Chapter 38 Running R from the UNIX Command Line

38.1 What is the UNIX Command line?

The command line is a very basic Terminal window with a prompt at which you can type commands, And do primitive but powerful things to your files. The UNIX computing environment was developed in the 1960s, and is still beloved and fetishized by brogrammers, who believe you are not truly a programmmer if you can’t code from the command line. This is silly.

The major attraction to UNIX in the 1960s is that it was much better than punch cards. Which isn’t saying much. We have had 60 years of software advancement and user interface improvements, so we (most of time) should not have to put up with the inherent user hostility of the UNIX environment.

UNIX is an early operating system, which is built around a ‘kernel’ which executes operating system commands, and a ‘shell’ which interprets your commands and sends them to the kernel for execution. The most common shell these days is named ‘bash’, which is a silly recursive brogrammer joke. You will sometimes see references to shell scripts or shell or bash programming. These are the same thing as command line programming.

UNIX is a common under-the-hood language across many computers today, as the Apple iOS is built on top of UNIX, and the various versions of the LinuxOS are built on a UNIX-like kernel, with a similar command shell.

The command line is often the least common denominator between different pieces of open-source software that were not designed to work together. It can occasionally be helpful to build a data pipeline from mismatched parts. However, there is a lot of low-quality user-hostile command line work involved to get it done, commonly referred to as “command-line bullshittery”. This is a common bottleneck that slows scientific productivity, and there is a vigorous discussion of it on the interwebs here and here (a counterpoint). Essentially, some argue that it is largely a waste of time and effort, while others see it as a valuable learning experience, like doing least squares regression by hand with a pencil.

Running R from the command line is a bit like spending a day tuning your car’s engine by yourself. There is a case to be made that this will improve the efficiency and performance of your car, but it is also usually more efficient to pay someone else to do it, unless you are a car expert with a lot of free time.

38.2 Why run R from the command line?

You can run R from the command line. It has none of the bells and whistles, nor any of the user conveniences of the RStudio Interactive Developer Environment (IDE). But it is how R was originally expected to be used when it was developed back in 2000 in New Zealand.

Running R from the command line allows you to do powerful things, like process multiple files at once, which can be handy when you have multiple files of sequencing data from distinct observations, or you have a multistep data wrangling pipeline with several slow steps. For many years, this was the only way to easily apply code across multiple files to build a complex data pipeline.

This is much less true today, with tools to handle file paths like the {here} and {fs} packages, run Python scripts from R with the {reticulate} package, run C++ scripts with Rcpp, and run bash, python, SQL, D3, and Stan scripts from Rmarkdown. You can use the {targets} package to manage multi-step data pipelines in different languages (similar to make). But some labs have been doing things at the command line for years, and find it hard to change.

38.3 How do you get started?

First, you need to open a terminal window. And to do that, you need to find it. This is akin to getting under the hood of a car, and computer makers don’t exactly encourage it.

38.3.1 On a Mac

Go to Finder/Applications/Utilities/Terminal

38.3.2 On a Windows PC

Go to Applications/Terminal

38.4 The Yawning Blackness of the Terminal Window

So, you have managed to open a terminal window, which has a standard UNIX prompt, ending in something like % or $. Not terribly helpful, is it? The bash shell is waiting for you to enter a command.
No user interface for you!

Let’s start with a introductory command, which can’t do any harm. Run the command below:
whoami

whoami

## peterhiggins

Remember that UNIX started out as an operating system for terminals, and knowing who was logged in was a helpful thing, especially if the person logged in was being charged for mainframe time by the minute.

You can string together two commands with a semicolon between them.

Try the following:

whoami;date

## peterhiggins
## Thu Oct 31 09:06:08 EDT 2024

OK, fine. This is sort of helpful. It was really important when you were on a terminal and paying by the minute for time on a mainframe back in 1969. And, on occasion, if you will need to use an entire computer cluster to run a script (or scripts) on a lot of data, you will likely have to use some of this command line knowledge. You can even schedule jobs (scripts) to run when your time is scheduled on the cluster with cron and crontab.

