Right Start Programming with R language

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## <span style='font-family:Arial; color: black; font-weight:400;'>Right Start Programming with R language</span>

### Part I: Getting started

.left[

<span style="font-weight: 600; font-size: 28px;">Stephen Balogun</span>

<span style="font-weight: 600; font-size: 28px;">Bilikisu Aderinto</span>

<span class="my_date">Sat, January 29 2022</span>

]

---

## Stephen Balogun

.left-column[
<img src="./imgs/Stephen.png" width="731" />
]

.right-column[

- A Public Health Physician

- A healthcare improvement safety expert - led me to data science

- Disease surveillance expert and epidemiologist

- Author, [{tidyndr}](https://CRAN.R-project.org/package=tidyndr)

- Co-founder: [r4hds](https://r4hds.netlify.app/)

- Co-organizer: [Abuja R user Group](https://www.meetup.com/Abuja-R-User-Group-Meetup/)

- <svg aria-hidden="true" role="img" viewBox="0 0 496 512" style="height:1em;width:0.97em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:currentColor;overflow:visible;position:relative;"><path d="M336.5 160C322 70.7 287.8 8 248 8s-74 62.7-88.5 152h177zM152 256c0 22.2 1.2 43.5 3.3 64h185.3c2.1-20.5 3.3-41.8 3.3-64s-1.2-43.5-3.3-64H155.3c-2.1 20.5-3.3 41.8-3.3 64zm324.7-96c-28.6-67.9-86.5-120.4-158-141.6 24.4 33.8 41.2 84.7 50 141.6h108zM177.2 18.4C105.8 39.6 47.8 92.1 19.3 160h108c8.7-56.9 25.5-107.8 49.9-141.6zM487.4 192H372.7c2.1 21 3.3 42.5 3.3 64s-1.2 43-3.3 64h114.6c5.5-20.5 8.6-41.8 8.6-64s-3.1-43.5-8.5-64zM120 256c0-21.5 1.2-43 3.3-64H8.6C3.2 212.5 0 233.8 0 256s3.2 43.5 8.6 64h114.6c-2-21-3.2-42.5-3.2-64zm39.5 96c14.5 89.3 48.7 152 88.5 152s74-62.7 88.5-152h-177zm159.3 141.6c71.4-21.2 129.4-73.7 158-141.6h-108c-8.8 56.9-25.6 107.8-50 141.6zM19.3 352c28.6 67.9 86.5 120.4 158 141.6-24.4-33.8-41.2-84.7-50-141.6h-108z"/></svg>: [stephenbalogun.github.io/stbalogun](https://stephenbalogun.github.io/stbalogun/) 😄

- <svg aria-hidden="true" role="img" viewBox="0 0 512 512" style="height:1em;width:1em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:currentColor;overflow:visible;position:relative;"><path d="M459.37 151.716c.325 4.548.325 9.097.325 13.645 0 138.72-105.583 298.558-298.558 298.558-59.452 0-114.68-17.219-161.137-47.106 8.447.974 16.568 1.299 25.34 1.299 49.055 0 94.213-16.568 130.274-44.832-46.132-.975-84.792-31.188-98.112-72.772 6.498.974 12.995 1.624 19.818 1.624 9.421 0 18.843-1.3 27.614-3.573-48.081-9.747-84.143-51.98-84.143-102.985v-1.299c13.969 7.797 30.214 12.67 47.431 13.319-28.264-18.843-46.781-51.005-46.781-87.391 0-19.492 5.197-37.36 14.294-52.954 51.655 63.675 129.3 105.258 216.365 109.807-1.624-7.797-2.599-15.918-2.599-24.04 0-57.828 46.782-104.934 104.934-104.934 30.213 0 57.502 12.67 76.67 33.137 23.715-4.548 46.456-13.32 66.599-25.34-7.798 24.366-24.366 44.833-46.132 57.827 21.117-2.273 41.584-8.122 60.426-16.243-14.292 20.791-32.161 39.308-52.628 54.253z"/></svg>: [@eppydoc]((https://twitter.com/eppydoc) 👍

