I'd was wondering how to best perform a test to determine test
disagreement (congruence test) in R?
Additional information can be found in Planet et al (DOI:
A common test seems the Shimodaira-Hasegawa Test (SH-test) which used to
be implemented in APE:
However, it seem to have disappeared in recent versions (e.g. ape 5.0).
Did this happen for a reason? Or maybe it has been replaced by a more
Failing this, is anyone aware of other software to perform SH-, KH- or
Thanks for any help!
Dr. Sebastian Müller
Department of Plant Sciences
University of Cambridge
Downing Street, Cambridge, CB2 3EA, UK
Phone: 0044 1223 748976
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