Fix Covy

[charliewang123]

• Reordered parameters: N, Y, W, G → N, W, G, Y

• Removed varzero = NULL initialization

• Moved pairs computation inside the sample size check and pre-allocated variab = numeric(nrow(pairs)) instead of growing with c()

• Cached pij() result in pij_val to avoid calling it twice per iteration

• Removed unnecessary sum() wrapping a scalar expression

• Updated man/Covy.Rd

• Updated tests to fix the parameter passing in the Covy() call

• Added N back to the signature and the docs

[Copilot]

Pull request overview

This PR fixes and optimizes the Covy() covariance estimator by reordering its arguments, reducing repeated computations, and improving how pairwise terms are accumulated, with corresponding doc/test updates.

Changes:

• Reordered Covy() parameters to N, w1, g1, w2, g2, W, G, Y, p, Ne, Ne_list and updated documentation accordingly.
• Refactored Covy() internals to pre-allocate variab and cache pij() results to avoid duplicate calls.
• Updated the Covy() unit test to match the new argument order.

Reviewed changes

Copilot reviewed 3 out of 3 changed files in this pull request and generated 2 comments.

File	Description
R/Covy.R	Reorders signature and refactors pairwise computation to avoid repeated calls and vector growth.
man/Covy.Rd	Updates usage/argument order to match the new Covy() signature.
tests/testthat/test-Covy.R	Updates the Covy() invocation to align with the reordered parameters.

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[Copilot]

The test call mixes a named argument (N = N) with positional arguments. This makes the test brittle to future signature changes (especially since this PR is about reordering args) and harder to read. Prefer passing all arguments by name (or pass N positionally as the first argument).

Suggested change

	c0010 <- Covy(N = N, 0,0,1,0, W, G, Y, p, Ne, Ne_list)
	c0010 <- Covy(N, 0,0,1,0, W, G, Y, p, Ne, Ne_list)

[Copilot]

The pairs creation and variab initialization are inside the if (...) { block but are not indented like the rest of the block. This makes it easy to misread the control flow and inconsistent with the surrounding style in this repo (e.g., other functions indent block bodies). Please indent these lines to clearly show they are guarded by the sample-size check.

Suggested change

	pairs <- expand.grid.unique(which(W == w1 & G == g1),
	which(W == w2 & G == g2),
	include.equals = FALSE)
	# Initialize
	variab = numeric(nrow(pairs))
	pairs <- expand.grid.unique(which(W == w1 & G == g1),
	which(W == w2 & G == g2),
	include.equals = FALSE)
	# Initialize
	variab = numeric(nrow(pairs))