Matrix calculus is a bit screwy when you realize that there are two possible notations to represent matrix derivatives (numerator vs. denominator layout; numerator layout is used in this guide). Plus, the notation is not very "speaking" for doing calculations unless you commit to memory some basic results.. which is why, as a physicist, I would recommend working in tensor calculus notation during calculations, and tr…
I was also surprised when I saw that there was no standard notation for Jacobian matrices. We use the numerator notation in the article, but point out that there are papers that use the denominator notation. I think I remember from engineering school that we used numerator notation so we stuck with that.
Index notation also seems natural for programming: an element A[i,j] or a slice Z[3,4,:] are precisely this.