- <svg aria-hidden="true" role="img" viewBox="0 0 448 512" style="height:1em;width:0.88em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:currentColor;overflow:visible;position:relative;"><path d="M416 32H31.9C14.3 32 0 46.5 0 64.3v383.4C0 465.5 14.3 480 31.9 480H416c17.6 0 32-14.5 32-32.3V64.3c0-17.8-14.4-32.3-32-32.3zM135.4 416H69V202.2h66.5V416zm-33.2-243c-21.3 0-38.5-17.3-38.5-38.5S80.9 96 102.2 96c21.2 0 38.5 17.3 38.5 38.5 0 21.3-17.2 38.5-38.5 38.5zm282.1 243h-66.4V312c0-24.8-.5-56.7-34.5-56.7-34.6 0-39.9 27-39.9 54.9V416h-66.4V202.2h63.7v29.2h.9c8.9-16.8 30.6-34.5 62.9-34.5 67.2 0 79.7 44.3 79.7 101.9V416z"/></svg>: [Stephen Balogun](https://www.linkedin.com/in/stbalogun/) 
]

---

## Bilikisu Aderinto

.f3[
&#x1F44B; Hi, I'm **Bilikisu Wunmi Aderinto**
]

.f3[
&#x1F426; [&commat;qbwoa](https://twitter.com/qbwoa)
]

.f3[
&#x1F9D1;&#x200D;&#x1F4BB; [baderinto.github.io](https://baderinto.github.io)
]

.f3[
&#x1F4BC; [Business Data Laboratory](https://business-datalab.com): **Principal Consultant/freelancer**
]

--
.f3[&#x1F469;[Abuja R user Group](https://www.meetup.com/Abuja-R-User-Group-Meetup/): **Founder, Co-organizer** 
]

--
.f3[&#x1F469;[R-Ladies Abuja](https://https://www.meetup.com/rladies-abuja/): **Co-founder, Organizer** 
]

---

class: top, center, hide-logo, abuja
background-image: url(imgs/LOGO.jfif)

# About Abuja R user Group

---

## What this course will teach you?

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- Part I: Getting started

- Workshop assumptions
    
    - Why use R?
    
    - Overview of data science/data analytics
    
    - Tabular data and its building blocks
    
    - Installing the required softwares
    
    - Setting up your R workspace
    
    - Using R and RStudio

]

.pull-right[

- Part II

- Importing your data

- Data cleaning and transformation
    
    - Basic data analysis
    
    - Plotting charts
    
- Part III

- Communicating your results
    
    - Summary
    
    - Next steps
]

---

## Who is this class for?

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- New R users

- No prior computer programming knowledge

- No assumed prior knowledge of statistics

]

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<img src="./imgs/assumptions.png" width="2083" />
]

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## What can R do for you?

.pull-left[

- Analysis

- Quantitative 
  - Qualitative (including text mining)
  - Specialized analysis (e.g. music)
    
- Visualizations

- Graphs
  - GIS maps
  - Games
  - Arts

- Websites

- Blogging
  - Personal/professional
]

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]

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## Example applications

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]

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]

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## Why should you choose R?

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- [Open source 😺](https://en.wikipedia.org/wiki/Open_source)

- [Free 🆓](https://www.gnu.org/philosophy/free-sw.html)

- [Strong R community/support 👪](https://community.rstudio.com/)

- [Reproducible 👩‍🔬](https://www.annualreviews.org/doi/10.1146/annurev-publhealth-012420-105110?url_ver=Z39.88-2003&rfr_id=ori%3Arid%3Acrossref.org&rfr_dat=cr_pub++0pubmed)

- Broad 📚

### R in Industries

- Google, Facebook, Microsoft, Twitter

- Norvatis WHO, Bioconductor (genomics data analysis), Janssen

]

