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Added README and code of conduct.
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‎.Rbuildignore‎

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^\.Rproj\.user$
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^LICENSE\.md$
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^data-raw$
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^README\.Rmd$
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^CODE_OF_CONDUCT\.md$

‎CODE_OF_CONDUCT.md‎

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# Contributor Covenant Code of Conduct
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## Our Pledge
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We as members, contributors, and leaders pledge to make participation in our
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community a harassment-free experience for everyone, regardless of age, body
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size, visible or invisible disability, ethnicity, sex characteristics, gender
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identity and expression, level of experience, education, socio-economic status,
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nationality, personal appearance, race, caste, color, religion, or sexual
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identity and orientation.
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We pledge to act and interact in ways that contribute to an open, welcoming,
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diverse, inclusive, and healthy community.
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## Our Standards
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Examples of behavior that contributes to a positive environment for our
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community include:
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* Demonstrating empathy and kindness toward other people
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* Being respectful of differing opinions, viewpoints, and experiences
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* Giving and gracefully accepting constructive feedback
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* Accepting responsibility and apologizing to those affected by our mistakes,
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and learning from the experience
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* Focusing on what is best not just for us as individuals, but for the overall
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community
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Examples of unacceptable behavior include:
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* The use of sexualized language or imagery, and sexual attention or advances of
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any kind
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* Trolling, insulting or derogatory comments, and personal or political attacks
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* Public or private harassment
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* Publishing others' private information, such as a physical or email address,
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without their explicit permission
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* Other conduct which could reasonably be considered inappropriate in a
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professional setting
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## Enforcement Responsibilities
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Community leaders are responsible for clarifying and enforcing our standards of
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acceptable behavior and will take appropriate and fair corrective action in
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response to any behavior that they deem inappropriate, threatening, offensive,
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or harmful.
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Community leaders have the right and responsibility to remove, edit, or reject
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comments, commits, code, wiki edits, issues, and other contributions that are
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not aligned to this Code of Conduct, and will communicate reasons for moderation
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decisions when appropriate.
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## Scope
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This Code of Conduct applies within all community spaces, and also applies when
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an individual is officially representing the community in public spaces.
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Examples of representing our community include using an official e-mail address,
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posting via an official social media account, or acting as an appointed
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representative at an online or offline event.
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## Enforcement
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Instances of abusive, harassing, or otherwise unacceptable behavior may be
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reported to the community leaders responsible for enforcement at aymeric.stamm@cnrs.fr.
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All complaints will be reviewed and investigated promptly and fairly.
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All community leaders are obligated to respect the privacy and security of the
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reporter of any incident.
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## Enforcement Guidelines
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Community leaders will follow these Community Impact Guidelines in determining
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the consequences for any action they deem in violation of this Code of Conduct:
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### 1. Correction
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**Community Impact**: Use of inappropriate language or other behavior deemed
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unprofessional or unwelcome in the community.
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**Consequence**: A private, written warning from community leaders, providing
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clarity around the nature of the violation and an explanation of why the
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behavior was inappropriate. A public apology may be requested.
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### 2. Warning
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**Community Impact**: A violation through a single incident or series of
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actions.
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**Consequence**: A warning with consequences for continued behavior. No
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interaction with the people involved, including unsolicited interaction with
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those enforcing the Code of Conduct, for a specified period of time. This
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includes avoiding interactions in community spaces as well as external channels
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like social media. Violating these terms may lead to a temporary or permanent
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ban.
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### 3. Temporary Ban
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**Community Impact**: A serious violation of community standards, including
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sustained inappropriate behavior.
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**Consequence**: A temporary ban from any sort of interaction or public
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communication with the community for a specified period of time. No public or
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private interaction with the people involved, including unsolicited interaction
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with those enforcing the Code of Conduct, is allowed during this period.
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Violating these terms may lead to a permanent ban.
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### 4. Permanent Ban
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**Community Impact**: Demonstrating a pattern of violation of community
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standards, including sustained inappropriate behavior, harassment of an
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individual, or aggression toward or disparagement of classes of individuals.
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**Consequence**: A permanent ban from any sort of public interaction within the
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community.
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## Attribution
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This Code of Conduct is adapted from the [Contributor Covenant][homepage],
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version 2.1, available at
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<https://www.contributor-covenant.org/version/2/1/code_of_conduct.html>.
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Community Impact Guidelines were inspired by
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[Mozilla's code of conduct enforcement ladder][https://github.com/mozilla/inclusion].
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For answers to common questions about this code of conduct, see the FAQ at
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<https://www.contributor-covenant.org/faq>. Translations are available at <https://www.contributor-covenant.org/translations>.
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[homepage]: https://www.contributor-covenant.org

