In parsermd: Formal Parser and Related Tools for R Markdown Documents

Call Rcpp from knitr

library(knitr)
opts_chunk$set(cache = TRUE) # because the compilation takes time, let's cache it

When the chunk option engine='Rcpp' is specified (or you write the chunk header as ```{Rcpp}), the code chunk will be compiled through Rcpp via sourceCpp():

Test for fibonacci:

```{Rcpp, fibCpp}

include

// [[Rcpp::export]] int fibonacci(const int x) { if (x == 0 || x == 1) return(x); return (fibonacci(x - 1)) + fibonacci(x - 2); }

Because `fibonacci` was defined with the `Rcpp::export` attribute it can now be called as a normal R function:

```r
fibonacci(10L)
fibonacci(20L)

You can define multiple functions (or helper functions that are not exported) within Rcpp code chunks:

```{Rcpp, multipleCpp}

include

using namespace Rcpp;

// [[Rcpp::export]] NumericVector convolveCpp(NumericVector a, NumericVector b) {

int na = a.size(), nb = b.size();
int nab = na + nb - 1;
NumericVector xab(nab);

for (int i = 0; i < na; i++)
    for (int j = 0; j < nb; j++)
        xab[i + j] += a[i] * b[j];

return xab;

}

// [[Rcpp::export]] List lapplyCpp(List input, Function f) {

List output(input.size());

std::transform(input.begin(), input.end(), output.begin(), f);
output.names() = input.names();

return output;

}

If you want to link to code defined in another package (e.g **RcppArmadillo**) then you need to provide an `Rcpp::depends` attribute. For example:

```{Rcpp, lmCpp}
// [[Rcpp::depends(RcppArmadillo)]]

#include <RcppArmadillo.h>

using namespace Rcpp;

// [[Rcpp::export]]
List fastLm(NumericVector yr, NumericMatrix Xr) {

    int n = Xr.nrow(), k = Xr.ncol();

    arma::mat X(Xr.begin(), n, k, false); // reuses memory and avoids extra copy
    arma::colvec y(yr.begin(), yr.size(), false);

    arma::colvec coef = arma::solve(X, y);      // fit model y ~ X
    arma::colvec resid = y - X*coef;            // residuals

    double sig2 = arma::as_scalar( arma::trans(resid)*resid/(n-k) );
                                                // std.error of estimate
    arma::colvec stderrest = arma::sqrt(
                    sig2 * arma::diagvec( arma::inv(arma::trans(X)*X)) );

    return List::create(Named("coefficients") = coef,
                        Named("stderr")       = stderrest
    );
}

A test:

fastLm(rnorm(10), matrix(1:20, ncol = 2))

Finally, you can pass additional arguments to sourceCpp() via the chunk option engine.opts. For example, we can specify engine.opts=list(showOutput=TRUE, rebuild=FALSE) to show the output of R CMD SHLIB.