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20251221 - convert from rmarkdown to quarto website
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‎.github/workflows/deploy_rmarkdown.yml‎

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# 2. Create a secret labeled `EMAIL` in the repo (Settings -> Security -> Secrets -> Actions), and copy the PAT for `EMAIL` into the secret labeled `EMAIL`
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on:
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push:
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branches:
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- main
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push:
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branches:
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- main
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name: deploywebsite
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name: Quarto Publish
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jobs:
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rmarkdown:
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name: Render-Website
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build-deploy:
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runs-on: ubuntu-latest
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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permissions:
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contents: write
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steps:
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- name: Checkout Repository
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uses: actions/checkout@v4 # update
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- name: Setup R
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uses: r-lib/actions/setup-r@v2 # update
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- name: Check out repository
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uses: actions/checkout@v4
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- name: Set up Quarto
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uses: quarto-dev/quarto-actions/setup@v2
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- name: Setup Python and Jupyter
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uses: actions/setup-python@v4
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with:
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python-version: '3.x' # Version range or exact version of a Python version to use, using SemVer's version range syntax
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- run: pip install jupyter
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- run: pip install -r requirements.txt
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- name: Install R
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uses: r-lib/actions/setup-r@v2
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- name: Session info
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run: Rscript -e 'sessionInfo()'
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- name: Setup pandoc
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uses: r-lib/actions/setup-pandoc@v2 # update
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- name: Install libcurl on Linux
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if: runner.os == 'Linux'
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run: sudo apt-get update -y && sudo apt-get install -y libcurl4-openssl-dev
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- name: Install package dependencies
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uses: r-lib/actions/setup-r-dependencies@v2 # update
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- name: Install remote packages
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run: |
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Rscript -e "install.packages('rstan', repos = c('https://mc-stan.org/r-packages/', getOption('repos')))"
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- name: Render blog
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run: Rscript -e 'rmarkdown::render_site()'
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- uses: actions/upload-artifact@v4 # update
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# Rscript -e 'remotes::install_github("DevPsyLab/petersenlab")'
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- name: Render and Publish
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uses: quarto-dev/quarto-actions/publish@v2
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with:
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target: gh-pages
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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- name: List files in workspace
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if: always()
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run: |
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ls -lh
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find . -type f
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- name: Archive production artifacts
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if: always() # ensures it runs even if previous steps fail
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uses: actions/upload-artifact@v4 # update
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with:
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name: site
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path: _site/
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# Need to first create an empty gh-pages branch
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# see https://pkgdown.r-lib.org/reference/deploy_site_github.html
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# and also add secrets for a GH_PAT and EMAIL to the repository
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# gh-action from Cecilapp/GitHub-Pages-deploy
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checkout-and-deploy:
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runs-on: ubuntu-latest
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needs: rmarkdown
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steps:
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- name: Checkout
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uses: actions/checkout@v4 # update
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- name: Download artifact
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uses: actions/download-artifact@v4 # update
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with:
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# Artifact name
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name: site # optional
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# Destination path
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path: _site # optional
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- name: Deploy to GitHub Pages
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uses: Cecilapp/GitHub-Pages-deploy@v3
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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with:
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build_dir: _site/ # "_site/" by default
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email: ${{ secrets.EMAIL }} # must be a verified email

R.Rmd renamed to R.qmd

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Large diffs are not rendered by default.

‎README.md‎

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# Data Analysis Guides
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This is the code that creates the Data Analysis Guides for the Developmental Psychopathology Lab.
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The Data Analysis Guides are located here: **https://devpsylab.github.io/DataAnalysis**
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The Data Analysis Guides are located here: **<https://devpsylab.github.io/DataAnalysis>**
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# License
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[![CC BY 4.0][cc-by-image]][cc-by]
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[cc-by]: https://creativecommons.org/licenses/by/4.0/
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[cc-by-image]: https://i.creativecommons.org/l/by/4.0/88x31.png
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[cc-by-shield]: https://img.shields.io/badge/License-CC%20BY%204.0-lightgrey.svg
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[cc-by]: <https://creativecommons.org/licenses/by/4.0/>
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[cc-by-image]: <https://i.creativecommons.org/l/by/4.0/88x31.png>
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[cc-by-shield]: <https://img.shields.io/badge/License-CC%20BY%204.0-lightgrey.svg>

