README.md

In RcppColMetric: Efficient Column-Wise Metric Computation Against Common Vector

RcppColMetric

Package: RcppColMetric 0.1.0 Author: Xiurui Zhu Modified: 2025-03-08 18:17:18 Compiled: 2025-03-08 18:17:53

The goal of RcppColMetric is to efficiently compute metrics between various vectors and a common vector. This is common in data science, such as computing performance metrics between each feature and a common response. Rcpp is used to efficiently iterate over vectors through compiled code. You may extend its utilities by providing custom metrics that fit into the framework.

Installation

You can install the released version of RcppColMetric from CRAN with:

install.packages("RcppColMetric")

Alternatively, you can install the developmental version of RcppColMetric from github with:

remotes::install_github("zhuxr11/RcppColMetric")

Examples

library(cbbinom)

We use cats from MASS to illustrate the use of the package.

library(MASS)
data(cats)
print(head(cats))
#>   Sex Bwt Hwt
#> 1   F 2.0 7.0
#> 2   F 2.0 7.4
#> 3   F 2.0 9.5
#> 4   F 2.1 7.2
#> 5   F 2.1 7.3
#> 6   F 2.1 7.6

Column-wise ROC-AUC

In binary classification modelling, it is a common practice to compute ROC-AUC of each feature (usually columns) against a common target. RcppColMetric provides a much faster version than its commonly used counterparts, e.g. caTools::colAUC().

library(caTools)
(col_auc_bench <- microbenchmark::microbenchmark(
  col_auc_r = caTools::colAUC(cats[, 2L:3L], cats[, 1L]),
  col_auc_cpp = col_auc(cats[, 2L:3L], cats[, 1L]),
  times = 100L,
  check = "identical"
))
#> Unit: microseconds
#>         expr     min       lq     mean   median       uq     max neval
#>    col_auc_r 514.600 544.2005 623.3241 613.2515 666.1505 985.601   100
#>  col_auc_cpp 200.401 222.2010 244.9679 236.0010 266.8010 391.501   100

As can be seen, the median speed of computation from RcppColMetric is 2.599 times faster.

If there are multiple sets of features and responses, you may use the vectorized version col_auc_vec(), which uses compiled code to speed up iterations and returns a list.

col_auc_vec(list(cats[, 2L:3L]), list(cats[, 1L]))
#> [[1]]
#>               Bwt      Hwt
#> F vs. M 0.8338451 0.759048

Column-wize mutual information

In classification modelling, it is another common practice to assess mutual information between features and a response if the features are discrete. RcppColMetric provides a much faster version than its commonly used counterparts, e.g. infotheo::mutinformation().

library(infotheo)
(col_mut_info_bench <- microbenchmark::microbenchmark(
  col_mut_info_r = sapply(round(cats[, 2L:3L]), infotheo::mutinformation, cats[, 1L]) %>%
    {matrix(., nrow = 1L, dimnames = list(NULL, names(.)))},
  col_mut_info_cpp = col_mut_info(round(cats[, 2L:3L]), cats[, 1L]),
  times = 100L,
  check = "identical"
))
#> Unit: microseconds
#>              expr      min       lq     mean   median        uq      max neval
#>    col_mut_info_r 1587.200 1685.351 1884.131 1766.001 1964.9510 4803.800   100
#>  col_mut_info_cpp  618.401  641.551  691.325  659.651  721.6015  943.101   100

As can be seen, the median speed of computation from RcppColMetric is 2.677 times faster.

If there are multiple sets of features and responses, you may use the vectorized version col_mut_info_vec(), which uses compiled code to speed up iterations and returns a list.

col_mut_info_vec(list(round(cats[, 2L:3L])), list(cats[, 1L]))
#> [[1]]
#>            Bwt       Hwt
#> [1,] 0.1346783 0.1620514

Extend the package with custom metric

You may implement your own metric by inheriting from RcppColMetric::Metric class with template arguments as feature SEXP (input, numeric here) and response SEXP (input, factor as integer here) types. For example, to compute range of each feature, define a RangeMetric class.

#include <RcppColMetric.h>
#include <Rcpp.h>
using namespace Rcpp;


// x: numeric (REALSXP), y: factor -> integer (INTSXP), output: numeric (REALSXP)
class 
RangeMetric: public RcppColMetric::Metric<REALSXP, INTSXP, REALSXP>
{
public:
  // Constructor
  RangeMetric(const RObject& x, const IntegerVector& y, const Nullable<List>& args = R_NilValue) {
    // This parameter is inherited from `Metric`, determining output dimension (number of rows)
    // For RangeMetric, the output dimension is 2 (min & max)
    output_dim = 2;
  }
  virtual Nullable<CharacterVector> row_names(const RObject& x, const IntegerVector& y, const Nullable<List>& args = R_NilValue) const override {
    // Determine the row names
    // If not used, it may return R_NilValue
    CharacterVector out = {"min", "max"};
    return out;
  }
  virtual NumericVector calc_col(const NumericVector& x, const IntegerVector& y, const R_xlen_t& i, const Nullable<List>& args = R_NilValue) const override {
    // Derive output value for each feature and the common response
    // For RangeMetric, the output is min & max
    NumericVector out = {min(x), max(x)};
    return out;
  }
};

Then, define the main function calling RcppColMetric::col_metric(), with corresponding feature SEXP (input, numeric here), response SEXP (input, factor as integer here) and output SEXP (output, numeric here) types.

NumericMatrix col_range(const RObject& x, const IntegerVector& y, const Nullable<List>& args = R_NilValue) {
  RangeMetric range_metric(x, y, args);
  NumericMatrix out = RcppColMetric::col_metric<REALSXP, INTSXP, REALSXP>(x, y, range_metric, args);
  return out;
}

Test this function with cats:

col_range(cats[, 2L:3L], cats[, 1L])
#>     Bwt  Hwt
#> min 2.0  6.3
#> max 3.9 20.5

To define vectorized version of the function, a wrapper function is defined to generate RangeMetric object (taking only x, y and args), and then passed on to the workhorse RcppColMetric::col_metric_vec().

RangeMetric gen_range_metric(const RObject& x, const IntegerVector& y, const Nullable<List>& args = R_NilValue) {
  RangeMetric out(x, y, args);
  return out;
}

// [[Rcpp::export]]
List col_range_vec(const List& x, const List& y, const Nullable<List>& args = R_NilValue) {
  List out = RcppColMetric::col_metric_vec<REALSXP, INTSXP, REALSXP>(x, y, &gen_range_metric, args);
  return out;
}

Test the vectorized function with cats:

col_range_vec(list(cats[, 2L:3L]), list(cats[, 1L]))
#> [[1]]
#>     Bwt  Hwt
#> min 2.0  6.3
#> max 3.9 20.5

RcppColMetric documentation built on April 4, 2025, 1:25 a.m.