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reproducibility_ws_setup.Rmd
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reproducibility_ws_setup.Rmd
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---
title: "Reproducible research"
subtitle: "Workshop setup instructions"
params:
make_version: 4.3
git_version: 2.32.0
---
1. Make sure that you have installed the [latest versions of R and RStudio](r_and_rstudio.html).
2. Install the tidyverse and the renv packages by copying the following code into the Console, after the prompt `>`
```{r install-tidyverse, eval = FALSE}
if (!require(tidyverse)) install.packages("tidyverse")
if (!require(renv)) install.packages("renv")
```
3. Download the data file we will use during the workshop by clicking on the following button and save it in your Desktop or another convenient location.
```{r echo = FALSE}
data_file <- read.csv("https://raw.githubusercontent.com/EDUCE-UBC/educer/main/data-raw/data_intro_ws.csv")
downloadthis::download_this(data_file,
output_name = "data",
output_extension = ".csv",
button_label = "Download data",
button_type = "default",
has_icon = TRUE,
icon = "fa fa-save",
class = "hvr-sweep-to-left",
csv2 = FALSE
)
```
## {.tabset .tabset-fade .tabset-pills}
### Windows 10
#### Terminal
Install [GitBash](https://gitforwindows.org/), which emulates Bash (a Unix shell) in Windows. All command-line instructions should be completed in GitBash and not the native Windows Command Prompt.
#### Git
1. Basic Git was installed automatically with your GitBash Terminal.
2. Test that Git is properly installed by opening GitBash and typing `git --version` <kbd>enter</kbd>. This should populate the window with information on your version of Git such as
```
git version `r params$git_version`.windows.1
```
3. Once you've installed Git, you'll need to activate it in RStudio:
- Open RStudio and go to Tools > Global Options > Git/SVN
- Click "Enable version control interface for RStudio projects"
- If necessary, enter the path for your Git executable where provided.
- The path should look approximately like `C:/Program Files/Git/bin/git.exe`
- Warning: do **not** use `C:/Program Files/Git/cmd/git.exe`. The path should include `bin`, **not** `cmd`.
- Warning: the path should end in `git.exe`, **not** in `git-bash.exe`
- Restart RStudio.
4. Finally, you need to change your environment variables to ensure you can run R scripts from GitBash:
- Open the Control Panel > System Properties > Advanced. In Windows 10 you can find this by searching for "environment".
- Click on the "Environment Variables..." button to open the settings for the environment variables.
- In the window that pops up select the `PATH` variable and click the "Edit" button below it.
- In the next window that pops up click the "Browse" button and navigate to the folder that contains the `Rscript.exe` file. The path should look approximately like `C:/Program Files/R/R-4.1.1/bin/Rscript.exe`.
- Test that everything worked by restarting GitBash and typing `Rscript --version` <kbd>enter</kbd>. This should populate the window with information information on your version of R such as
```{bash, echo = FALSE}
Rscript --version
```
#### GitHub
1. If you do not already have one, sign up for a [GitHub account](https://github.com/).
2. Configure your GitHub user name and email (the email address you used to register on GitHub). To do this, open GitBash and type:
```{bash eval = FALSE}
git config --global user.name '<your GitHub username>'
git config --global user.email '<[email protected]>'
```
#### Make
1. Download the [Make *without guile* (version `r params$make_version`)](https://sourceforge.net/projects/ezwinports/files/), file name `` `r paste0("make-", params$make_version, "-without-guile-w32-bin.zip")` ``.
2. Unzip the folder.
3. Copy all of its contents to `C:\Program Files\Git\mingw64\`.
Merge all of the contents of the folders but do NOT overwrite/replace any existing files.
4. Check that Make is installed by typing `make --version` <kbd>enter</kbd> in GitBash. This should populate the window with information on your version of Make such as
```
GNU Make `r params$make_version`.
Built for Windows32
Copyright (C) 1988-2016 Free Software Foundation, Inc.
License GPLv3+: GNU GPL verison 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.
```
### macOS
#### Terminal
The native Terminal on macOS is Unix-based and, therefore, can be used in this workshop. You can access it under Applications > Utilities > Terminal.app
#### Git
1. Download and [install Git](https://git-scm.com/downloads).
2. Test that Git is properly installed by opening your Terminal and typing `git --version` <kbd>enter</kbd>. This should populate the window with information on your version of Git such as
```
git version `r params$git_version`
```
3. Once you've installed Git, you'll need to activate it in RStudio:
- Open RStudio and go to Tools > Global Options > Git/SVN
- Click "Enable version control interface for RStudio projects"
- If necessary, enter the path for your Git executable where provided (see picture below).
- Restart RStudio.
#### GitHub
1. If you do not already have one, sign up for a [GitHub account](https://github.com/).
2. Configure your GitHub user name and email (the email address you used to register on GitHub). To do this, open the Terminal and type:
```{bash eval = FALSE}
git config --global user.name '<your GitHub username>'
git config --global user.email '<[email protected]>'
```
#### Make
1. Download and install the Mac command line developer tools (including Make) by opening your Terminal and typing: `xcode-select --install` <kbd>enter</kbd>. In the window that opens, click "Install" to allow the installation of the full developer’s packet.
2. Check that Make is installed by typing `make --version` <kbd>enter</kbd> in your Terminal. This should populate the window with information on your version of Make such as
```
GNU Make `r params$make_version`.
Copyright (C) 2006 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.
There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A
PARTICULAR PURPOSE.
This program built for i386-apple-darwin11.3.0
```