require(inline)
require(RcppArmadillo)

## extract cosine similarity between columns
cosine <- function(x) {
    y <- t(x) %*% x
    res <- 1 - y / (sqrt(diag(y)) %*% t(sqrt(diag(y))))
    return(res)
}

cosineRcpp <- cxxfunction(
  signature(Xs = "matrix"),
  plugin = c("RcppArmadillo"),
  body='
    Rcpp::NumericMatrix Xr(Xs);  // creates Rcpp matrix from SEXP
    int n = Xr.nrow(), k = Xr.ncol();
    arma::mat X(Xr.begin(), n, k, false); // reuses memory and avoids extra copy
    arma::mat Y = arma::trans(X) * X; // matrix product
    arma::mat res = (1 - Y / (arma::sqrt(arma::diagvec(Y)) * arma::trans(arma::sqrt(arma::diagvec(Y)))));
    return Rcpp::wrap(res);
')

mat <- matrix(rnorm(100000), ncol=1000)

x <- cosine(mat)
y <- cosineRcpp(mat)
identical(x, y)
[1] TRUE