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Well, I share that concern. But note that the low Rook value was not only
based on the result of Q-2R assymetric testing. I also played R-BP and
NN-RP, which ended unexpectedly bad for the Rook, and sets the value of
the Rook compared to that of the minor pieces. While the value of the
Queen was independently tested against that of the minor pieces by playing
Q-BNN.

The low difference between R and B does make sense to me now, as the wider
board should upgrade the Bishop a lot more than the Rook. The Bishop gets
extra forward moves, and forward moves are worth a lot more than lateral
moves. I have seen that in testing cylindrical pieces, (indicated by *),
where the periodic boundary condition w.r.t. the side edges effectifely
simulates an infinitely wide board. In a context of normal Chess pieces,
B* = B+P, while R* = R + 0.25P. OTOH, Q* = Q+2P. So it doesn't surprise
me that on wider boards R loses compared to Q and B.

I can think of several systematic errors that lead to unrealistically poor
performance of the Rook in asymmetric playtesting from an opening position.
One is that Capablanca Chess is a very violent game, where the three
super-pieces are often involved in inflicting an early chekmate (or nearly
so, where the opponent has to sacrifice so much material to prevent the
mate, that he is lost anyway). The Rooks initially offer not much defense
against that. But your chances for such an early victory would be strongly
reduced if you were missing a super-piece. So perhaps two Rooks would do
better against Q after A and C are traded. This explanation would do
nothing for explaining poor Rook performance of R vs B, but perhaps it is
B that is strong (it is also strong compared to N). The problem then would
be not so much low R value, but high Q value, due to cooperativity between
superpieces. So perhaps the observed scores should not be entirely
interpreted as high base values for Q, C and A, but might be partly due to
super-piece pair bonuses similar to that for the Bishop pair. Which I would
then (mistakenly) include in the base value, as the other super-pieces are
always present in my test positions.

Another possible source of error is that the engine plays a strategy that
is not well suited for playing 2R vs Q. Joker80's evaluation does not
place a lot of importance to keeping all its pieces defended. In general
this might be a winning strategy, giving the engine more freedom in using
its pieces in daring attacks. But 2R vs Q might be a case where this
backfires, and where you can only manifest the superiority of your Rook
force by very careful and meticulous, nearly allergic defense of your
troops, slowly but surely pushing them forward. This is not really the
style of Joker's play. So it would be interesting to do the asymmetreic
playtesting for Q vs 2R also with other engines. But TJchess10x8 only
became available long after I started my piece value project, TSCP-G does
not allow setting up positions (although now I know a work-around for
that, forcing initial moves with both ArchBishops to capture all pieces to
delete, and then retreating them before letting the engine play). And Smirf
initially could not play automatically at all, and when I finally made a WB
adapter for it so that it could, fast games by it where more decided by
timing issues than by play quality (many losses on time with scores like
+12!). And Fairy-Max is really a bit too simplistic for this, not knowing
the concept of a Bishop pair or passed pawns, besides being a slower
searcher.