‎README.Rmd‎

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---
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output: github_document
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---
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<!-- README.md is generated from README.Rmd. Please edit that file -->
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```{r, include = FALSE}
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knitr::opts_chunk$set(
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collapse = TRUE,
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comment = "#>",
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fig.path = "man/figures/README-",
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out.width = "100%"
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)
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```
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# inphr
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<!-- badges: start -->
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<!-- badges: end -->
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The goal of {inphr} is to provide a set of functions for performing null
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hypothesis testing on samples of persistence diagrams using the theory of
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permutations. Currently, only two-sample testing is implemented. Inputs can be
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either samples of persistence diagrams themselves or vectorizations. In the
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former case, they are embedded in a metric space using either the Bottleneck or
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Wasserstein distance. In the former case, persistence data becomes functional
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data and inference is performed using tools available in the
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[{fdatest}](https://permaverse.github.io/fdatest/) package.
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## Installation
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You can install the development version of inphr from
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[GitHub](https://github.com/) with:
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``` r
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# install.packages("pak")
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pak::pak("tdaverse/inphr")
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```
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## Example
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Let us start by loading the package:
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```{r}
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library(inphr)
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```
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The package contains three sets of persistence diagrams, which can be used for
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testing. They are available in the package as `trefoils1`, `trefoils2`, and
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`archspirals`. The first two sets contain persistence diagrams computed from
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noisy samples of trefoil knots, while the third set contains persistence
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diagrams computed from noisy samples of 2-armed Archimedean spirals. Each set
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contains 24 persistence diagrams, each computed from a sample of 120 points
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sampled from the respective shape, with Gaussian noise added (standard
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deviation = 0.05). The persistence diagrams were computed using the
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[`TDA::ripsDiag()`] function with a maximum scale of 6 and up to dimension 2.
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You can use the `two_sample_test()` function to perform a two-sample test on
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these persistence diagrams. For example, to test whether the first 5
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persistence diagrams from the first set are significantly different from the
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first 5 persistence diagrams from the second set, you can run:
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```{r}
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two_sample_test(trefoils1[1:5], trefoils2[1:5], B = 100L)
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```
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To test whether the first 5 persistence diagrams from the first set are
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significantly different from the first 5 persistence diagrams from the third
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set, you can run:
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```{r}
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two_sample_test(trefoils1[1:5], archspirals[1:5], B = 100L)
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```
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## Contributions
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Contributions are welcome! Please feel free to open an issue or a pull request
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if you have any suggestions or improvements. The package is still in its early
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stages, so any feedback is appreciated.
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### Code of Conduct
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Please note that the {inphr} project is released with a [Contributor Code of
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Conduct](https://contributor-covenant.org/version/2/1/CODE_OF_CONDUCT.html). By
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contributing to this project, you agree to abide by its terms.
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### Acknowledgements
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This project was funded by [an ISC grant from the R
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Consortium](https://r-consortium.org/all-projects/2024-group-1.html#modular-interoperable-and-extensible-topological-data-analysis-in-r)
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and done in coordination with Jason Cory Brunson and with guidance from Bertrand
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Michel and Paul Rosen. It builds upon conversations with Mathieu Carrière and
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Vincent Rouvreau who are among the authors of the
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[GUDHI](https://gudhi.inria.fr) library. Package development also benefited
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from the support of colleagues at the [Department of Mathematics Jean
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Leray](https://www.math.sciences.univ-nantes.fr) and the use of equipment at
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[Nantes University](https://english.univ-nantes.fr).

‎README.md‎

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<!-- README.md is generated from README.Rmd. Please edit that file -->
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# inphr
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<!-- badges: start -->
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<!-- badges: end -->
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The goal of {inphr} is to provide a set of functions for performing null
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hypothesis testing on samples of persistence diagrams using the theory
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of permutations. Currently, only two-sample testing is implemented.
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Inputs can be either samples of persistence diagrams themselves or
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vectorizations. In the former case, they are embedded in a metric space
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using either the Bottleneck or Wasserstein distance. In the former case,
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persistence data becomes functional data and inference is performed
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using tools available in the
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[{fdatest}](https://permaverse.github.io/fdatest/) package.
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## Installation
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You can install the development version of inphr from
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[GitHub](https://github.com/) with:
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``` r
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# install.packages("pak")
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pak::pak("tdaverse/inphr")
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```
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## Example
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Let us start by loading the package:
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``` r
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library(inphr)
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```
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The package contains three sets of persistence diagrams, which can be
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used for testing. They are available in the package as `trefoils1`,
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`trefoils2`, and `archspirals`. The first two sets contain persistence
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diagrams computed from noisy samples of trefoil knots, while the third
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set contains persistence diagrams computed from noisy samples of 2-armed
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Archimedean spirals. Each set contains 24 persistence diagrams, each
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computed from a sample of 120 points sampled from the respective shape,
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with Gaussian noise added (standard deviation = 0.05). The persistence
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diagrams were computed using the \[`TDA::ripsDiag()`\] function with a
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maximum scale of 6 and up to dimension 2. You can use the
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`two_sample_test()` function to perform a two-sample test on these
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persistence diagrams. For example, to test whether the first 5
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persistence diagrams from the first set are significantly different from
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the first 5 persistence diagrams from the second set, you can run:
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``` r
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two_sample_test(trefoils1[1:5], trefoils2[1:5], B = 100L)
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#> [1] 0.9782132
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```
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To test whether the first 5 persistence diagrams from the first set are
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significantly different from the first 5 persistence diagrams from the
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third set, you can run:
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``` r
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two_sample_test(trefoils1[1:5], archspirals[1:5], B = 100L)
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#> [1] 0.008047755
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```
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## Contributions
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Contributions are welcome! Please feel free to open an issue or a pull
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request if you have any suggestions or improvements. The package is
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still in its early stages, so any feedback is appreciated.
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### Code of Conduct
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Please note that the {inphr} project is released with a [Contributor
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Code of
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Conduct](https://contributor-covenant.org/version/2/1/CODE_OF_CONDUCT.html).
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By contributing to this project, you agree to abide by its terms.
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### Acknowledgements
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This project was funded by [an ISC grant from the R
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Consortium](https://r-consortium.org/all-projects/2024-group-1.html#modular-interoperable-and-extensible-topological-data-analysis-in-r)
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and done in coordination with Jason Cory Brunson and with guidance from
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Bertrand Michel and Paul Rosen. It builds upon conversations with
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Mathieu Carrière and Vincent Rouvreau who are among the authors of the
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[GUDHI](https://gudhi.inria.fr) library. Package development also
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benefited from the support of colleagues at the [Department of
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Mathematics Jean Leray](https://www.math.sciences.univ-nantes.fr) and
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the use of equipment at [Nantes
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University](https://english.univ-nantes.fr).

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