Support distmat as lower triangular for PAM #77
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
asardaes
changed the title
asardaes
force-pushed
the
feature/lower-triangular-distmat
branch
from
a72e187 to
0eaed23
Compare
asardaes
force-pushed
the
feature/lower-triangular-distmat
branch
from
b4f31a8 to
b7295e4
Compare
asardaes
force-pushed
the
feature/lower-triangular-distmat
branch
from
ecb41b2 to
b16581d
Compare
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Up until now, all the
proxy::distwrappers included in this package returned complete matrices regardless of the values of their input parameters. When discussing the space requirements for a cross-distance matrix's lower triangular, the dominant factor is the numerator inn² / 2, but when it comes to real use cases in current hardware, that half can be significant in terms of required RAM. Therefore, I've updated the code so that distances that can result in symmetric matrices can be handled with only the lower triangular values, but strictly speaking this will be a breaking change with respect to previous versions.Documentation has been updated, in particular to mention the
DistmatLowerTriangularreference class that can help in some common scenarios.