Merge pull request #22 from nih-cfde/pr15-updates

copilot adds to readme

Author: cgreene

.Rbuildignore

@@ -9,3 +9,4 @@
 terraform/
 DEVELOPER.md
 ^README\.Rmd$
+^CODE_OF_CONDUCT\.md$

CODE_OF_CONDUCT.md

@@ -0,0 +1,139 @@
+# Code of Conduct
+
+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.
+
+Additionally, we follow the Contributor Covenant Code of Conduct, as found below.
+
+## Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socioeconomic status,
+nationality, personal appearance, race, caste, color, religion, or sexual
+identity and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+- Demonstrating empathy and kindness toward other people
+- Being respectful of differing opinions, viewpoints, and experiences
+- Giving and gracefully accepting constructive feedback
+- Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+- Focusing on what is best not just for us as individuals, but for the overall
+  community
+
+Examples of unacceptable behavior include:
+
+- The use of sexualized language or imagery, and sexual attention or advances of
+  any kind
+- Trolling, insulting or derogatory comments, and personal or political attacks
+- Public or private harassment
+- Publishing others' private information, such as a physical or email address,
+  without their explicit permission
+- Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official email address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement.
+Instances of abusive, harassing, or otherwise unacceptable behavior may be reported to community leaders responsible for enforcement.
+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.
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series of
+actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or permanent
+ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior, harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within the
+community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.1, available at
+[https://www.contributor-covenant.org/version/2/1/code_of_conduct.html][v2.1].
+
+Community Impact Guidelines were inspired by
+[Mozilla's code of conduct enforcement ladder][mozilla coc].
+
+For answers to common questions about this code of conduct, see the FAQ at
+[https://www.contributor-covenant.org/faq][faq]. Translations are available at
+[https://www.contributor-covenant.org/translations][translations].
+
+[faq]: https://www.contributor-covenant.org/faq
+[homepage]: https://www.contributor-covenant.org
+[mozilla coc]: https://github.com/mozilla/diversity
+[translations]: https://www.contributor-covenant.org/translations
+[v2.1]: https://www.contributor-covenant.org/version/2/1/code_of_conduct.html

LICENSE

@@ -1,2 +1,2 @@
 YEAR: 2025
-COPYRIGHT HOLDER: programets authors
+COPYRIGHT HOLDER: programets authors

README.Rmd

@@ -19,32 +19,151 @@ knitr::opts_chunk$set(
 [![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)
 <!-- badges: end -->
 
-The goal of programets is to compile public metrics from iCite, Google Analytics, GitHub, and related sources to help researchers understand how their NIH project engages with the broader research community. The package is designed to highlight how project impact evolves over time, such as in response to publications or events.
+**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.
+
+## What Does It Do?
+
+The package provides unified access to:
+
+- **NIH RePORTER** - Project metadata, funding details, and associated publications
+- **iCite** - Citation metrics including Relative Citation Ratio (RCR) for PubMed publications
+- **GitHub** - Repository metrics (stars, forks, commits, contributors, issues, PRs) for projects tagged with NIH Core Project Numbers
+- **Google Analytics** - Web traffic and engagement data for project websites
+- **Europe PMC** - Literature search across millions of publications
 
 ## Installation
 
-You can install the development version of programets from [GitHub](https://github.com/) with:
+Install the development version from GitHub:
 
 ``` r
 # install.packages("pak")
 pak::pak("nih-cfde/programets")
 ```
 
-## Example Usage
+**Requirements:**
+- R >= 4.1.0
+- For GitHub data: A Personal Access Token is recommended for higher rate limits
 
-Query the NIH RePORTER:
+## Quick Start
+
+### 1. Query NIH RePORTER for Project Information
+
+Retrieve comprehensive project metadata including publications, funding details, and principal investigators:
 
 ```{r reporter_example}
 library(programets)
 
+# Get project info for one or more NIH Core Project Numbers
 proj_info <- get_core_project_info(c("u24ca289073"))
 proj_info |> colnames()
 ```
 
-Tag your GitHub repositories with NIH Core Project Numbers to download common metrics:
+Available fields include: project title, abstract, funding amounts, dates, PIs, publications (PMIDs), and more.
+
+### 2. Get GitHub Repository Metrics
+
+If your project repositories are tagged with NIH Core Project Numbers as topics, you can collect engagement metrics:
 
 ```{r git_example}
+# Fetch GitHub metrics for repos tagged with your project number
 df <- get_github_by_topic(c("u24ca289073"))
 df |> colnames()
 ```
 
+Metrics include: stars, watchers, forks, open/closed issues, open/closed PRs, commit count, contributor count, and more.
+
+**Tip:** Tag your GitHub repositories with your NIH Core Project Number (e.g., `u24ca289073`) to enable discovery.
+
+### 3. Get Citation Metrics from iCite
+
+Calculate impact metrics including the Relative Citation Ratio (RCR) for your publications:
+
+```{r icite_example, eval=FALSE}
+# Get citation metrics for PubMed IDs
+pmids <- c(26001965, 25015380)
+citation_data <- icite(pmids)
+
+# View RCR and other metrics
+dplyr::select(citation_data, pmid, title, year, 
+              relative_citation_ratio, citation_count)
+```
+
+### 4. Search Europe PMC for Publications
+
+Query millions of publications with flexible search syntax:
+
+```{r epmc_example, eval=FALSE}
+# Search for publications related to CRISPR
+crispr_pubs <- epmc_search(query = "crispr", page_limit = 2)
+
+# Search by author
+author_pubs <- epmc_search(query = 'AUTH:"Smith J"', page_limit = 1)
+```
+
+### 5. Access Google Analytics Data
+
+Retrieve web traffic data for project websites (requires authentication):
+
+```{r ga_example, eval=FALSE}
+# Authenticate with Google (first time only)
+googleAnalyticsR::ga_auth()
+
+# Get traffic data
+traffic <- ga_dataframe(
+  property_id = "123456789",
+  start_date = "2024-01-01",
+  end_date = "2024-12-31",
+  metrics = c("activeUsers", "sessions"),
+  dimensions = c("date", "country")
+)
+```
+
+## Authentication
+
+### GitHub
+For increased API rate limits, set up a Personal Access Token:
+
+```{r github_token, eval=FALSE}
+# Create a token with: usethis::create_github_token()
+# Then use it in your calls:
+df <- get_github_by_topic(c("u24ca289073"), token = "your_token_here")
+```
+
+### Google Analytics
+First-time setup requires authentication:
+
+```{r ga_auth, eval=FALSE}
+# Opens browser for Google account authorization
+googleAnalyticsR::ga_auth()
+
+# For non-interactive use, see DEVELOPER.md for service account setup
+```
+
+## Use Cases
+
+- **Impact Reporting**: Generate comprehensive reports combining publication citations, web traffic, and GitHub engagement
+- **Trend Analysis**: Track how metrics evolve over time in response to publications, presentations, or events
+- **Portfolio Management**: Compare metrics across multiple projects or funding opportunities
+- **Compliance**: Document project outputs and community engagement for progress reports
+
+## Documentation
+
+- **Function Reference**: See `?get_core_project_info`, `?icite`, `?get_github_by_topic`, etc.
+- **Vignettes**: Browse vignettes for detailed workflows
+- **Developer Notes**: See `DEVELOPER.md` for advanced setup (service accounts, encryption)
+
+## Getting Help
+
+- File issues at: https://github.com/nih-cfde/programets/issues
+- Review examples in the vignettes
+- Check function documentation with `?function_name`
+
+## Authors
+
+- Sean Davis ([email protected])
+- David Mayer ([email protected])
+
+## License
+
+MIT
+