At this point, it would be helpful to open a window with your Documents folder, and keep it side by side with the window in which you are reading this e-book. We will start working with files and directories, and it is helpful to see changes in your file/folder structure in real time. As we run commands in the bash shell, check them against what you see in the folder window. You may find that some files (dotfiles, starting with a period) are hidden from the user to prevent problems that occur when these are deleted.

38.5 Where Are We?

OK, let’s start looking at files and directories. Start with the pwd command, which does not stand for password, but for print working directory.

Run the code below in your Terminal window.

pwd

## /Users/peterhiggins/Documents/RCode/rmrwr-book

You can see the full path to your current directory. This can be a bit obscure if you are just looking at your folder structure, particularly at the beginning of the path. Fortunately, the {here} package handles a lot of this for you when you are working in Rstudio projects.
We think of the directory as a tree, with a root - in this case, Users, and various branches as you build out folders and subfolders.
We can move up and down the folders of the directory paths with the cd command, for change directory.

Try this command in your Terminal Window, and see if you can figure out what it does.

cd ..

cd .. changes the directory up one level closer to the root directory. Note that there is a required space between cd and the ... You can also go directly to the root directory with cd /. It is straightforward to go up the directory tree, as each folder only has one parent. But it is tricky to go down the directory tree, as there are many possible branches/children, and you do not inherently know the names of these branches. We need to list the contents of your current directory with ls to know what is there.

