## Introduction to {targets} for effective workflows in R **Joel Nitta** AsiaR Meetup <span style = 'font-size: 120%;'>2022/05/07</span> <br><br><img src="https://docs.ropensci.org/targets/logo.svg" alt="drawing" height="350" style="float:right;margin:-200px 0px"> <br><br><br>https://joelnitta.github.io/asiaR-targets-intro --- ## Self-introduction .pull-left[ @joel_nitta https://joelnitta.com - Project Research Associate @ [Tokyo University](http://iwasakilab.k.u-tokyo.ac.jp/) - Research interests: Ecology and evolution of __ferns__ - Hobbies: Running (after my 6YO!) ] .pull-right[ <img src="https://github.com/joelnitta/joelnitta-site/blob/master/static/media/headers/research_img2.jpg?raw=true" alt="drawing" height="400"/> .small[Photo: J-Y Meyer] ] --- ## Outline of today's talk - Introduction to {targets} - Live coding To follow along with live coding, install [R](https://www.r-project.org/), [RStudio](https://www.rstudio.com/products/rstudio/download/), and [targets](https://github.com/ropensci/targets) --- ## Why {targets}? -- ### To make your code more reproducible --- ## What is reproducibility? -- > The ability for others (or your future self) to re-run your code and get the same results -- - Not "yes" or "no" - Reproducibility = **mindset** - Many aspects - Computing environment - Data availability - **Code automation** --- ## Workflows in R  **Which steps** need to be run **in what order**? .footnote[R for Data Science https://r4ds.had.co.nz/] --- ## Workflows in R  If **one part** of a workflow changes, **how does it affect other parts?** **How much of it do we need to re-run?** --- ## What is {targets}? .pull-left[ - Automates workflow - Only runs necessary steps - Can run workflow steps in parallel (speeds up analysis) - Provides proof that **results** are derived **from code** ] <img src="https://docs.ropensci.org/targets/logo.svg" alt="drawing" height="350" style="float:right"> --- ## Resources - Github https://github.com/ropensci/targets - Package website https://docs.ropensci.org/targets/ - User manual https://books.ropensci.org/targets/ - Targetopia https://wlandau.github.io/targetopia/ - {tarchetypes} website https://docs.ropensci.org/tarchetypes/ - Discussion board https://github.com/ropensci/targets/discussions --- ## Live Coding - `tar_script()`: Write a generic workflow script - `tar_visnetwork()`: Visualize the state of the workflow - `tar_make()`: Run the workflow - `tar_load()`: Load a target from the workflow - `tar_outdated()`： List which steps will be run next time --- class: inverse, center, middle # Live Coding --- ## Example workflows - Gapminder workflow - https://github.com/joelnitta/targets_gapminder_example - Variant calling workflow - https://github.com/joelnitta/targets_vcf_example - My projects on github - https://github.com/joelnitta/#reproducible-data-analysis- --- ## Summary - Write your workflow plan in `_targets.R` - Run your workflow with `tar_make()` - Check the status of your workflow with `tar_visnetwork()` --- ## If you want to learn more... User manual https://books.ropensci.org/targets/ <img src="https://4.bp.blogspot.com/--ZNd-68qDog/Vq8822mkoUI/AAAAAAAA3gM/-NwzZtON8Dk/s800/setsumeisyo_woman.png" alt="drawing" height="250" style="float:right;margin:0px 0px"> --- class: inverse, center, middle # Thank you!