need more flexible function-internal references to data.frame columns

[davebraze]

There are places in the code where we do stuff like this:

data_den <- matrix(numeric(0), nrow(data[data$type!='oob',]), n_lines)

Such that references to particular data.frame columns are hardwired, either by name or by position. We need to make this more flexible, so that a user can optionally specify the column to be used (by either name or position), but with reasonable defaults.