.pull-right[

<footer>
  <sup>1</sup>
  
  <a "http://makemeanalyst.com/companies-using-r/">
  <span style="font-size:80%;">Companies using R</span>
  </a>
  <br/>
  
  <sup>2</sup><a "https://r4hds.netlify.app/why_r">
   <span style="font-size:80%;">Why you should use R</span>
  </a>
</footer>

]

---

## Data Science - Overview

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- A combination of

- computer programming
    
    - Scientific reasoning 
    
    - Data comprehension
    
- Varying mix of the above, depending on the specialization

]

.pull-right[
<img src="./imgs/datascience component2.png" width="560" />
]

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## Data Science - Workflow

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- Getting your data (Excel, csv, etc) into R

- Formatting your data appropriately

- Identifying patterns (exploration)

- Plotting graphs

- Performing statistics

- Passing the information

]

.pull-right[
<img src="./imgs/datascience workflow.png" width="1336" />
]

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## Tabular data

.pull-left[

- Rows are horizontal, columns are vertical

- Should be __*tidy*__ each:

- variable must have its own column
    
    - observation must have its own row
    
    - value must have its own cell
]

.pull-right[
<img src="./imgs/tidy data.png" width="1600" />

> "Tidy datasets are alike, but every messy dataset is messy in its own way"
  >
  > - Hadley Wickham
]

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## Tidy data

.pull-left[

What makes this data *"untidy"*?
<img src="./imgs/untidy data.png" width="728" />
]

.pull-right[
What makes this data "*tidy"*?

<img src="./imgs/tidy.png" width="766" />
]

---

## Atomic vectors (variables) in R

.pull-left[

- These are building blocks of tabular data

- Four common atomic variables

- Double (continuous variables)
  
  - Integer (discrete or count variables)
  
  - Characters (strings) - surrounded by quotes
  
  - Logical (boolean) - `TRUE/FALSE`, `T/F`

- __*Variables can be converted from one form to another*__

- Others: augmented (s3 atomic) vectors and dataframes
]

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]

---

## Requirements

- [<svg aria-hidden="true" role="img" viewBox="0 0 581 512" style="height:1em;width:1.13em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:currentColor;overflow:visible;position:relative;"><path d="M581 226.6C581 119.1 450.9 32 290.5 32S0 119.1 0 226.6C0 322.4 103.3 402 239.4 418.1V480h99.1v-61.5c24.3-2.7 47.6-7.4 69.4-13.9L448 480h112l-67.4-113.7c54.5-35.4 88.4-84.9 88.4-139.7zm-466.8 14.5c0-73.5 98.9-133 220.8-133s211.9 40.7 211.9 133c0 50.1-26.5 85-70.3 106.4-2.4-1.6-4.7-2.9-6.4-3.7-10.2-5.2-27.8-10.5-27.8-10.5s86.6-6.4 86.6-92.7-90.6-87.9-90.6-87.9h-199V361c-74.1-21.5-125.2-67.1-125.2-119.9zm225.1 38.3v-55.6c57.8 0 87.8-6.8 87.8 27.3 0 36.5-38.2 28.3-87.8 28.3zm-.9 72.5H365c10.8 0 18.9 11.7 24 19.2-16.1 1.9-33 2.8-50.6 2.9v-22.1z"/></svg> software](https://cran.r-project.org)

- [RStudio](https://www.rstudio.com/products/rstudio/download/)

- [some R packages](#installation-required-r-packages)

- A compiler (optional):

- [Rtools on Windows](https://cran.r-project.org/bin/windows/Rtools/)
    
    - [Xcode command line tools on macOS](https://developer.apple.com/programs/register/)
    
- Good internet connection

---

## Installation - R

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- Visit the [`CRAN` website](https://cran.r-project.org): <br/> https://cran.r-project.org

- Follow the instructions provided

]

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<img src="./imgs/cran.png" width="100%" />
]

---

## Installation - RStudio

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- Visit the [RStudio website](https://www.rstudio.com/products/rstudio/download/)

- Scroll down a bit and download the free version.

