Last updated: 2020-07-04

Checks: 6 1

Knit directory: Hands-on-Training/

This reproducible R Markdown analysis was created with workflowr (version 1.6.2). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.

R Markdown file: uncommitted changes

The R Markdown file has staged changes. To know which version of the R Markdown file created these results, you’ll want to first commit it to the Git repo. If you’re still working on the analysis, you can ignore this warning. When you’re finished, you can run wflow_publish to commit the R Markdown file and build the HTML.

Environment: empty

Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.

Seed: set.seed(20200702)

The command set.seed(20200702) was run prior to running the code in the R Markdown file. Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.

Session information: recorded

Great job! Recording the operating system, R version, and package versions is critical for reproducibility.

Cache: none

Nice! There were no cached chunks for this analysis, so you can be confident that you successfully produced the results during this run.

File paths: relative

Great job! Using relative paths to the files within your workflowr project makes it easier to run your code on other machines.

Repository version: e86e1de

Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.

The results in this page were generated with repository version e86e1de. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.

Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated: 


Ignored files:
    Ignored:    .Rhistory
    Ignored:    .Rproj.user/

Untracked files:
    Untracked:  Folder/

Unstaged changes:
    Modified:   analysis/commandline.Rmd

Staged changes:
    Modified:   analysis/commandline.Rmd

Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.

These are the previous versions of the repository in which changes were made to the R Markdown (analysis/commandline.Rmd) and HTML (docs/commandline.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.

File Version Author Date Message
Rmd e86e1de Laura Vairus 2020-07-04 Change
Rmd 4818263 HomeUser 2020-07-04 command line tutorial
html 4818263 HomeUser 2020-07-04 command line tutorial

Command Line Basics - Terminal

In this tutorial, we will learn some basic Unix/Linux commands to perform tasks in the command line.
The command line is an interface that allows you to store, manage, and process data.
Terminal is an app that gives you access to the command line.

(Note: This tutorial was made for Mac users. For Windows users, follow the tutorial here)

To start, open Terminal using the computer’s search button.
Whenever you’re in Terminal, you are “standing” in a certain file on your computer.
From there, you can move around folders, create files, and much more.

For now, here are a few basic commands and their functions to get you started:

Command Denotation Function
pwd (present working directory) shows you the folder you are currently in
ls (list files) lists all of the items in your current folder
cd (change directory) move from folder to folder
mkdir (make directory) creates a folder in your current folder
touch (touch) creates a file
mv (move/rename) moves or renames files/folders
cp (copy) copies a file to a new location
cp -r (copy recursive) copies a folder and everything in it to a new location
rm (remove here) deletes a file
rm -rf (remove here recursive force) deletes a folder

Hands-On Practice

  • Follow along the commands on Terminal to practice

Find out what folder you are currently in

pwd


Find out what files/folders you have in that folder

ls


Go back one folder

cd ..
  • cd .. will take you back to the parent folder of the one you are currently in

Go to your home directory

cd
  • cd ~ will have the same effect

Go into your Desktop folder

cd ~/Desktop/
  • The command line is case sensitive, so capitals are important!

Make a folder named “Folder” in your Desktop

mkdir Folder


Make a text file named “file.txt”

touch file.txt


Move “file.txt” into “Folder”

mv file.txt Folder/
  • mv works for moving both files and folders

Rename the file to “file2.txt”

mv file.txt file2.txt
  • Remember you have to enter “Folder” to work with your file

Make a copy of “file2.txt” and move it to your Documents

cp file2.txt ~/Documents/file2.txt
  • To copy files, you must enter the name of the file you want to copy, a space, and then the path to where you want to move it.
  • the .. takes the file from the Desktop to the home directory, it’s parent folder; into the Documents folder; and drops it inside

Copy “Folder” and the file inside it to your Documents

cp -r Folder ../Documents/Folder
  • Remember you have to go to your Desktop to work with “Folder”
  • The -r (recursive) copies everything inside the folder
  • If you don’t use -r, the command line will give you an error saying “Folder is a directory (not copied)”

Delete the file2.txt that you copied into Documents

rm file2.txt


Delete the “Folder” that you copied into Documents

rm -rf Folder
  • -rf stands for “recusive” and “force”
  • Recursive deletes everything inside the folder
  • Force forces the system to delete the folder. This is a safety feature to make sure you don’t accidentally delete anything
  • REMEMBER: Be careful whenever you delete a file/folder because you can’t undo it; Once it’s gone, it’s gone

Extra Notes

  • Paths
    • When moving to a folder, you must type out the full “path” to it
    • For example, let’s say you want to go to a folder (named “Folder”) in your Desktop.
    • Right now, you are in your “home directory.” If you type cd Folder, Terminal will give you an error, saying “there is no such file or directory.” This is because the command line only looks in your current folder, and there is no “Folder” in your home directory
    • Instead, you have to type cd Desktop/Folder. The command line looks for “Desktop” in your home directory, then for “Folder” in your Desktop.
  • Tab (auto-completion)
    • Pressing tab can be extremely helpful and time-saving
    • After typing in the first few letters of a file/folder you want to interact with, pressing tab will autocomplete the name of it
    • In the case of mutiple files/folders with similar starting letters, pressing tab twice will print a list of the possiblilities
    • If tab doesn’t seem to work, that might indicate that you’re in the wrong folder
  • Arrow Keys
    • This is another time-saving trick
    • You can use the up and down keys to copy in previous commands into you current line
    • This can be helpful if you had just a one-letter typo in a long, complicated, previous command

For Windows Users


sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS High Sierra 10.13.6

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.4.6    rstudioapi_0.11 whisker_0.4     knitr_1.29     
 [5] magrittr_1.5    workflowr_1.6.2 R6_2.4.1        rlang_0.4.6    
 [9] stringr_1.4.0   tools_4.0.2     xfun_0.15       git2r_0.27.1   
[13] htmltools_0.5.0 ellipsis_0.3.1  yaml_2.2.1      digest_0.6.25  
[17] rprojroot_1.3-2 tibble_3.0.1    lifecycle_0.2.0 crayon_1.3.4   
[21] later_1.1.0.1   vctrs_0.3.1     promises_1.1.1  fs_1.4.2       
[25] glue_1.4.1      evaluate_0.14   rmarkdown_2.3   stringi_1.4.6  
[29] compiler_4.0.2  pillar_1.4.4    backports_1.1.8 httpuv_1.5.4   
[33] pkgconfig_2.0.3