Try the ls command in your Terminal window

cd /Users/peterhiggins/Documents/;
ls

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## Screenwriting Contests.docx
## Sean Common App academic honors list.docx
## Sean Common App activities list.docx
## Sean Higgins Bordogni.mp4
## Sean Higgins Brag Sheet.docx
## Sean Investment Summary.docx
## Sean Resume Tabular VBorder.docx
## Sean Resume Tabular.docx
## Sean Resume.docx
## Sean Summer Priorities 2016.docx
## Seattle Talk Dec 2012
## SecureIBD.pptx
## Severe UC protocol
## SevereUC_Tofa_Presentation_IBD_Forum.pptx
## SevereUC_Tofa_Presentation_Pfizer.pptx
## Shail CT
## ShareRmd.html
## Sheehan Pfizer IBD Fellowship.docx
## Sherman Prize Nominee Questions.docx
## Shoreline West Tour Information.docx
## Short PA slides.pptx
## Shotwave thread.docx
## Should we accel IFX - survey.pdf
## Signing Clinical Research Infusion Orders.pdf
## SingleCell_DDW_2021_ISS.pdf
## SkinCancer.IBD.Gentics_Yanhua_PDRH.docx
## Slade UC review Walter
## SoMe_use_2020.png
## Social Media for GI.pptx
## Soulfege t shirts
## Source Code PT1.docx
## Specialty Pharmacist Referral Process_11162021.pptx
## Specific Aims.pdf
## Stairs.docx
## Stelara paper.docx
## Stelara paper_revised_PDRH_KCC.docx
## Structure of Aim 3.docx
## Surgery Topics
## Surveys
## T32 Competitive Renewal 2017 FINAL WM.pdf
## T32 Fellowship Annual Orientation 2022.pptx
## T32 summary statement.pdf
## T32_current_text_14June2019.docx
## TOPPIC ML draft v5SCM_YL_AKW_PDRH.docx
## TabaCrohn IBD J club.docx
## Tables.docx
## Taiwan talks
## Takeda Grants_Letter of Request_IBD School Videos_Medication Series_2018_.docx
## Takeda_IBD School Videos_Submission.pdf
## Task List 2020-2.docx
## Task List 2020-5.docx
## Task List 2020.docx
## Task List 2021.docx
## Task List 2022.docx
## Task List 2024.docx
## Tenure Plan
## Testing signatures with Adobe.pdf
## The Innovative IBD Center.docx
## The Risk of SARS.R1.Markup.docx
## Thiopurine talks Manitoba 2011
## Thiopurines talks Vandy
## Tidymodels.docx
## Timelines for K submission.pdf
## Timelines for K submission.pptx
## Tips for Submitting DDW Abstracts for 2022.docx
## Tofa Inpatient
## Tofa in ICI Figure Legends_Final Draft_V2.docx
## Tofa inpatient induction Protocol_02NOV2018_PHforEdits.docx
## Tofa_Presentation_2_10_2021.pptx
## Toffee Separation Tips.docx
## Topics to Discuss with Bill.docx
## Trip to Hawaii 2023 GUILD.docx
## UC CD Impact Manuscript Tables__19Feb2021_PDRH.docx
## UC and CD Impact Manuscript_Draft 2_9Jan2022_PDRH.docx
## UC and CD Impact Manuscript_Draft1_19Feb2021_PDRH.docx
## UC2.jpg
## UCB Pt video 2010 Grant App
## UCRx_DDW_2021_ISS.pdf
## UC_protocol_comments_2020.docx
## UEGW 2010
## UEI stidham files
## UM IBD Clinical Trials IBD referral form.docx
## UM Severe UC Protocol.docx
## UM Severe UC Protocolv3.0.docx
## UPA_U_ACHIEVE 1st draft_PDRH.docx
## US_R01 outcomes I.1.docx
## US_R01 outcomes I.1_Dillman.docx
## Untitled.docx
## Upa ASUC Concept Page.docx
## Upa IBD J Club.pdf
## Upa IBD J Club.pptx
## Upa M14-234 SS3 maintenance  Q and A ECCO 2022.docx
## Upa outpatient vs Prednisone_PDRH.docx
## V8 Infliximab Outcomes_PDRH.docx
## VINDICO IBD
## VINDICO_PRO.pptx
## VideoVisitSchedulingQuickApptsforProviders.pdf
## VincentChen_K specific aims 2020-10-25.docx
## VirtualPtEdMar2020.v2.pdf
## Walk Letter of Reference.docx
## Walk Letter of Reference.pdf
## WebEx
## Weekly Clinical T32 Seminar 2023.docx
## Why not excel.docx
## Zoom
## Zwift
## Zwift-Gift-Card.pdf
## aga institute council july 2020 meeting.pdf
## algorithms_thiopurine.pdf
## base-r-cheatsheet.pdf
## biomakers_fibrosisPDRH.docx
## blue_down_arrow - Gravit Designer.html
## bmj_imputation.pdf
## bowel disease_2108_PDRH.docx
## ccf_verily.docx
## cgh_factors_utilization.pdf
## clare_stocks_long_term.xlsx
## cycling core exercises.docx
## draft letter to patients.docx
## draft_GUILD_abstract.docx
## draft_tokenization letter Risa_Uste.docx
## early-career-faculty_Dec-2020.xlsx
## epic cancel_reschedule appointments.ppt
## epic schedule viewing_close.ppt
## escalator.html
## exercise1.xlsx
## exercise2.xlsx
## fellow graduation 2020.docx
## flag_contest_submission_PDRH.pdf
## hershey_long_term.xlsx
## hexStickers.jpg
## higgins2x3.jpg
## higgins_signature.docx
## iBike Rides
## imaging_stricture.xlsx
## introduce_clare.docx
## jama_cushing_crohn_review_2021.pdf
## learnr app diagram.jpg
## learnr app diagram.pptx
## letter Lowrimore.docx
## medicaldata_NHS_R_2021.pptx
## medicaldata_Rmedicine21.pdf
## medicaldata_Rmedicine21.pptx
## medicaldata_image_hex.ai
## messy_bp.xlsx
## mockstudy manuscript draft.docx
## nejm1966_beecher_ethics.pdf
## nejm_indomethacin.pdf
## nejm_statins.pdf
## orange_green_down_arrow - Gravit Designer.html
## orange_green_down_arrow- Gravit Designer.pdf
## pdrh_IBD_email.xlsx
## personal statement fellowship_PDRH.docx
## peterhiggins.jpg
## pink_down_arrow - Gravit Designer.html
## pink_up_arrow - Gravit Designer.pdf
## rehab schedule.docx
## seq-6.pdf
## signature.docx
## signature.fld
## signature.html
## signature.pdf
## signature.png
## sorted_steno.xlsx
## starting biologics.pptx
## stiff_bcl.R
## submitJanssen_IBD School Videos_12Jul2018.pdf
## tidyr_pivot.png
## tidyr_pivot.xcf
## tofa_checkpoint.pdf
## twitter.com.webarchive
## ucla1.jpg
## untidy_sheets.pptx
## user_testing_learnr tutorials.pptx
## weiser_topics.docx
## wga_min20.pdf
## zwift_training_pacepartner.xlsx
## {"Attachments"-[{"__type"-"F.textClipping
## ~$ Severe UC Protocol.docx
## ~$Big data with Arrow and DuckDB with demo.pptx
## ~$Jun2021_ibdTrials.pptx
## ~$T Review Higgins.docx
## ~$sk List 2020-5.docx
## ~$sk List 2020.docx
## ~$sk List 2021.docx

