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02b_rstudio-projects.qmd
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---
title: "Projects in Rstudio"
subtitle: "Project Management"
editor: visual
---
## General Project Organisation
**Good project layout helps ensure:**
- Integrity of data
- Portability of the project
- work is easy to revisit after a break and onboard new collaborators
- supports tool building which takes advantage of the shared structure.
::: callout-info
### Principles
- Everything required is contained in the project or sourced automatically.
- Use paths relative to the project root directory.
- Separate data, methods, and output, while making the relationship between them clear.
- Document the contents of your project and how to use them.
- Use R package development and community conventions.
- Do not manually edit raw data.
- Keep a [clean pipeline](https://dynamicecology.wordpress.com/2016/08/22/ten-commandments-for-good-data-management/) of data processing from raw to analytical.
:::
## Rstudio Projects
Rstudio projects are a convenient way to manage research projects, providing the scaffolding for self contained and portable work.
### Features
- Self contained and portable
- Clean environment on load
- Working directory and files tab set to project root
## Posit Cloud projects
For the rest of the course, we will be working in a project where I have already set up the computational environment. This will save a lot of time by avoiding having to run a long installation scripts during the class or debug individual installation problems.
### Launch Posit Cloud project
To access this project, please click on the **supplied project link**
This should drop you into the **ACCE DTP Reproducible research in R Workspace**. If not, navigate to the space from the menu on the top left.
In there you will find a project called **wood-survey**. Click on **+ Copy** to create your own copy of the project.
You now have your own copy of the project.
## Rstudio IDE Global Options
You can customise your RStudio IDE to suit your preferences. To access the global options, click on **Tools \> Global Options**.
Let's go ahead and set up some useful options:
::: panel-tabset
## General
In the General tab you can customise default configurations for your R Sessions & Workspace.
- **Restore .RData into workspace at startup**: This will stop R from loading an .RData file into your workspace when you start RStudio.
- **Save workspace to .RData on exit: Never**: This will ensure your workspace is never saved to an .RData file when you exit RStudio.
- **Always save history (even when not saving .RData)**: This tells RStudio NOT to save your history to a .Rhistory file.
**These settings ensure a clean fresh environment each time you start RStudio.**
## Code
In the Code Editing tab you can customise how you would like your code to be edited.
- **Auto-detect code indention**: This will automatically detect the appropriate indentation of your code.
- **Use native pipe operator**: When using the insert Pipe command (Cmd/Ctrl + Shift + M), the native pipe operator `|>` instead of the magrittr pipe operator `%>%` will be inserted.
- **Soft-wrap R source files**: This will wrap your code to the next line when it reaches the end of the screen.
- **Continue comment when inserting new line**: This will continue the comment when you press enter at the end of a line that is a comment.
In the display tab you can customise how you would like your code to be displayed.
 - **Highlight selected line**: This will highlight the line of code that you are currently working on. - **Highlight R function calls**: This will highlight the function calls in your code. - **Use rainbow parentheses**: This will colour code your parentheses to make it easier to see where they open and close.
## Appearance
In the Appearance panel you are able to customise the appearance of the IDE including text size, font, and editor theme.
:::
### Creating projects locally
To create a new project locally in Rstudio, you can either use **File \> New Project \> New Directory**, or in the console (you only need to run this once, so you don't want it to be part of a repeatable script) run:
```{r}
#| eval: false
usethis::create_project("~/Desktop/wood-survey")
```
::: {.alert .alert-danger}
In general, do not use such hard code paths in repeatable scripts. They might not work across operating systems and are unlikely to generalise across someone elses file system.
:::
You will also need to run the `setup/install.R` script. See the [setup instructions](setup.qmd) for more details.