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README.Rmd
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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
```
# {{projectname}}
<!-- Standard badges and licenses: -->
<!-- [](https://doi.org/[ZENODO_DOI]) Uncomment when deposited to Zenodo -->
[-MIT-green.svg)](https://opensource.org/licenses/MIT)
[-CC0_1.0-lightgrey.svg)](http://creativecommons.org/publicdomain/zero/1.0/)
[-CC_BY_4.0-blue.svg)](http://creativecommons.org/publicdomain/zero/1.0/)
<!-- If the repository is or will be related to a manuscript, keep the following
text. Otherwise replace it with a high-level summary and relevant citation,
contact, or re-use information. -->
This repository contains data and R code which are supplements to:
_Paper Title_, by
Author [](https://orcid.org/AUTHOR_ORCID_ID),
Author [](https://orcid.org/AUTHOR_ORCID_ID),
and Author [](https://orcid.org/AUTHOR_ORCID_ID),
(20XX)
Please cite that paper, when referring to this work. Please also cite
the permanent archive of repository (Zenodo reference (<https://doi.org/[ZENODO_DOI]>)
when reusing or referring directly to data and code.
## Repository Structure and Reproducibility
<!-- Modify this appropriate if you change project structure -->
- `data/` contains data from the study
and a data dictionary describing all variables.
- `R/` contains functions used in this analysis.
- `reports/` contains R Markdown/Quarto reports generated in the analysis
- `outputs/` contains figures and other outputs
- This project uses the [{targets}](https://wlandau.github.io/targets-manual/)
framework to organize build steps for analysis pipeline. The steps are
defined in the `_targets.R` file and the workflow can be executed by running
`run.R` via `source("run.R")` in your R terminal or `Rscript run.R` in
your system shell. The schematic figure below summarizes the steps. (The figure is generated using
`mermaid.js` syntax and should display as a graph on GitHub. It can also
be viewed by pasting the code into <https://mermaid.live>.)
```{r, echo=FALSE, message = FALSE, results='asis'}
# This block renders the {targets} workflow as a graph in mermaid.js form,
# which is displayed by default on GitHub.
mer <- targets::tar_mermaid(targets_only = TRUE, outdated = FALSE,
callr_function = NULL, envir = new.env(), reporter = "silent",
legend = FALSE, color = FALSE)
cat(
"```{mermaid}",
mer[1],
"subgraph Project Workflow",
mer[3:length(mer)],
"linkStyle 0 stroke-width:0px;",
"```",
sep = "\n"
)
```
- This project was built with `r R.version$version.string`. This project uses the [{renv}](https://rstudio.github.io/renv/) framework to
record R package dependencies and versions. Packages and versions used are recorded in
`renv.lock` and code used to manage dependencies is in `renv/` and other files
in the root project directory. On starting an R session in the working directory, run `renv::restore()`
to install R package dependencies.
## Code of Conduct
Please note that this project is released with a [Contributor Code of
Conduct](https://contributor-covenant.org/version/2/1/CODE_OF_CONDUCT.html). By
contributing to this project, you agree to abide by its terms.
## Reproducibility
Template SHA: {{template_sha}}