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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 = "#>"
)
```
<!-- badges: start -->
<!-- badges: end -->
## About
This workshop-style module provides an introduction to the emerging field of Data Science in R, including data analysis and visualization, with a particular focus on its utility for biological insight. Students will be provided with biological datasets, and introduced to R packages and code used to examine data. In the first half of each class, students will be lectured on methods and shown demonstrations; in the second half of each class, students will use tools to analyze real data; laptop computers are required. Methods for filtering, sorting, and transforming data will be discussed along with visualization tools and options. Particular attention will be paid to code interpretation and data provenance methods by learning to generate reproducible data output files. For a final project, students will be given a new dataset to analyze using the tools learned during the course, and will share findings with the class in a short oral presentation. Although specific datasets will be used for analysis in class, this workshop will provide broadly applicable tools to reproducibly analyze and visualize data across the biological sciences.
**This repository serves a website with an integrated learning experience that you can access freely at [www.tidybiology.org](http://www.tidybiology.org)**
## Admin
For contributors, here are few notes to make it easier to create materials to embed within this learning platform
#### App organization
This repository serves several shinyapps.io containers. For example, the landing site is a single shiny app, each module is a single shiny app, the map and quiz pages are shiny apps. In this way, we can both prevent too many users at one time from slowing a single system (performance), and we can make sure this doesn't grow into a monolithic unnavigable mess (organization).
#### File organization
The top level index page lives at the root. All other module pages (and auxillary map and quiz pages) live in the `code` dir. Within `code`, a single module.Rmd page for the entire module calls objects within the corresponding `num-objects` dir (e.g. 1-objects, 7-objects). The module.Rmd file and the object directory are then uploaded to shinyapps to serve that page in its own container.
#### Parent/Child chunks
All of the single module.Rmd pages are considered 'parent' pages, and call 'child' chunks/pages which live in the `num-objects` dir. The reason for this organizations is that these child chunks are designed to be re-used and re-mixed across different modules. If we want to make a new module, or a new track with new modules, then we can simply re-use some of the child chunks.
#### File Naming
Modules are given random, but unique numbers. They are based on the original tidybiology organization, based on "class 1", "class 2", etc.
#### Types of files (child chunks)
- Slides: make some slides to show content
- Video: embed video from YouTube link to deliver material
- Activity: something you do in the flow of learning to reinforce it (feel free to pre-populate inline-chunks)
- Quiz: just like an activity, something you do in the flow of learning
- Exercise: integrates all of the activities from a module (it’s the final…it’s also what you do “in class”)
- Project = integrates all of the learning from a track (it’s a change to practice everything)