You will see a listing of all files and folders in the current directory. You can get more details by adding the option (sometimes called a flag) -l

cd /Users/peterhiggins/Documents/;
ls -l

The full listing will give you more details, including read & write permissions, file size, date last saved, etc.
Many UNIX commands have options, or flags, that modify what they do.

Find a folder inside of your Documents folder. We will now go down a level in the directory tree. In my case, I will use the Powerpoint folder.
In your Terminal window:

change the directory to the Powerpoint directory
list the contents of this folder

cd /Users/peterhiggins/Documents/Powerpoint;
ls

## 2016IBDClinTrialsforMDsDearborn.pptx
## 2016IntegratedDeckorMDsGB.pptx
## 2019 SCSG GI Symposium IBD SoA  -  Read-Only.pptx
## ADTC Flowchart-draft-RWS_14FEB2015.docx
## Acutely Ill IBD Patient protocol for ADTC-RWS.docx
## Annual Research Career Review 2021PH.pptx
## BE LGD Dearborn 2016.04.12.pptx
## CCF_Clinical_Trials.pptx
## CP1_Higgins Intro.pptx
## CP2_DiagnosingIBD_KC.pptx
## CP3_FMT_MMM.pptx
## CP4_SurgeryRegenbogen.pptx
## CP5_NutritionIBD_EH.pptx
## CP6_Infections2018.pptx
## CP7_PsychologicalStress_Riehl IBDFlint2018.pptx
## CP8_SteroidsWaljee.pptx
## CP9_ClinicalTrials2018.pptx
## ECCO 2022 UPA-UC ext duration oral_v2.0_3Feb2022_for QC.pptx
## ECCO22_Template.pptx
## Feasibility and Pilot Studies CTA.pptx
## FibrosisIBDCedars2016.pdf
## Getting Started in RStudio.pptx
## Higgins CCFA CTPROs in IBD.pptx
## Higgins CCFACT2017FundingClinicalResearch.pptx
## Higgins HK 2017IBD Nursing and Quality of Care.pptx
## Higgins HK 2017The Gut Microbiota and the Pathophysiology of IBD.pptx
## Higgins Microbiota for IBD Patient Ed.pptx
## HigginsAI talk for DDW2019.pptx
## HigginsDec2018AJG_SmokingStatus.pptx
## HigginsFALKMadridThioMtx2017.pptx
## Higgins_CCC_2018_Refractory_Rising_Bar_v3.pptx
## IBD Part 1 Higgins USMN.pptx
## IBD Part 2 Higgins USMN.pptx
## IBD Part 3 Higgins USMN.pptx
## IBD Part 4 Higgins USMN.pptx
## IBD and PTSD.pptx
## IBDUpdate.pptx
## IOIBD.Fibrosis.Higgins.2018.Amsterdam.pptx
## Integrated Slide Deck Dearborn 2016.04.12.pptx
## MER Stress Management Dearborn 4-14.pptx
## MichiganMedicine-IBDTemplate.potx
## Outcome Measures CTA.pptx
## PDRH RCR 2020.pptx
## PDR_Higgins_DeficienciesInIBD_AIBD2021.pptx
## PennThioMTX2017Higgins.pptx
## Pilot Feasibility Studies.pptx
## PragueRefractoryRisingBar2017.pptx
## Pregnancy in IBD.pptx
## Presentation1.pptx
## Regenbogen CRS for GI CME Course2016.pptx
## Senior Slide Show.pptx
## Social Media for GI.pptx
## SuperRough AI.pptx
## T32 Fellowship Annual Orientation 2023.pptx
## T32 GI Clinical Pink Sheet analysis.pptx
## T32 GI Fellowship Presentation 2023.pptx
## ThomsonRectalStumpComplicationsIBD2_13.pptx
## UEGweek2020.pptx
## UMHS IBD ADTC Encounter Note-DRAFT-RWS_15FEV2015.docx
## UMHS Talk- Moving Beyond AntiTNF 4-2016 FINAL v2.pptx
## UMich COVID-19  IBD.pptx
## Update on COVID and IBD.pptx
## Vertebrate Animals for K.pptx
## VirtualPtEdMar2020.v2.pptx
## VirtualPtEdMar2022Jan.pptx
## VirtualPtEd_2022_Deck.pptx
## VirtualPtEd_2022_Feb.pptx
## Writers Room.pptx
## ibd_meds_surgery_metan.pptx

