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<!DOCTYPE html>
<html lang="" xml:lang="">
<head>
<title>cheatsheets.knit</title>
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<body>
<textarea id="source">
class: title-slide
count: false
.title[
# Cheat Sheets
]
.subtitle[
## Open Science Tools
]
.author[
### Claudio Zandonella & Davide Massidda
]
.institute[
]
---
## RStudio Keyboard Shortcuts
.pull-left-50[
<table class="table" style="font-size: 15px; width: auto !important; margin-left: auto; margin-right: auto;">
<thead>
<tr>
<th style="text-align:left;"> Command </th>
<th style="text-align:left;"> Windows &amp; Linux </th>
<th style="text-align:left;"> MacOS </th>
</tr>
</thead>
<tbody>
<tr grouplength="4"><td colspan="3" style="border-bottom: 1px solid;"><strong>Basic</strong></td></tr>
<tr>
<td style="text-align:left;padding-left: 2em;" indentlevel="1"> Run current line </td>
<td style="text-align:left;"> Ctrl+Enter </td>
<td style="text-align:left;"> Cmd+Return </td>
</tr>
<tr>
<td style="text-align:left;padding-left: 2em;" indentlevel="1"> Jump to Word </td>
<td style="text-align:left;"> Ctrl+Left/Right </td>
<td style="text-align:left;"> Option+Left/Right </td>
</tr>
<tr>
<td style="text-align:left;padding-left: 2em;" indentlevel="1"> Jump to Start/End </td>
<td style="text-align:left;"> Ctrl+Home/End </td>
<td style="text-align:left;"> Cmd+Home/End </td>
</tr>
<tr>
<td style="text-align:left;padding-left: 2em;" indentlevel="1"> Delete Line </td>
<td style="text-align:left;"> Ctrl+D </td>
<td style="text-align:left;"> Cmd+D </td>
</tr>
<tr grouplength="8"><td colspan="3" style="border-bottom: 1px solid;"><strong>Life Hack</strong></td></tr>
<tr>
<td style="text-align:left;padding-left: 2em;" indentlevel="1"> Insert assignment operator </td>
<td style="text-align:left;"> Alt+- </td>
<td style="text-align:left;"> Option+- </td>
</tr>
<tr>
<td style="text-align:left;padding-left: 2em;" indentlevel="1"> Insert pipe operator </td>
<td style="text-align:left;"> Ctrl+Shift+M </td>
<td style="text-align:left;"> Cmd+Shift+M </td>
</tr>
<tr>
<td style="text-align:left;padding-left: 2em;" indentlevel="1"> Comment/uncomment </td>
<td style="text-align:left;"> Ctrl+Shift+C </td>
<td style="text-align:left;"> Cmd+Shift+C </td>
</tr>
<tr>
<td style="text-align:left;padding-left: 2em;" indentlevel="1"> Reflow Comment </td>
<td style="text-align:left;"> Ctrl+Shift+/ </td>
<td style="text-align:left;"> Cmd+Shift+/ </td>
</tr>
<tr>
<td style="text-align:left;padding-left: 2em;" indentlevel="1"> Reformat Selection </td>
<td style="text-align:left;"> Ctrl+Shift+A </td>
<td style="text-align:left;"> Cmd+Shift+A </td>
</tr>
<tr>
<td style="text-align:left;padding-left: 2em;" indentlevel="1"> Find in Files </td>
<td style="text-align:left;"> Ctrl+Shift+F </td>
<td style="text-align:left;"> Cmd+Shift+F </td>
</tr>
<tr>
<td style="text-align:left;padding-left: 2em;" indentlevel="1"> Show help for function at cursor </td>
<td style="text-align:left;"> F1 </td>
<td style="text-align:left;"> F1 </td>
</tr>
<tr>
<td style="text-align:left;padding-left: 2em;" indentlevel="1"> Check Spelling </td>
<td style="text-align:left;"> F7 </td>
<td style="text-align:left;"> F7 </td>
</tr>
</tbody>
</table>
]
.pull-right-50[
<table class="table" style="font-size: 15px; width: auto !important; margin-left: auto; margin-right: auto;">
<thead>
<tr>
<th style="text-align:left;"> Command </th>
<th style="text-align:left;"> Windows &amp; Linux </th>
<th style="text-align:left;"> MacOS </th>
</tr>
</thead>
<tbody>
<tr grouplength="4"><td colspan="3" style="border-bottom: 1px solid;"><strong>Pro Tricks</strong></td></tr>
<tr>
<td style="text-align:left;padding-left: 2em;" indentlevel="1"> Move Lines Up/Down </td>
<td style="text-align:left;"> Alt+Up/Down </td>
<td style="text-align:left;"> Option+Up/Down </td>
</tr>
<tr>
