Ported a short MATLAB script to R and one result came back as a matrix

You have them the wrong way round. MATLAB's .* is the matrix product and * is elementwise, same as R's *, so s should match as written. Look at w instead. c() gives a plain vector, not a column, and R recycles it across the matrix.

Backwards. In MATLAB * between matrices is the matrix product and .* is elementwise. R has it the other way round. * is elementwise and %*% is the product.

s <- A %*% w
s
#>      [,1]
#> [1,] 1.00
#> [2,] 1.25

w is fine as a plain vector. %*% treats it as a column when that's what makes the shapes fit. B matched only because A .* A and A * A are both elementwise. Dropping the dot was right for that line and wrong for the other.

Right, I had them swapped. The dot is MATLAB's elementwise marker, which is exactly why R never needed one. The c() point holds, though, a plain vector has no orientation and %*% picks one for it.

The R line computes something real, just not MATLAB's A * w. R recycles w down each column, so row i is multiplied by w[i]. That is MATLAB's A .* w with w as a column. Your 2 by 2 result is correct for that expression.

And it does that without a word because the lengths divide. Recycling warns only when the longer length isn't a multiple of the shorter one, and four elements over two weights divides evenly. A three-element w would at least have complained. When the weights really are per row I'd rather write sweep(A, 1, w, "*") and have the intent on the page.

Same trap, more symbols. MATLAB A^2 is the matrix power, A * A. R A^2 squares each element. MATLAB A' transposes, t(A) in R for a real matrix. MATLAB A \ b solves the system, solve(A, b) in R, and / between matrices is a solve in MATLAB too, while R divides element by element. Go through the script and check every *, ^ and / with a matrix on both sides.

That was it, thank you. s <- A %*% w gives 1 and 1.25 now. It comes back as a 2 by 1 matrix, so it goes through drop() before landing in the data frame. The full script has an A^2 further down too, and pgr's list caught it before it could become the next mystery.