FES 720 Introduction to R

How Computers Work

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FES 720: Intro to R

Which House will the Apple be in … ?

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By the end of today, you will:

Understand the different parts of a computer and how they interact
Navigate through your computer using the command line
Create and delete folders and files

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The worst prediction in history?

The world will need no more than “about five computers”

Thomas Watson, IBM Corporation, 1940s

Source: https://imgs.xkcd.com/comics/number_of_computers.png

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A computer is an INFORMATION PROCESSOR

Computers take in information or data (INPUT),

crunch it (PROCESSING),

spit out the results (OUTPUT),

and store the data and/or the result (MEMORY).

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Your microwave oven is a very simple computer

INPUT: numbered keypad

PROCESSING: convert key presses to cooking time and temperature

MEMORY: clock

OUTPUT: e.g., Cook for 3 minutes at high temperature … DINNER!

$59.99 from Target

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Output …

Mmm.. dinner

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Your laptop is a more complex computer

INPUT: keyboard, mouse, scanner, …

PROCESSING & MEMORY: central processing unit (CPU) interprets and executes program instructions, and communicates with input, output, and secondary storage. It has a small amount of temporary memory.

OUTPUT: screen, printer, video, …

SECONDARY STORAGE: hard drives, external drives, flash. These can store large amounts of data and software

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HARDWARE is the physical computer and peripherals

Bits of a computer …

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SOFTWARE tells the computer what to do

Planned, step-by-step instructions.

Two kinds of software:

System software: Operating system (e.g., Windows, MacOS, Unix)
Applications software: Word, Excel, unix programs, .. R!

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An operating system versus permanent physical circuits

Operating systems …

do a variety of DIFFERENT things;
INTERACT with the user in COMPLEX ways;
can CHANGE what it does and how it interacts

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The operating system is an intermediary between applications and hardware

It manages the computers resources (CPU, memory, drives, outputs)
Establishes a user interface (graphical or command-line)
Executes and provides services for applications software.

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User Interfaces allow humans to interact easily with computers

You are probably mostly familiar with GRAPHICAL USER interfaces (GUI, “goo-ee”).

GUIs allow users to interact with mouse/finger movements and clicks.

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R uses a COMMAND-LINE interface (CLI).

CLI are less user-friendly at first, but much more powerful:

Can keep permanent record of commands
Can automate some/many/all steps by calling this record

All personal computers have GUI and CLI access!

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An Application Programming Interface (API) allows software to interact easily

Analagous to a GUI, but for software ‘users’.

Usually an abstraction of underlying specific instructions.

Allows software to work on many/all operating systems.

https://en.wikipedia.org/wiki/Application_programming_interface

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File systems and directory structure

A file system allows us to access specific data/information on a computer.

Naming is derived from office filing systems for paper documents.

“FILE” = a group of data, e.g., a Word document, R code, image, …

“FOLDER” (or DIRECTORY) = a collection or group of files.

Can be HIERARCHICAL, i.e., allow subfolders.

“PATH” = Full location of a (sub)directory: e.g., “C:\Simon\Teaching\FES720"

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Path: The address of a folder or file

It is hierarchical like a postal address:

Simon Queenborough
301 Prospect St
New Haven
CT
USA

“PATH” = Full location of a (sub)directory:

"C:\Simon\Teaching\FES720\"

or file

"C:\Simon\Teaching\FES720\myRfile.txt"

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Path can be absolute or relative

The PATH can be absolute (i.e., it includes the ‘country’ and ‘state’):

"C:\Simon\Teaching\FES720\"

Or, relative to your working directory.

If your working directory is ‘Teaching/’:

"FES720\"

Note: Working with relative paths allows your code to transfer between different computers and users much more easily (we will come back to this).

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PATHS: shortcuts

Relative paths can also be specified using shortcut codes.

So, if the working directoy = C:\Simon\Teaching\FES720\

Path = “.” indicates the current working directory

Path = “.” = C:\Simon\Teaching\FES720\

Path = “..” indicates the directory one level above the current working directory

Path = “..” = C:\Simon\Teaching\

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Use paths to move files around in your code

Let’s assume we have the following hierarchical directory stucture:

─ R-project-1
  |   └─ analysis.r
  ├─ raw_data
  |   ├─ 2015
  |   ├─ 2016
  |   └─ 2017
  ├─ processed_data
  |   └─ data_all_yrs.csv
  ├─ results
  └─ figures
      └─ plot1.png

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Use paths to move files around in your code

─ R-project-1
  |   └─ analysis.r
  ├─ raw_data
  |   ├─ 2015
  |   ├─ 2016
  |   └─ 2017
  ├─ processed_data
  |   └─ data_all_yrs.csv
  ├─ results
  └─ figures
      └─ plot1.png

Suppose we want to:

read data from raw_data/2015/ and raw_data/2016/,
process it and write the file to processed_data/,
read that file in, run an analysis and make a figure to save into figures/

Two ways to move around:

bad: use setwd() a lot
good: use relative paths from the main directory (R-project-1/) to read and write

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File names

Uniquely identifies a file.

Different OS have different naming conventions and allowed characters.

DRIVE: C:

USER or ROOT: Simon

DIRECTORY: Teaching

SUBDIRECTORY: FES720

FILENAME: myRfile

FILE EXTENSION: .txt

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File and path names are TEXT

# You will use this function in the lesson
getwd()

# Notice the speech marks/quotation marks:
"C:\Simon\Teaching\FES720\"

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File systems in Mac, Windows, and Linux

R can run in all three OSs, but there are minor differences.

Backslash (\, windows) vs slash (Mac, Linux)

https://www.howtogeek.com/181774/why-windows-uses-backslashes-and-everything-else-uses-forward-slashes/

File encodings (non-ASCII text, e.g., text with accents, apostrophes, etc.)

https://en.wikipedia.org/wiki/Text_file

Line endings (newline, return+newline)

https://en.wikipedia.org/wiki/Newline

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File utilities allow you to manage the file system

In a GUI, you can create, delete, rename, move, copy, change metadata, etc. files and folders.

You can do the same in a CLI.

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File utilities from the CLI allow:

automation of data cleaning and processing,
- e.g, read in various data files from multiple (sequential?) years, process, and write to new file/s.
creation and removal of temporary folders and files to store intermediate or temporary steps
- e.g., in file encoding and unencoding

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Reading:

Zen and the Art of File and Folder Organization

https://www.howtogeek.com/howto/15677/zen-and-the-art-of-file-and-folder-organization/

We will discuss various options for organising R projects later in the course