• This is very cool, but you didn't mention it takes forever to run. (And for a busy guy, too!)

    The bash script clocked in for me at about 34 minutes. I haven't had the patience to let the
    g <- graph.adjacency(y, mode="directed", weighted=TRUE, add.rownames=TRUE)

    ...run all the way through yet, but somewhere more than 20 minutes.

  • I may also have found an error in your showlinkage function, but debugging it is beyond me. (This whole thing is beyond me, but excellent and well done.)

    Line 20:
    df <- df1==1 | rownames(df)==package), which(df[which(rownames(df)==package), ]==1)), c(which(df[package]==1 | rownames(df)==package), which(df[which(rownames(df)==package), ]==1))]

    Seems to be missing a left paren somewhere before
    "df <- df1==1 | rownames(df)==package)" and df1 is undefined elsewhere? This maybe a typo for subsetting df[]?

    The other issue is line 5---are you intending to use "<<-" scoping assignment for rc? That shouldn't matter if it doesn't already exist, right?

    Again, this is super cool. Any pointers you can give for replicating are appreciated.

  • I was wondering if you ever thought of changing the
    page layout of your site? Its very well written; I love
    what youve got to say. But maybe you could a little more in the way of content so people
    could connect with it better. Youve got an awful lot of
    text for only having 1 or 2 images. Maybe you could
    space it out better?