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Prepare v0.9.0-beta release
- Add comprehensive .gitignore for R projects - Add MIT LICENSE file - Add DESCRIPTION file with package metadata - Add setup.R script for easy installation - Add RELEASE_NOTES.md with detailed release information - Update README.md with v0.9.0-beta branding and quick start guide - Add pre-publication warnings and status indicators
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‎.gitignore‎

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# R specific
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.Rproj.user
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.Rhistory
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.RData
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.Ruserdata
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.Rapp.history
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*.Rproj
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.Rproj.user/
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# OS generated files
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.DS_Store
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.DS_Store?
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._*
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.Spotlight-V100
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.Trashes
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ehthumbs.db
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Thumbs.db
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# Temporary files
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*~
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*.tmp
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*.temp
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*.swp
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*.swo
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# Stan compiled models
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*.rds
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*.rda
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*.RData
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# Large data files (uncomment if needed)
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# *.csv
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# data/raw_*.csv
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# OSF sync folder
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osf/
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results/Fit population/
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results/Fit population/
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# IDE files
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.vscode/
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.idea/
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# Logs
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*.log
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# Backup files
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*.bak
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*.backup

‎DESCRIPTION‎

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Package: Hierarchical-Interoception
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Type: Package
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Title: Hierarchical Bayesian Modelling of Interoceptive Psychophysics
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Version: 0.9.0-beta
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Authors@R: c(
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person("Arthur S.", "Courtin", role = c("aut", "cre"), email = "arthur.courtin@clin.au.dk"),
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person("Jesper Fischer", "Ehmsen", role = "aut"),
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person("Leah", "Banellis", role = "aut"),
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person("Francesca", "Fardo", role = "aut"),
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person("Micah", "Allen", role = "aut")
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)
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Description: This package provides tools for hierarchical Bayesian modeling of
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interoceptive psychophysics data, specifically for Heart Rate Discrimination
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Task (HRDT) and Respiratory Resistance Sensitivity Task (RRST). It includes
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Stan models, power analysis tools, and educational resources for researchers
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working with interoceptive psychophysics.
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License: MIT + file LICENSE
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URL: https://github.com/[username]/Hierarchical-Interoception
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BugReports: https://github.com/[username]/Hierarchical-Interoception/issues
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Depends: R (>= 4.0.0)
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Imports:
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brms,
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cmdstanr,
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tidyverse,
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posterior,
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bayesplot,
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tidybayes,
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rstan,
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here,
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loo,
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shiny,
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flextable,
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pracma,
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furrr
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Suggests:
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knitr,
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rmarkdown,
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testthat
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VignetteBuilder: knitr
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RoxygenNote: 7.2.3
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Encoding: UTF-8
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LazyData: true

‎LICENSE‎

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MIT License
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Copyright (c) 2025 Arthur S. Courtin, Jesper Fischer Ehmsen, Leah Banellis, Francesca Fardo, Micah Allen
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.

‎README.md‎

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# Hierarchical-Interoception
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# Hierarchical-Interoception v0.9.0-beta
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⚠️ **Pre-publication Release**: This is pre-peer-review research software. The methods and results are under review. Use with appropriate caution for research applications.
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This repository is the companion of our pre-print "Hierarchical Bayesian Modelling of Interoceptive Psychophysics" (https://doi.org/10.1101/2025.08.27.672360).
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Another is a shiny app which researchers can use to explore the results of our power analysis, e.g. to justify sample size of future studies.
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## Table of Contents
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1. [Structure of the repository](#structure-of-the-repository)
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2. [Using the BRMS Demo](#using-the-brms-demo)
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3. [Shiny App Deployment and Usage](#shiny-app-deployment-and-usage)
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3. [Dependencies](#dependencies)
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3. [Citation](#citation)
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3. [Contact](#contact)
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1. [Quick Start](#quick-start)
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2. [Structure of the repository](#structure-of-the-repository)
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3. [Using the BRMS Demo](#using-the-brms-demo)
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4. [Shiny App Deployment and Usage](#shiny-app-deployment-and-usage)
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5. [Dependencies](#dependencies)
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6. [Citation](#citation)
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7. [Contact](#contact)
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## Quick Start
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1. **Clone the repository**:
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```bash
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git clone https://github.com/[username]/Hierarchical-Interoception.git
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cd Hierarchical-Interoception
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```
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2. **Set up the environment**:
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```r
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# Run the setup script
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source("setup.R")
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```
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3. **Try the BRMS demo**:
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- Open `app & demo/BRMS demo.Rmd`
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- Run the code to see a complete analysis workflow
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4. **Explore power analysis**:
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```r
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shiny::runApp("app & demo/shiny app.R")
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```
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## Structure of the repository
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‎RELEASE_NOTES.md‎

