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https://github.com/karoliskoncevicius/matrixtests
R package for computing multiple hypothesis tests on rows/columns of a matrix or a data.frame
https://github.com/karoliskoncevicius/matrixtests
anova fast hypothesis-testing matrix package r rows t-test wilcoxon-test
Last synced: 28 days ago
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R package for computing multiple hypothesis tests on rows/columns of a matrix or a data.frame
- Host: GitHub
- URL: https://github.com/karoliskoncevicius/matrixtests
- Owner: karoliskoncevicius
- Created: 2017-03-14T21:53:02.000Z (almost 8 years ago)
- Default Branch: master
- Last Pushed: 2024-06-07T16:18:32.000Z (7 months ago)
- Last Synced: 2024-10-11T18:48:25.878Z (2 months ago)
- Topics: anova, fast, hypothesis-testing, matrix, package, r, rows, t-test, wilcoxon-test
- Language: R
- Homepage: https://cran.r-project.org/web/packages/matrixTests/index.html
- Size: 608 KB
- Stars: 36
- Watchers: 4
- Forks: 5
- Open Issues: 18
-
Metadata Files:
- Readme: README.md
- Funding: .github/FUNDING.yml
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# Matrix Tests #
A package dedicated to running multiple statistical hypothesis tests on rows and columns of matrices.
## Goals ##
1. Fast execution via vectorization.
2. Convenient and detailed output format.
3. Compatibility with tests implemented in base R.
4. Careful handling of missing values and edge cases.
## Examples ##
#### 1. Bartlett's test on columns ####
Bartlett's test on every column of iris dataset using Species as groups:
```r
col_bartlett(iris[,-5], iris$Species)
```
```
obs.tot obs.groups var.pooled df statistic pvalue
Sepal.Length 150 3 0.26500816 2 16.005702 0.0003345076070163084
Sepal.Width 150 3 0.11538776 2 2.091075 0.3515028004158132768
Petal.Length 150 3 0.18518776 2 55.422503 0.0000000000009229038
Petal.Width 150 3 0.04188163 2 39.213114 0.0000000030547839322
```
#### 2. Welch t-test on rows ####
Welch t-test performed on each row of 2 large (million row) matrices:
```r
X <- matrix(rnorm(10000000), ncol = 10)
Y <- matrix(rnorm(10000000), ncol = 10)
row_t_welch(X, Y) # running time: 2.4 seconds
```
Confidence interval computations can be turned-off for further increase in speed:
```r
row_t_welch(X, Y, conf.level = NA) # running time: 1 second
```
## Available Tests ##
| Variant | Name | Function |
|----------------------------------|---------------------------------------|------------------------------------|
| **Location tests (1 group)** | Single sample Student's t.test | `row_t_onesample` |
| | Single sample Wilcoxon's test | `row_wilcoxon_onesample` |
| **Location tests (2 groups)** | Equal variance Student's t.test | `row_t_equalvar` |
| | Welch adjusted Student's t.test | `row_t_welch` |
| | Two sample Wilcoxon's test | `row_wilcoxon_twosample` |
| **Location tests (paired)** | Paired Student's t.test | `row_t_paired` |
| | Paired Wilcoxon's test | `row_wilcoxon_paired` |
| **Location tests (2+ groups)** | Equal variance oneway anova | `row_oneway_equalvar` |
| | Welch's oneway anova | `row_oneway_welch` |
| | Kruskal-Wallis test | `row_kruskalwallis` |
| | van der Waerden's test | `row_waerden` |
| **Scale tests (2 groups)** | F variance test | `row_f_var` |
| **Scale tests (2+ groups)** | Bartlett's test | `row_bartlett` |
| | Fligner-Killeen test | `row_flignerkilleen` |
| | Levene's test | `row_levene` |
| | Brown-Forsythe test | `row_brownforsythe` |
| **Association tests** | Pearson's correlation test | `row_cor_pearson` |
| **Periodicity tests** | Cosinor | `row_cosinor` |
| **Distribution tests** | Kolmogorov-Smirnov test | `row_kolmogorovsmirnov_twosample` |
| **Normality tests** | Jarque-Bera test | `row_jarquebera` |
| | Anderson-Darling test | `row_andersondarling` |
## Further Information ##
For more information please refer to the [Wiki](https://github.com/karoliskoncevicius/matrixTests/wiki) page:
1. [Installation Instructions](https://github.com/karoliskoncevicius/matrixTests/wiki/Installation)
2. [Design Decisions](https://github.com/karoliskoncevicius/matrixTests/wiki/Design-Decisions)
3. [Speed Benchmarks](https://github.com/karoliskoncevicius/matrixTests/wiki/Benchmarks)
4. [Bug Fixes and Improvements to Base R](https://github.com/karoliskoncevicius/matrixTests/wiki/Bug-Fixes-and-Improvements-to-Base-R)
## See Also ##
### Literature ###
**Computing thousands of test statistics simultaneously in R**, *Holger Schwender, Tina Müller*.\
Statistical Computing & Graphics. Volume 18, No 1, June 2007.
### Packages ###
CRAN:
1. `ttests()` in the [**Rfast**](https://CRAN.R-project.org/package=Rfast) package.
2. `row.ttest.stat()` in the [**metaMA**](https://CRAN.R-project.org/package=metaMA) package.
3. `MultiTtest()` in the [**ClassComparison**](https://CRAN.R-project.org/package=ClassComparison) package.
4. `bartlettTests()` in the [**heplots**](https://CRAN.R-project.org/package=heplots) package.
5. `harmonic.regression()` in the [**HarmonicRegression**](https://CRAN.R-project.org/package=HarmonicRegression) package.
BioConductor:
1. `lmFit()` in the [**limma**](https://bioconductor.org/packages/release/bioc/html/limma.html) package.
2. `rowttests()` in the [**genefilter**](https://bioconductor.org/packages/release/bioc/html/genefilter.html) package.
3. `mt.teststat()` in the [**multtest**](https://www.bioconductor.org/packages/release/bioc/html/multtest.html) package.
4. `row.T.test()` in the [**HybridMTest**](https://www.bioconductor.org/packages/release/bioc/html/HybridMTest.html) package.
5. `rowTtest()` in the [**viper**](https://bioconductor.org/packages/release/bioc/html/viper.html) package.
6. `lmPerGene()` in the [**GSEAlm**](https://www.bioconductor.org/packages/release/bioc/html/GSEAlm.html) package.
GitHub:
1. `rowWilcoxonTests()` in the [**sanssouci**](https://github.com/pneuvial/sanssouci) package.
2. `matrix.t.test()` in the [**pi0**](https://github.com/gitlongor/pi0) package.
3. `wilcoxauc()` in the [**presto**](https://github.com/immunogenomics/presto) package.