# matrixStats: Functions that Apply to Rows and Columns of Matrices (and to Vectors)

## Introduction

The matrixStats package provides highly optimized functions for
computing common summaries over rows and columns of matrices,
e.g. `rowQuantiles()`

. There are also functions that operate on
vectors, e.g. `logSumExp()`

. Their implementations strive to minimize
both memory usage and processing time. They are often remarkably
faster compared to good old `apply()`

solutions. The calculations are
mostly implemented in C, which allow us to optimize beyond what is
possible to do in plain R. The package installs out-of-the-box on all
common operating systems, including Linux, macOS and Windows.

## Example

With a matrix

`> x <- matrix(rnorm(20 * 500), nrow = 20, ncol = 500)`

it is many times faster to calculate medians column by column using

`> mu <- matrixStats::colMedians(x)`

than using

`> mu <- apply(x, MARGIN = 2, FUN = median)`

Moreover, if performing calculations on a subset of rows and/or columns, using

`> mu <- colMedians(x, rows = 33:158, cols = 1001:3000)`

is much faster and more memory efficient than

`> mu <- apply(x[33:158, 1001:3000], MARGIN = 2, FUN = median)`

## Benchmarks

For formal benchmarking of matrixStats functions relative to alternatives, see the Benchmark reports.

## Design goals

The objectives of the **matrixStats** package is to perform operations
on matrices (i) as faster as possible, while (ii) not using
unnecessary amounts of memory. These objectives drive the design,
including the choice of the different defaults.

## Installation

R package matrixStats is available on CRAN and can be installed in R as:

`install.packages("matrixStats")`

### Pre-release version

To install the pre-release version that is available in Git branch `develop`

on GitHub, use:

`remotes::install_github("HenrikBengtsson/matrixStats", ref="develop")`

This will install the package from source. Because of this and because this package also compiles native code, Windows users need to have Rtools installed and macOS users need to have Xcode installed.

## Contributing

To contribute to this package, please see CONTRIBUTING.md.