SPSS.Rmd renamed to SPSS.qmd

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title: "SPSS"
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---
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```{r setup, include = FALSE}
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knitr::opts_chunk$set(
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echo = TRUE,
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error = TRUE,
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comment = "")
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```
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# When to use `SPSS` {#whenSPSS}
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We use [R](R.html) for almost all data analysis.
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However, [R](R.html) is code-based and has a steep learning curve.
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As a result, undergraduate students in the lab most often use `SPSS` or [`jamovi`](jamovi.html) for their research projects (e.g., [Honors projects](https://devpsylab.github.io/LabWiki/honors.html) and [SROP projects](https://devpsylab.github.io/LabWiki/expectations-SROP.html)), because `SPSS` and [`jamovi`](jamovi.html) have a point-and-click interface.
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We use [R](R.qmd) for almost all data analysis.
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However, [R](R.qmd) is code-based and has a steep learning curve.
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As a result, undergraduate students in the lab most often use `SPSS` or [`jamovi`](jamovi.qmd) for their research projects (e.g., [Honors projects](https://devpsylab.github.io/LabWiki/honors.html) and [SROP projects](https://devpsylab.github.io/LabWiki/expectations-SROP.html)), because `SPSS` and [`jamovi`](jamovi.qmd) have a point-and-click interface.
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# Creating a `SPSS` Syntax File to Import a `.csv` Data File {#import}
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# Recode Variables {#recode}
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https://stats.oarc.ucla.edu/spss/modules/creating-and-recoding-variables/ (archived at https://perma.cc/YJ2H-SRZM)
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<https://stats.oarc.ucla.edu/spss/modules/creating-and-recoding-variables/> (archived at <https://perma.cc/YJ2H-SRZM>)
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https://wlm.userweb.mwn.de/SPSS/wlmsreco.htm (archived at https://perma.cc/G4FN-PYPV)
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<https://wlm.userweb.mwn.de/SPSS/wlmsreco.htm> (archived at <https://perma.cc/G4FN-PYPV>)
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## Average Across Variables {#averageVars}
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```
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1. Create plot of interaction
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- see McCabe et al. (2018) and following links:
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- https://github.com/connorjmccabe/InterActive
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- https://connorjmccabe.shinyapps.io/interactive/ (archived at https://perma.cc/93G6-ALDP)
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- <https://github.com/connorjmccabe/InterActive>
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- <https://connorjmccabe.shinyapps.io/interactive/> (archived at <https://perma.cc/93G6-ALDP>)
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# Best Practices {#bestPractices}
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‎_quarto.yml‎

