update scripts to future proof against R 4.0.0+ updates

Merged Michaja Pehl requested to merge github/fork/0UmfHxcvx5J7JoaOhFSs5mncnisTJJ6q/develop into develop
  • https://stat.ethz.ch/pipermail/r-announce/2020/000653.html

    R now uses a stringsAsFactors = FALSE default, and hence by default no longer converts strings to factors in calls to data.frame() and read.table().

  • this breaks all instances of levels() being used on data.frames read using read.csv()

  • switching to unique() solves this

  • unique() used on factors (R < 4.0.0, currently on the cluster) still returns the same values as levels(), but as a factor, which does not cause problems (but is a little ugly in interactive use)

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