Entropy from counts

[ms609]

rather than probabilities.
To optimize calls from TreeSearch.

[Copilot]

Pull Request Overview

This PR adds support for computing entropy directly from counts (integers) via a new entropy_int C++ function, exposes it in R as Ntropy(), and updates documentation and tests to cover this new capability.

• Introduce a log2_table lookup for fast integer entropy computations and register entropy_int via Rcpp.
• Add Ntropy() in R (with roxygen and NAMESPACE export) as an alias for entropy_int.
• Update tests and Rd documentation to verify both Entropy() and Ntropy() outputs.

Reviewed Changes

Copilot reviewed 7 out of 7 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
tests/testthat/test-information.R	Adjust test expectations order and add tests for entropy_int/Ntropy.
src/information.h	Define log2_table, compute it at load time, and implement entropy_int.
src/RcppExports.cpp	Register the new _TreeDist_entropy_int entry for R interface.
man/Entropy.Rd	Document Ntropy() alias and update argument/value descriptions.
R/tree_distance_utilities.R	Add Ntropy() wrapper with roxygen comments.
R/RcppExports.R	Expose entropy_int() in R for internal use.
NAMESPACE	Export Ntropy.

Comments suppressed due to low confidence (2)

tests/testthat/test-information.R:3

• [nitpick] The test description still refers only to Entropy; consider updating it to mention entropy_int/Ntropy so it's clear what behavior is being validated.

test_that("Entropy is calculated correctly", {

R/RcppExports.R:16

• [nitpick] Since entropy_int() is internal, you might prefix it with a dot (e.g. .entropy_int) or add a roxygen @export tag if it's meant for end users to avoid confusion.

entropy_int <- function(n) {

[Copilot]

Consider moving #include <Rcpp.h> from the header into the implementation file (.cpp) to reduce header dependencies and compile-time coupling.

[Copilot]

[nitpick] It may be safer to limit the linkage of log2_table by placing it in an anonymous namespace or marking it static to avoid potential symbol conflicts in large projects.

Suggested change

	double log2_table[LOG_MAX];
	static double log2_table[LOG_MAX];

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 99.09%. Comparing base (bc7bc10) to head (0891e4e).

Additional details and impacted files

@@           Coverage Diff           @@
##           master     #133   +/-   ##
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  Coverage   99.08%   99.09%           
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  Files          37       37           
  Lines        2625     2638   +13     
=======================================
+ Hits         2601     2614   +13     
  Misses         24       24           

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