Great!
You moved to a new directory and listed it.
Now we will get fancy, and make a new directory within this directory with the mkdir command.

Try this in your Terminal window:

pwd;
mkdir new_files;
ls

You have now made a new directory (folder) within the previous directory (pwd = present working directory), named new_files. Verify this in your Documents folder.
You can now make changes to this directory
and list the contents (it should currently be empty).

Try this out in your Terminal Window (note edit the cd command to your own directory path).

cd /Users/peterhiggins/Documents/Powerpoint/new_files;
ls

Note that you can abbreviate the current directory with ., so that you could have also used cd ./new_files

You can create a new (empty) file in this directory with the touch command. Sometimes you need to create a new file, then write data to it.

Try this out

touch file_name;
ls

You can also create a file with data inside it with the cat > command.

Type in the following lines into your Terminal window. When complete, type control-D to be done and return to the Terminal prompt. cat stands for concatenate.

cat > file2.txt
cat1
cat2
cat3

Now you can list the contents of this file with the cat command below.

Give this a try

cat file2.txt

You can also list the directory of your new_files folder with ls to see the new folder contents.

Try this

ls

Note that you don’t need to use the Terminal to run bash commands. You can do this from an Rmarkdown file.
Take a moment to run pwd in your Terminal, to get the current directory.

Now open Rstudio, and a new Rmarkdown document.
Copy the path to the current directory from the Terminal.
Switch back to the Rmarkdown document.
Select one of the R code chunks (note the {r} at the top) and delete it.
Now click on the Insert dropdown at the top of the document, and insert a Bash chunk.
Now you can add UNIX commands (separated by a semicolon) to this code chunk, like

cd (paste in path here);
pwd;
ls;
cat file2.txt

Then run this chunk.

Now you can run terminal commands directly from Rmarkdown!

38.6 Cleaning Up

OK, now we are done with the file file2.txt and the directory new_files. Let’s get rid of them with rm (for removing files) and rmdir for removing directories.
In order, we will - Make sure we are in the right directory - remove the file with rm file2.txt - go up one level of the directory with cd .. - remove the directory with rmdir new_files

Give this a try

pwd;
rm file2.txt;
cd ..;
rmdir new_files

Verify all of this in your Documents window.
This is great. But you can imagine a situation in which you mistakenly rm a file (or directory) that you actually needed. Unlike your usual user interface, when a file is removed at the command line, it is gone. It is not in the trash folder. It is really gone. There is something to be said for modern user interfaces, which are built for humans, who occasionally make mistakes. Sometimes we do want files or folders back.

