Removing individuals

[thoree]

I am not allowed to remove individuals 201, 202 and 203 in the pedigree below:

[magnusdv]

Thanks, I agree this looks like a bug.

The command pedtools::removeIndividuals(x, ids) which works behind the scenes here, is not very advanced: it removes ids and all their descendants. In your example that leaves an empty pedigree, hence the error message.

The problem of removing individuals (so that the result is a proper pedigree) is surprisingly confusing in general. For instance, suppose you remove individual 203 in your example. What should be the result? Here are 3 possibilities:

• Keep all the others, but loose the father-daughter connection between 201 and 102.
• Remove 201 as well, since he is a "single parent". Then 202 must also go (by the same argument), leaving only the bottom trio.
• Remove 203 and all her descendants (102 and 205), leaving the upper-left trio.

The last strategy, i.e., removing all descendants, is the one currently adopted by removeIndividuals().

As your example shows, the implementation clearly has room for improvement. I'll look into it!

[magnusdv]

This feature was rewritten in QuickPed 3.0.0, splitting the "Remove individuals" in two:

• Up: Removes ancestors. In the example above this corresponds to the first of the three options.
• Down: Removes descendants, e.g., the third option.