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# Release Notes
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## v0.9.0-beta (2025-01-XX)
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### Pre-publication Release
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⚠️ **Important**: This is pre-peer-review research software. The methods and results are under review. Use with appropriate caution for research applications.
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### What's New
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This is the initial release of the Hierarchical-Interoception toolkit, providing comprehensive tools for hierarchical Bayesian modeling of interoceptive psychophysics data.
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### Features
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- **Hierarchical Psychometric Models**: Complete Stan implementations for HRDT and RRST data
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- **Parameter Recovery Validation**: Extensive validation of model parameter recovery
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- **Power Analysis Tools**: Interactive Shiny app for power analysis exploration
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- **Educational Resources**: Complete BRMS demo with step-by-step workflow
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- **Population Fitting**: Tools for deriving normative priors from large datasets
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- **Model Comparison**: LOO-based model comparison between different psychometric functions
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### Components
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- **Stan Models**: Population fitting, power analysis, and parameter recovery models
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- **Analysis Scripts**: Complete analysis pipeline from data preparation to visualization
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- **Shiny App**: Interactive power analysis explorer with three main panels
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- **BRMS Demo**: Educational R Markdown with complete workflow example
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- **Raw Data**: HRDT and RRST datasets for analysis and validation
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### Getting Started
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1. Clone the repository
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2. Run `source("setup.R")` to install dependencies
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3. Follow the BRMS demo for basic usage
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4. Use the Shiny app for power analysis exploration
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### Dependencies
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- R (>= 4.0.0)
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- Stan/CmdStan via cmdstanr
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- brms, tidyverse, posterior, bayesplot, tidybayes
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- shiny, flextable, here, loo, pracma, furrr
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### Known Issues
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- Some large RData files may cause slow repository cloning
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- Stan compilation required on first use
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- Path resolution may vary across operating systems
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### Citation
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If you use this software in your research, please cite:
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```
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Courtin, A.S., Fischer Ehmsen, J., Banellis, L., Fardo, F., & Allen, M. (2025).
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Hierarchical Bayesian Modelling of Interoceptive Psychophysics.
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bioRxiv. https://doi.org/10.1101/2025.08.27.672360
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```
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### Roadmap
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- **v1.0.0**: Planned after peer review acceptance
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- **v0.9.1+**: Bug fixes and minor improvements before v1.0.0
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### Support
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For questions or issues, please:
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1. Check the README.md for usage instructions
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2. Open an issue on the GitHub repository
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3. Contact the authors directly
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---
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*This software is released under the MIT License. See LICENSE file for details.*

‎setup.R‎

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# Hierarchical-Interoception Setup Script
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# This script helps set up the environment for using this research software
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cat("Setting up Hierarchical-Interoception v0.9.0-beta...\n")
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# Check if renv is available, if not install it
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if (!require("renv", quietly = TRUE)) {
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cat("Installing renv for dependency management...\n")
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install.packages("renv")
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}
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# Initialize renv if not already done
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if (!file.exists("renv.lock")) {
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cat("Initializing renv...\n")
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renv::init()
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}
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# Restore dependencies
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cat("Installing/updating dependencies...\n")
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renv::restore()
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# Check for cmdstanr and Stan installation
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if (require("cmdstanr", quietly = TRUE)) {
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cat("Checking Stan installation...\n")
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if (!cmdstanr::cmdstan_version()) {
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cat("Installing CmdStan...\n")
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cmdstanr::install_cmdstan()
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}
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} else {
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cat("Warning: cmdstanr not available. Please install manually.\n")
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}
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cat("Setup complete! You can now use the Hierarchical-Interoception tools.\n")
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cat("Start with the BRMS demo: app & demo/BRMS demo.Rmd\n")
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cat("Or run the Shiny app: shiny::runApp('app & demo/shiny app.R')\n")

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