38.7 Other helpful file commands

Here are some file commands worth knowing

cat filename - to print out whole file to your monitor
less filename - to print out the first page of a file, and you can scroll through each page one at a time
head filename - print first 10 lines of a file
tail filename - print last 10 lines of a file
cp file1 file2 - copy file1 to file2
mv file1.txt file.2.txt file3.txt new_folder - move 3 files to a new folder

38.8 What about R?

So now you can get around directories, and find your files in the Terminal window, but you really want to run R.
You can launch an R session from the Terminal Window (if you have R installed on your computer) by typing the letter R at the Terminal prompt

Launch R

You get the usual R intro, including version number, and the R> prompt.
Now you can run R in interactive mode with available datasets, or your own datasets.

Try a few standard tidyverse commands with the mtcars dataset.
Give the examples below a try.

You can use q() to quit back to the terminal (and reply “n” to not save the workplace image).

head(mtcars)

##                    mpg cyl disp  hp drat    wt  qsec vs am
## Mazda RX4         21.0   6  160 110 3.90 2.620 16.46  0  1
## Mazda RX4 Wag     21.0   6  160 110 3.90 2.875 17.02  0  1
## Datsun 710        22.8   4  108  93 3.85 2.320 18.61  1  1
## Hornet 4 Drive    21.4   6  258 110 3.08 3.215 19.44  1  0
## Hornet Sportabout 18.7   8  360 175 3.15 3.440 17.02  0  0
## Valiant           18.1   6  225 105 2.76 3.460 20.22  1  0
##                   gear carb
## Mazda RX4            4    4
## Mazda RX4 Wag        4    4
## Datsun 710           4    1
## Hornet 4 Drive       3    1
## Hornet Sportabout    3    2
## Valiant              3    1

mtcars %>% 
  filter(mpg > 25) %>% 
  select(starts_with('m')|starts_with('c'))

##                 mpg cyl carb
## Fiat 128       32.4   4    1
## Honda Civic    30.4   4    2
## Toyota Corolla 33.9   4    1
## Fiat X1-9      27.3   4    1
## Porsche 914-2  26.0   4    2
## Lotus Europa   30.4   4    2

38.9 What about just a few lines of R?

Sometimes you will want to call R, run some code, and be done with R.
You can call R, run a few lines, and quit in one go.
You can add the flag -e (for evaluate) to the call to R,
and put the R commands in quotes.

Try the example below (note that this will not work if you are still in R - be sure you are back in the terminal with the % or $ prompt)

R -e "head(mtcars)"

or this example - note that single or double quotes does not matter - as long as they match.

Try this

R -e 'install.packages(palmerpenguins)'

You can also string together several commands with the semicolon between them.

Try the example below.

R -e 'library(palmerpenguins);data(penguins);tail(penguins)'

38.10 Running an R Script from the Terminal

Now we are stepping up a level - you have an R script that you have carefully created and saved as the myscript.R file. How do you run this from the Terminal?
This is straightforward - you can call the Rscript command with your file name.

Pick out a short R file you have written, make sure you are in the right directory where the file is, and use it as in the example below.

Rscript myscript.R

This launches R, runs your script, saves resulting output (if your script includes save or ggsave commands), closes R, and sends you back to the Terminal. Very nice!

38.11 Rendering an Rmarkdown file from the Terminal

This is a little different, as you can’t just run an Rmarkdown file. Normally you would use the dropdown button to knit your file from Rstudio. But you can use the rmarkdown::render command to render your files to HTML, PDF, Word, Powerpoint, etc. Pick out a small Rmd file like output_file.Rmd below, make sure you are in the right directory where the file is, and try something like the example below.
Note that this is one case where nesting different types of quotes (single vs. double) can come in handy.
It helps to use single quotes around your filename and double quotes around the rmarkown::render command.

Try it out

Rscript -e "rmarkdown::render('output_file.Rmd')"

So there you have it!
Just enough to get you started with R from the command line.

For further reading, check out these helpful links: