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Rewrites lingering github.com / *.sr.ht references to this Gitea instance, translating GitHub and Sourcehut URL shapes to Gitea's (/blob/<ref>/ and sr.ht /tree/<ref>/item/ -> /src/branch/<ref>/, /tree/<tag> -> /src/tag/<tag>, /actions/workflows/X -> /actions?workflow=X, /edit/ -> /_edit/). Left pointing at the old hosts on purpose: pull-request links (PRs were not migrated), forks that were never migrated, and GitHub-only surfaces Gitea lacks. OpenPGP identity proofs are untouched by design.
111 lines
3.5 KiB
Markdown
111 lines
3.5 KiB
Markdown
# megapermute
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A million permutation hypothesis test utility.
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## Installation
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1. If you don't already have rust installed, [install it](https://www.rust-lang.org/tools/install).
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2. Then run: `cargo install --git https://git.swaits.com/swaits/megapermute`
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## Usage
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`megapermute` is a command-line utility which reads two input files,
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`control.dat` and `treatment.dat`. Each is a text file containing a list of
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numbers, treated internally as 64-bit floating point numbers.
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- `control.dat`: the control sample
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- `treatment.dat`: the treatment sample
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With these two files in the current directory, running `megapermute` computes
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the empircal difference in means and p-value for the null hypothesis, that H_0
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is equivalent to H_a. You can think of p-value like the probability that the
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null hypothesis is true.
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### Example
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Given the following two input files:
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```bash
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~/tmp
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❯ bat control.dat
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───────┬───────────────────────
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│ File: control.dat
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───────┼───────────────────────
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1 │ 52
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2 │ 104
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3 │ 146
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4 │ 10
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5 │ 51
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6 │ 30
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7 │ 40
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8 │ 27
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9 │ 46
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───────┴───────────────────────
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~/tmp
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❯ bat treatment.dat
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───────┬───────────────────────
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│ File: treatment.dat
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───────┼───────────────────────
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1 │ 94
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2 │ 197
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3 │ 16
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4 │ 38
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5 │ 99
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6 │ 141
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7 │ 23
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───────┴──────────────────────
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```
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Running `megapermute` should yield results like this:
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```bash
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~/tmp
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❯ megapermute
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mu_control = 56.22222222222222
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mu_treatment = 86.85714285714286
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(mu_treatment - mu_control) = 30.63492063492064
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p-value = 0.139556
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```
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## Performance
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My goal with this was to take advantage of multiple cores by using
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[`rayon`](https://crates.io/crates/rayon) iterators to compute the permutation
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hypothesis test quickly. As of January 2022, this application can do one
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million permutations on the example dataset listed above in 39.4 ms (N=69,
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SD=2.6 ms), which is on the order of 25M permutations/second.
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```bash
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~/tmp
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❯ hyperfine megapermute
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Benchmark 1: megapermute
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Time (mean ± σ): 39.4 ms ± 2.6 ms [User: 499.3 ms, System: 10.2 ms]
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Range (min … max): 35.1 ms … 48.4 ms 69 runs
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```
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Benchmark machine info:
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```bash
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~/tmp
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❯ neofetch
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'c. stephenwaits@SWaits-Mac-01.local
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,xNMM. --------------------------------
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.OMMMMo OS: macOS 11.6.1 20G224 x86_64
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OMMM0, Host: MacBookPro16,1
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.;loddo:' loolloddol;. Kernel: 20.6.0
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cKMMMMMMMMMMNWMMMMMMMMMM0: Uptime: 31 days, 21 hours, 23 mins
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.KMMMMMMMMMMMMMMMMMMMMMMMWd. Packages: 149 (brew)
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XMMMMMMMMMMMMMMMMMMMMMMMX. Shell: zsh 5.8
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;MMMMMMMMMMMMMMMMMMMMMMMM: Resolution: 3840x2160, 1920x1080
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:MMMMMMMMMMMMMMMMMMMMMMMM: DE: Aqua
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.MMMMMMMMMMMMMMMMMMMMMMMMX. WM: Amethyst
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kMMMMMMMMMMMMMMMMMMMMMMMMWd. Terminal: WezTerm
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.XMMMMMMMMMMMMMMMMMMMMMMMMMMk CPU: Intel i9-9880H (16) @ 2.30GHz
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.XMMMMMMMMMMMMMMMMMMMMMMMMK. GPU: Intel UHD Graphics 630, AMD Radeon Pro 5500M
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kMMMMMMMMMMMMMMMMMMMMMMd Memory: 21514MiB / 32768MiB
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;KMMMMMMMWXXWMMMMMMMk.
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.cooc,. .,coo:.
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```
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