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project:
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type: website
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website:
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title: "Data Analysis Guides for the Developmental Psychopathology Lab"
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repo-url: https://github.com/DevPsyLab/DataAnalysis
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repo-actions: [edit, source, issue]
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google-analytics: G-TYR0QMREEW
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sidebar:
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style: "floating"
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contents:
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- text: "ABCD Data"
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href: abcdData.qmd
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- text: "Bayesian Analysis"
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href: bayesian.qmd
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- text: "Data Management"
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href: dataManagement.qmd
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- text: "Developmental Scaling"
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href: developmentalScaling.qmd
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- text: "Directed Acyclic Graphs"
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href: dags.qmd
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- text: "Electroencephalography/Event-Related Potentials"
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href: eegERP.qmd
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- text: "Exploratory Data Analysis"
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href: eda.qmd
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- text: "Factor Analysis"
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href: factorAnalysis.qmd
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- text: "Figures"
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href: figures.qmd
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- text: "Git, GitLab, and GitHub"
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href: git.qmd
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- text: "Hierarchical Linear Modeling"
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href: hlm.qmd
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- text: "High-Performance Computing"
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href: hpc.qmd
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- text: "Item Response Theory"
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href: irt.qmd
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- text: "jamovi"
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href: jamovi.qmd
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- text: "JATOS (Just Another Tool for Online Studies)"
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href: jatos.qmd
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- text: "jsPsych"
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href: jsPsych.qmd
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- text: "LAMP (Linux, Apache, MySQL, PHP)"
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href: lamp.qmd
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- text: "Longitudinal Data Analysis"
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href: lda.qmd
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- text: "Markdown"
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href: markdown.qmd
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- text: "Mediation"
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href: sem.qmd#mediation
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- text: "Moderation/Interaction"
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href: regression.qmd#moderation
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- text: "Mplus"
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href: mplus.qmd
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- text: "Multiple Imputation"
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href: multipleImputation.qmd
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- text: "Open Science Framework"
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href: osf.qmd
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- text: "Principal Component Analysis"
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href: pca.qmd
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- text: "Python"
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href: https://devpsylab.github.io/pythonDataAnalysisGuides
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- text: "R"
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href: R.qmd
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- text: "Regression"
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href: regression.qmd
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- text: "SPSS"
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href: SPSS.qmd
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- text: "Statistics"
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href: statistics.qmd
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- text: "Structural Equation Modeling"
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href: sem.qmd
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navbar:
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logo: images/labLogo.png
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search: true
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tools:
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- icon: github
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menu:
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- text: "Source Code"
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href: https://github.com/DevPsyLab/DataAnalysis
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- text: "Report a Bug"
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href: https://github.com/DevPsyLab/DataAnalysis/issues/new
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- icon: twitter
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href: https://twitter.com/devpsylab
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- icon: facebook
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href: https://www.facebook.com/DevPsyLab
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- icon: instagram
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href: https://www.instagram.com/dev_psy_lab
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left:
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- text: "Datasets"
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menu:
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- text: "ABCD Study Data"
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href: abcdData.qmd
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- text: "Analysis Techniques"
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menu:
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- text: "Bayesian Analysis"
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href: bayesian.qmd
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- text: "Data Management"
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href: dataManagement.qmd
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#- text: "Developmental Scaling"
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# href: developmentalScaling.qmd
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- text: "Directed Acyclic Graphs"
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href: dags.qmd
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- text: "Electroencephalography/Event-Related Potentials"
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href: eegERP.qmd
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- text: "Exploratory Data Analysis"
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href: eda.qmd
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- text: "Factor Analysis"
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href: factorAnalysis.qmd
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- text: "Figures"
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href: figures.qmd
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- text: "Hierarchical Linear Modeling"
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href: hlm.qmd
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- text: "Item Response Theory"
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href: irt.qmd
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- text: "Longitudinal Data Analysis"
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href: lda.qmd
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- text: "Mediation"
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href: sem.qmd#mediation
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- text: "Moderation/Interaction"
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href: regression.qmd#moderation
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- text: "Multiple Imputation"
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href: multipleImputation.qmd
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- text: "Principal Component Analysis"
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href: pca.qmd
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- text: "Regression"
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href: regression.qmd
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- text: "Statistics"
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href: statistics.qmd
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- text: "Structural Equation Modeling"
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href: sem.qmd
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- text: "Software/Frameworks"
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menu:
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- text: "Git, GitLab, and GitHub"
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href: git.qmd
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- text: "High-Performance Computing Cluster"
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href: hpc.qmd
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- text: "jamovi"
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href: jamovi.qmd
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- text: "JATOS (Just Another Tool for Online Studies)"
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href: jatos.qmd
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- text: "jsPsych"
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href: jsPsych.qmd
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- text: "LAMP (Linux, Apache, MySQL, PHP)"
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href: lamp.qmd
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- text: "Markdown"
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href: markdown.qmd
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- text: "Mplus"
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href: mplus.qmd
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- text: "Open Science Framework"
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href: osf.qmd
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- text: "Python"
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href: https://devpsylab.github.io/pythonDataAnalysisGuides
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- text: "R"
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href: R.qmd
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- text: "SPSS"
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href: SPSS.qmd
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- text: "About"
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href: about.qmd
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right:
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- text: "Lab Wiki"
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href: https://devpsylab.github.io/LabWiki
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- text: "Lab Website"
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href: https://developmental-psychopathology.lab.uiowa.edu
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format:
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html:
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highlight-style: a11y
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theme: cosmo
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css: ["styles.css", "includes/custom.css", "font/css/roboto.css"]
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toc: true
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toc-depth: 5
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toc-title: Contents
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toc-location: right
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execute:
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error: true
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warning: false
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code-link: true
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number-sections: true
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code-fold: show
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anchor-sections: true
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df-print: paged
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code-tools:
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source: true
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toggle: true
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link-external-newwindow: true
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#include-in-header:
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# - "includes/google_analytics.html"
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include-after-body:
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- "includes/footer.html"
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license: CC BY
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author-meta: "Isaac T. Petersen"
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date-meta: today

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