您可以跟踪在散列map中发现的顶点位置 set中的重复顶点只需执行一次过程:

#include <Rcpp/Lightest>
#include <map>
#include <set>
#include <tuple>

typedef std::tuple<double, double, double> Point3;

// [[Rcpp::export()]]
Rcpp::List duplicated_vertices(Rcpp::NumericMatrix x) {
    std::map<Point3, Rcpp::IntegerVector> positions;
    std::set<Point3> duplicates;

    for (R_len_t i = 0; i < x.ncol(); ++i) {
        Point3 vertex = { x(0, i), x(1, i), x(2, i) };
        if (positions.count(vertex) == 0) {
            Rcpp::IntegerVector position = { i + 1 };
            positions.emplace(vertex, position);
        } else {
            duplicates.insert(vertex);
            positions.at(vertex).push_back(i + 1);
        }
    }

    Rcpp::List result;
    for (const Point3& vertex: duplicates) {
        result.push_back(positions.at(vertex));
    }

    return result;
}

在我的机器上，与duplicated()相比，我获得了大约10倍的加速:

> set.seed(123)
> N <- 150
> M <- matrix(sample(c(1, 2, 3), N * 3, replace = TRUE), 3, N)
> 
> microbenchmark::microbenchmark(
+   Rcpp = dupes(M),
+   R = duplicated(t(M), fromLast = TRUE),
+   cpp_map = duplicated_vertices(M)
+ )
Unit: microseconds
    expr   min     lq    mean median    uq    max neval
    Rcpp 458.7 468.50 490.049  476.6 487.5 1092.7   100
       R 329.2 339.45 408.056  347.6 361.7 5103.3   100
 cpp_map  45.1  47.60  59.972   48.9  52.0  880.7   100