1

When using R in org mode source blocks, any NA (i.e. missing) values in tables get replaced with nil. Why is this?

And is there a way to change this (globally, or at the file level)? I regularly create reports using Org Babel that are to be read by non-Org users and while they do understand NA, nil means nothing to them.

2

I believe the reason lies in org-babel-R-write-object-command

(defconst org-babel-R-write-object-command "{
    function(object,transfer.file) {
        object
        invisible(
            if (
                inherits(
                    try(
                        {
                            tfile<-tempfile()
                            write.table(object, file=tfile, sep=\"\\t\",
                                        na=\"nil\",row.names=%s,col.names=%s,
                                        quote=FALSE)
                            file.rename(tfile,transfer.file)
                        },
                        silent=TRUE),
                    \"try-error\"))
                {
                    if(!file.exists(transfer.file))
                        file.create(transfer.file)
                }
            )
    }
}(object=%s,transfer.file=\"%s\")"

Try changing na=\"nil\" to na=\"NA\" or removing that argument.

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