<td style="text-align:left;padding-left: 2em;" indentlevel="1"> Copy Lines Up/Down </td>
<td style="text-align:left;"> Shift+Alt+Up/Down </td>
<td style="text-align:left;"> Cmd+Option+Up/Down </td>
</tr>
<tr>
<td style="text-align:left;padding-left: 2em;" indentlevel="1"> Add Cursor Above/below </td>
<td style="text-align:left;"> Ctrl+Alt+Up/Down </td>
<td style="text-align:left;"> Ctrl+Option+Up/Down </td>
</tr>
<tr>
<td style="text-align:left;padding-left: 2em;" indentlevel="1"> Add Cursor Selection </td>
<td style="text-align:left;"> Alt+mouse selction </td>
<td style="text-align:left;"> Option+mouse selction </td>
</tr>
<tr grouplength="2"><td colspan="3" style="border-bottom: 1px solid;"><strong>RMarkdown</strong></td></tr>
<tr>
<td style="text-align:left;padding-left: 2em;" indentlevel="1"> Knit Document </td>
<td style="text-align:left;"> Ctrl+Shift+K </td>
<td style="text-align:left;"> Cmd+Shift+K </td>
</tr>
<tr>
<td style="text-align:left;padding-left: 2em;" indentlevel="1"> Insert R chunk </td>
<td style="text-align:left;"> Ctrl+Alt+I </td>
<td style="text-align:left;"> Command+Option+I </td>
</tr>
<tr grouplength="4"><td colspan="3" style="border-bottom: 1px solid;"><strong>Devtools</strong></td></tr>
<tr>
<td style="text-align:left;padding-left: 2em;" indentlevel="1"> Load All </td>
<td style="text-align:left;"> Ctrl+Shift+L </td>
<td style="text-align:left;"> Cmd+Shift+L </td>
</tr>
<tr>
<td style="text-align:left;padding-left: 2em;" indentlevel="1"> Test Package </td>
<td style="text-align:left;"> Ctrl+Shift+T </td>
<td style="text-align:left;"> Cmd+Shift+T </td>
</tr>
<tr>
<td style="text-align:left;padding-left: 2em;" indentlevel="1"> Document Package </td>
<td style="text-align:left;"> Ctrl+Shift+D </td>
<td style="text-align:left;"> Cmd+Shift+D </td>
</tr>
<tr>
<td style="text-align:left;padding-left: 2em;" indentlevel="1"> Insert Roxygen Skeleton </td>
<td style="text-align:left;"> Ctrl+Alt+Shift+R </td>
<td style="text-align:left;"> Cmd+Option+Shift+R </td>
</tr>
</tbody>
</table>
]
---
## Bash Cheatsheet
.pull-left-70[
.code-size-12[
```bash
#---- Navigating ----#
pwd # Print working directory
cd <directory> # Change directory
ls <directory> # List files
-l # Long list with details
-a # List also hidden files and directories
-h # Return file size in readable units
#---- Modifying ----#
mkdir <directory> # Create directory
touch <file> # Create file
mv <source><dest> # Move (or rename) file or directory
cp <source><dest> # Copy file
-r # For directories
rm <file> # Remove file
rmdir <directory> # Remove directory
#----- Other -----#
echo <message> # Print message in console
cat <file> # Print file in console
less <file> # Open file in a screen
```
]
]
---
## Git Cheatsheet
.move-up-30[
.pull-left-50[
.code-small[
```bash
#---- Configure Settings ----#
git config --list # Check configuration settings
git config --global user.name "<My Name>" # Configure username
git config --global user.email "<[email protected]>" # Configure email
git config --global merge.conflictstyle diff3 # Configure conflict style
#---- Initialize Git Repo ----#
git init <path> # Initialize local repository
git clone <repository-URL> # Clone remote repository
#---- Tracking Files ----#
git status # Check repository status
# Staging
git add <files> # Add selected files to staging area
git add --all # Add all files to staging area
git rm --cached <file> # Remove selected files from staging area
git reset # Remove all files from staging area
# Commit
git commit # Create commit
# Options
-a # Commit all changes of tracked files
-m "<message>" # Inline commit message
git log # Get commit history
git log --oneline # Get commit history (compact)
```
]
]
.pull-right-50[
.code-small[
```bash
git diff # Changes since the last commit
git diff <commit-ID> # Changes since a specified commit
git diff <commit-ID-A> <commit-ID-B> # Changes from commit-A to commit-B.
