contains nothing not needed to run the example.  We don't care how you got to that data only that it causes problems for some function or functions in the aster package (or aster2 package if you are trying to use that).  And just a data frame plus pred, fam, and famlist (if not using the default for that) won't tell anyone much about what your data are about.

Ideally, this script should be runnable from the (unix, linux, Mac OS X, Windows) command-line by 

    R CMD BATCH --vanilla example.R

If you're not familiar with the command-line, you can do the same thing from within R with the R statement

    system("R CMD BATCH --vanilla example.R")

The "-- vanilla" in the above command makes R start in a clean environment so what it does for you it will also do for us.  Thus the file "example.R" needs to define everything it uses. Also, when reading a data file *do not* provide a absolute link on your own hard drive, but just read the file from the same directory

    read.csv(file = "example_data.csv")

or

    load("example.rda")

if loading a previously saved RData file made with

    save(pred, fam, redata, file = "example.rda")

(or perhaps more objects besides pred, fam, redata -- include whatever is needed to make the example run and nothing else)

More information on batch processing here.