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Merge pull request #21 from nih-cfde/15-add-readme
Add basic readme
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‎.Rbuildignore‎

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^.lintr$
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.vscode$
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terraform/
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DEVELOPER.md
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DEVELOPER.md
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^README\.Rmd$
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^CODE_OF_CONDUCT\.md$

‎.gitignore‎

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**/.quarto/
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docs
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.vscode/
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terraform/
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terraform/
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/.quarto/
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**/*.quarto_ipynb

‎CODE_OF_CONDUCT.md‎

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# Code of Conduct
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We abide the [CU code of conduct](https://www.cu.edu/ope/aps/2027) as part of our association with the University of Colorado Anshutz Medical Campus.
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Additionally, we follow the Contributor Covenant Code of Conduct, as found below.
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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, socioeconomic 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 email 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.
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Instances of abusive, harassing, or otherwise unacceptable behavior may be reported to community leaders responsible for enforcement.
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Please open a [new security advisory notice](https://github.com/CU-DBMI/.github/security/advisories/new) (using defaults or “n/a” where unable to fill in the form) to privately notify us of any incidents of this nature.
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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][v2.1].
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Community Impact Guidelines were inspired by
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[Mozilla's code of conduct enforcement ladder][mozilla coc].
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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][faq]. Translations are available at
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[https://www.contributor-covenant.org/translations][translations].
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[faq]: https://www.contributor-covenant.org/faq
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[homepage]: https://www.contributor-covenant.org
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[mozilla coc]: https://github.com/mozilla/diversity
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[translations]: https://www.contributor-covenant.org/translations
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[v2.1]: https://www.contributor-covenant.org/version/2/1/code_of_conduct.html

‎LICENSE‎

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YEAR: 2025
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COPYRIGHT HOLDER: programets authors
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COPYRIGHT HOLDER: programets authors

‎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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# programets
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<!-- badges: start -->
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[![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)
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<!-- badges: end -->
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**programets** is an R package for collecting and analyzing academic impact metrics for NIH-funded research projects. It aggregates data from multiple public sources to help researchers, program managers, and evaluators understand how their projects engage with the broader research community over time.
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## What Does It Do?
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The package provides unified access to:
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- **NIH RePORTER** - Project metadata, funding details, and associated publications
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- **iCite** - Citation metrics including Relative Citation Ratio (RCR) for PubMed publications
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- **GitHub** - Repository metrics (stars, forks, commits, contributors, issues, PRs) for projects tagged with NIH Core Project Numbers
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- **Google Analytics** - Web traffic and engagement data for project websites
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- **Europe PMC** - Literature search across millions of publications
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## Installation
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Install the development version from GitHub:
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``` r
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# install.packages("pak")
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pak::pak("nih-cfde/programets")
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```
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**Requirements:**
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- R >= 4.1.0
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- For GitHub data: A Personal Access Token is recommended for higher rate limits
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## Quick Start
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### 1. Query NIH RePORTER for Project Information
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Retrieve comprehensive project metadata including publications, funding details, and principal investigators:
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```{r reporter_example}
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library(programets)
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# Get project info for one or more NIH Core Project Numbers
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proj_info <- get_core_project_info(c("u24ca289073"))
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proj_info |> colnames()
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```
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Available fields include: project title, abstract, funding amounts, dates, PIs, publications (PMIDs), and more.
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### 2. Get GitHub Repository Metrics
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If your project repositories are tagged with NIH Core Project Numbers as topics, you can collect engagement metrics:
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```{r git_example}
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# Fetch GitHub metrics for repos tagged with your project number
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df <- get_github_by_topic(c("u24ca289073"))
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df |> colnames()
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```
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Metrics include: stars, watchers, forks, open/closed issues, open/closed PRs, commit count, contributor count, and more.
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**Tip:** Tag your GitHub repositories with your NIH Core Project Number (e.g., `u24ca289073`) to enable discovery.
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### 3. Get Citation Metrics from iCite
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Calculate impact metrics including the Relative Citation Ratio (RCR) for your publications:
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```{r icite_example, eval=FALSE}
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# Get citation metrics for PubMed IDs
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pmids <- c(26001965, 25015380)
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citation_data <- icite(pmids)
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# View RCR and other metrics
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dplyr::select(citation_data, pmid, title, year,
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relative_citation_ratio, citation_count)
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```
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### 4. Search Europe PMC for Publications
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Query millions of publications with flexible search syntax:
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```{r epmc_example, eval=FALSE}
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# Search for publications related to CRISPR
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crispr_pubs <- epmc_search(query = "crispr", page_limit = 2)
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# Search by author
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author_pubs <- epmc_search(query = 'AUTH:"Smith J"', page_limit = 1)
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```
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### 5. Access Google Analytics Data
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Retrieve web traffic data for project websites (requires authentication):
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```{r ga_example, eval=FALSE}
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# Authenticate with Google (first time only)
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googleAnalyticsR::ga_auth()
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# Get traffic data
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traffic <- ga_dataframe(
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property_id = "123456789",
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start_date = "2024-01-01",
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end_date = "2024-12-31",
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metrics = c("activeUsers", "sessions"),
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dimensions = c("date", "country")
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)
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```
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## Authentication
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### GitHub
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For increased API rate limits, set up a Personal Access Token:
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```{r github_token, eval=FALSE}
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# Create a token with: usethis::create_github_token()
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# Then use it in your calls:
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df <- get_github_by_topic(c("u24ca289073"), token = "your_token_here")
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```
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### Google Analytics
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First-time setup requires authentication:
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```{r ga_auth, eval=FALSE}
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# Opens browser for Google account authorization
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googleAnalyticsR::ga_auth()
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# For non-interactive use, see DEVELOPER.md for service account setup
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```
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## Use Cases
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- **Impact Reporting**: Generate comprehensive reports combining publication citations, web traffic, and GitHub engagement
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- **Trend Analysis**: Track how metrics evolve over time in response to publications, presentations, or events
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- **Portfolio Management**: Compare metrics across multiple projects or funding opportunities
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- **Compliance**: Document project outputs and community engagement for progress reports
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## Documentation
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- **Function Reference**: See `?get_core_project_info`, `?icite`, `?get_github_by_topic`, etc.
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- **Vignettes**: Browse vignettes for detailed workflows
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- **Developer Notes**: See `DEVELOPER.md` for advanced setup (service accounts, encryption)
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## Getting Help
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- File issues at: https://github.com/nih-cfde/programets/issues
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- Review examples in the vignettes
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- Check function documentation with `?function_name`
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## Authors
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- Sean Davis ([email protected])
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- David Mayer ([email protected])
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## License
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MIT
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