git checkout <commit-ID> # Point HEAD to specific commit/branch
git revert <commit-ID> # Undo commit (forward-way)
git reset <commit-ID> # Undo commit (disruptive-way)
#---- Collaboration ----#
git remote -v # List remote (verbose)
git remote add <name> <url> # Add remote
git pull <remote-name> <branch-name> # Pull commits from remote
git push <remote-name> <branch-name> # Push commit to remote
-u # Set upstream remote branch
git branch --set-upstream-to="<remote/branch>" # Set upstream remote branch
#---- Branching ----#
git branch # List branches
git branch -vv # List branches (verbose)
git branch -vvr # List remote branches (verbose)
git branch <branch-name> # Create new branch
git checkout -b <new-branch-name> # Create and move to new branch
git merge <branch-name> # Merge target branch
git merge --abort # Abort merge
git branch -d <branch-name> # Delete local Branch
git push <remote-name> --delete <branch-name> # Delete remote Branch
```
]
]
]
---
.pull-left-50[
## `targets` Cheatsheet
.code-size-12[
```r
# Define targets
tar_target(<target_name>, <expression>)
tar_target(<target_name>, <path-to-file>, format = "file")
tarchetypes::tar_render(
<target_name>, <path-to-document>
)
# Check pipeline
tar_manifest()
tar_visnetwork()
# Run analysis
tar_make()
# Load Results
tar_read()
tar_load()
```
]
]
.pull-right-50[
## `renv` Cheatsheet
.code-size-12[
```r
# Initialize project
init()
# Install package
install.packages()
# Capture dependencies
snapshot()
# Restore dependencies
restore()
```
]
]
---
## Docker Cheatsheet
.pull-left-50[
.code-small[
```bash
#---- Images ----#
docker build -t <name-image>:<tag> . # Build an image from Dockerfile
docker images # List all images
docker image ls # List all images
docker image rm <id-image> # Remove Image
#---- Container ----#
docker run --name <container-name> <image>:<tag> # Run a container from an Image
# Other flags and options
--rm # Remove at exit
-it # Interactive terminal
-d # Detached mode
-v <host-path>:<container-path> # Attach a volume or bind mount
-e <name>=<value> # Define environment variable
-p <host-port>:<container-port> # Map port
docker ps -a # List all containers
docker container ls -a # List all containers
docker stop <container-name> # Stop container
docker start <container-name> # Start container
docker rm <container-name> # Remove container
docker cp <container-name>:<path> <host-path> # Copy from container to host
docker cp <host-path> <container-name>:<path> # Copy from host to container
docker exec -it <name-container> bin/bash # Connect to container bin/bash
```
]
]
.pull-right-50[
.code-small[
```bash
#---- Volumes ----#
docker volume create <name-volume> # Create named volume
docker volume ls # List all volumes
docker volume rm <volume id> # Remove volume
#---- Docker Compose ----#
docker-compose up # Start service
docker-compose down # Stop service
#---- Docker Hub ----#
docker pull <username>/<name-repo>:<tag> # Pull image
docker push <username>/<name-repo> # Push image
docker login --username=<username> --email=<email@com> # Login
docker tag <image-id> <username>/<name-repo>:<tag> # Tag image for repository
```
]
]
---
class: inverse, center
# God Progammer Mode Achieved!
<img src="images/exercises/stallman.png" width="40%" style="display: block; margin: auto;" />
</textarea>
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