- Follow the installation prompt.
]

.right-column[
<img src="./imgs/rstudio.png" width="100%" />
]

---

## Setting up your workspace

.pull-left[

- Modify default settings

- From the __*Tools*__ tab, go to __*Global Options...*__ (the last listed item)

- Confirm that the places highlighted are unchecked

<img src="./imgs/workspace_1.png" width="3432" />
]

.pull-right[

<img src="./imgs/workspace2.png" width="2157" />
]

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## Setting up your workspace - Project

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- Use R projects

- Makes your work easy to share with others

- Identified by a "__*.Rproj*__" file in the folder

- Create R project

- Click on the __*File*__ tab, then

- Click on __*New project*__ (should be the second option from the listed items)

- Create from "New" or "Existing" folders

]

.pull-right[

]

---

## Navigating RStudio

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- 3 - 4 window panes

- Use the Editor pane for your codes

- Send codes from the __*editor*__ to the __*console*__ either using the __*run*__ tab (it has a drop-down) or use "Ctrl + Enter"

]

.right-column[

<img src="./imgs/rstudio pane.png" width="1702" />
]

---

## Installation - Required R packages

- tidyverse, lubridate, skimr packages

<br/>
    
    
    install.packages("tidyverse", dependencies = TRUE)

install.packages("lubridate", dependencies = TRUE)

install.packages("skimr", dependencies = TRUE)

- You do not have to repeat the steps above if you have installed the packages before now

- You need internet connection to install a package

---

## R functions

- Essentially the "heart" of R

- R can perform simple arithmetic like `1 + 1`

- Most functions follow this format:

function_name(object, 1st argument, 2nd argument, etc)

- Example, assuming you have a population of 10 and you want to sample 2 persons (without replacement)

install.packages(tidyverse, dependencies = TRUE)

- You can have functions with no arguments e.g. `Sys.Date()`

---

## R packages

.pull-left[

- All R functions are contained in *packages*

- *R packages* are a collection of *functions* that perform related tasks

- R comes with pre-installed packages

- Additional packages extend the functions of base R. They can be installed depending on your needs

- *CRAN* and *GitHub* are two common package repositories

- You can also write your own package!!!

]

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]

---

## Assigning values

.right-column[

- R can let you "save" a value for re-use

- To save a value, decide on the name you want to give it

- Common naming conventions are:

- snakecase: this_is_a_snake_case
    
    - camelcase: thisIsACamelCase

- Use meaningful names

- Caution!! Existing values of a similar name will be overwritten so names have to be unique

- You can include comments in your code using `#`

]

.left-column[

]
---

## Arithmetic operators

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- addition sign (+)

- substraction sign (-)

- division sign (/)

- multiplication sign (*)

- Exponential sign (^)

- integer division (%/%)

- modulo division (%%) - remainder

- greater than (>) e.g. 5 > 3

- less than (<) e.g. 5 < 3

]

.pull-right[

- greater than or equal to (>=) e.g. `5 >= 10/2`

- less than or equal to (<=) e.g. `5 <= 10/2`

- equal to (==) e.g. `1/49 * 49 == 1`

- not equal to (!=) e.g. `4 != 2*2`

- not/negate (!) e.g. `!TRUE`

- or (|) e.g. `4 > 6 | 3`

- and (&) e.g. `4 > 6 & 3`

]

---

## Summary

- R is free, versatile and used in various industries

- R can ingest several types of data and cross-communicates with several other analytic software

- Data is not always tidy. You may need to manipulate the data to get it in the right format

- Set up your working environment, use R project

- Most interactions with R will be via functions. Functions are organized into packages.

- If you want to keep objects in memory, you must assign them to a name.

- Most arithmetic operators are similar to what you would expect.

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# Questions