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https://github.com/HenrikBengtsson/matrixStats
R package: Methods that Apply to Rows and Columns of Matrices (and to Vectors)
https://github.com/HenrikBengtsson/matrixStats
cran matrix package performance r vector
Last synced: about 2 months ago
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R package: Methods that Apply to Rows and Columns of Matrices (and to Vectors)
- Host: GitHub
- URL: https://github.com/HenrikBengtsson/matrixStats
- Owner: HenrikBengtsson
- Created: 2014-06-14T23:59:10.000Z (about 10 years ago)
- Default Branch: develop
- Last Pushed: 2024-05-14T18:50:56.000Z (about 2 months ago)
- Last Synced: 2024-05-15T15:14:49.963Z (about 2 months ago)
- Topics: cran, matrix, package, performance, r, vector
- Language: R
- Homepage: https://cran.r-project.org/package=matrixStats
- Size: 6.19 MB
- Stars: 198
- Watchers: 24
- Forks: 33
- Open Issues: 53
-
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
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README
# 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
```r
> x <- matrix(rnorm(20 * 500), nrow = 20, ncol = 500)
```
it is [many times faster] to calculate medians column by column using
```r
> mu <- matrixStats::colMedians(x)
```
than using
```r
> mu <- apply(x, MARGIN = 2, FUN = median)
```
Moreover, if performing calculations on a subset of rows and/or
columns, using
```r
> mu <- colMedians(x, rows = 33:158, cols = 1001:3000)
```
is much faster and more memory efficient than
```r
> 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.
[many times faster]: https://www.jottr.org/2015/01/matrixStats-0.13.1.html
[Benchmark reports]: https://github.com/HenrikBengtsson/matrixStats/wiki/Benchmark-reports
## Installation
R package matrixStats is available on [CRAN](https://cran.r-project.org/package=matrixStats) and can be installed in R as:
```r
install.packages("matrixStats")
```
### Pre-release version
To install the pre-release version that is available in Git branch `develop` on GitHub, use:
```r
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](https://cran.r-project.org/bin/windows/Rtools/) installed and macOS users need to have [Xcode](https://developer.apple.com/xcode/) installed.
## Contributing
To contribute to this package, please see [CONTRIBUTING.md](CONTRIBUTING.md).