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Bioconductor / MatrixGenerics

S4 Generic Summary Statistic Functions that Operate on Matrix-Like Objects
https://bioconductor.org/packages/MatrixGenerics
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HEADS UP: New default for `ties.method` of {col,row}Ranks() #24

Open HenrikBengtsson opened 3 years ago

HenrikBengtsson commented 3 years ago

Background

matrixStats uses ties.method = "max" as the default for colRanks() and rowRanks() for legacy reasons, but we want eventually update to ties.method = "average" to align it with base::rank(), cf. https://github.com/HenrikBengtsson/matrixStats/issues/142.

The process for this migration with be:

  1. Give a deprecation warning if ties.method is not explicitly specified (long time; several releases)
  2. Give a defunct error if ties.method is not explicitly specified (long time; several releases)
  3. Switch the new default to ties.method = "average"

This will have to take a long time in order to make sure end-users out there will notice this and update their code. I hope this will minimize the risk for existing code all of a sudden start producing different results.

Issue

MatrixGenerics gives an ERROR when I revdep check asserting !isTRUE(missing(ties.method)), cf. https://github.com/HenrikBengtsson/matrixStats/blob/feature/default-rank-ties.method/revdep/R_MATRIXSTATS_TIES_METHOD_MISSING%3Ddefunct/problems.md#matrixgenerics