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<!DOCTYPE html>
<html lang="" xml:lang="">
<head>
<title>R@GARD | Intro to R programming</title>
<meta charset="utf-8" />
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<textarea id="source">
class: center, middle, inverse, title-slide
.title[
# <a href="mailto:R@GARD" class="email">R@GARD</a> | Intro to R programming
]
.subtitle[
## ⚔
]
.author[
### Jill Bilodeaux, Kewalin Samart <br/>JRaviLab
]
.institute[
### University of Colorado Anschutz Medical Campus<br/>
]
.date[
### <a href="mailto:jill.bilodeaux@cuanschutz.edu" class="email">jill.bilodeaux@cuanschutz.edu</a> | <a href="mailto:kewalin.samart@cuanschutz.edu" class="email">kewalin.samart@cuanschutz.edu</a>
]
---
---
# Why R?
.pull-left[
### R is free
### R is popular
### R is powerful
### R is flexible
### R is well-supported
]
.pull-right[
### R has a strong community!
<img src="https://github.com/allisonhorst/stats-illustrations/raw/main/rstats-artwork/code_hero.jpg" alt="RStats community by Allison Horst: A person in a cape that reads 'code hero' who looks like they are flying through the air while typing on a computer while saying 'I’m doing a think all on my own!' The coder’s arms and legs have ropes attached to two hot air balloons lifting them up, with labels on the balloons including 'teachers', 'bloggers', 'friends', 'developers'. Below the code hero, several people carry a trampoline with labels 'support' and 'community' that will catch them if they fall" width="60%" />
]
---
# Why R?
**R is fun!**
.pull-left[
`beeper::beep(3)`
<img src="https://github.com/allisonhorst/stats-illustrations/raw/main/rstats-artwork/beepr.jpg" alt="beepr: A cartoon alligator running excitedly toward a computer with musical notes coming out of it. Text reads 'beepr::beep()s when your analysis is done running!'" width="70%" />
]
.pull-right[
`Rcade::games$Pacman` & `Rcade::games$`2048``
<img src="img/rcade_pacman.png" alt="Pacman from the Rcade package with the four characters, Blinky, Pinky, Inky, and Clyde" width="30%" />
<img src="img/rcade_2048.png" alt="Rcade package snapshot of the 2048 game" width="20%" />
]
---
# R community
A few global R communities in addition to RFoundation, RForwards, RStudio, and the Rconsortium.
.pull-left[
<img src="https://cdn.shortpixel.ai/spai/w_600+q_lossy+ret_img+to_webp/https://www.numfocus.org/wp-content/uploads/2016/07/ropensci-logo-300.png" alt="8 R community logos: rOpenSci, useR, R-Ladies, AfricaR, ArabR, AsiaR, miR, LatinR" width="25%" /><img src="https://user2021.r-project.org//img/artwork/user-logo-color.png" alt="8 R community logos: rOpenSci, useR, R-Ladies, AfricaR, ArabR, AsiaR, miR, LatinR" width="25%" /><img src="https://community-cdn.rstudio.com/uploads/default/original/3X/e/6/e61d5c8d76feee06efb84f95880e3fc4e12cf269.png" alt="8 R community logos: rOpenSci, useR, R-Ladies, AfricaR, ArabR, AsiaR, miR, LatinR" width="25%" /><img src="https://africa-r.org/author/avatar_hu73f0541d09985efc907138a8670305ca_97180_270x270_fill_lanczos_center_2.png" alt="8 R community logos: rOpenSci, useR, R-Ladies, AfricaR, ArabR, AsiaR, miR, LatinR" width="25%" /><img src="https://arabr.github.io/img/arab-r-logo2.png" alt="8 R community logos: rOpenSci, useR, R-Ladies, AfricaR, ArabR, AsiaR, miR, LatinR" width="25%" /><img src="https://pbs.twimg.com/profile_images/1491075015730954244/pzpN5s2V_400x400.jpg" alt="8 R community logos: rOpenSci, useR, R-Ladies, AfricaR, ArabR, AsiaR, miR, LatinR" width="25%" /><img src="https://mircommunity.com/img/mir_logo_small.png" alt="8 R community logos: rOpenSci, useR, R-Ladies, AfricaR, ArabR, AsiaR, miR, LatinR" width="25%" /><img src="https://github.com/LatinR/latinr/raw/master/man/figures/logo.png" alt="8 R community logos: rOpenSci, useR, R-Ladies, AfricaR, ArabR, AsiaR, miR, LatinR" width="25%" />
<br> <br>
Find your local R chapter on Twitter, [Meetup.com](//meetup.com), [RLadies.org](//rladies.org), or the [R community explorer](https://benubah.github.io/r-community-explorer)!
]
.pull-right[
<img src="https://github.com/allisonhorst/stats-illustrations/raw/main/rstats-artwork/code_hero.jpg" alt="RStats community logo again by Allison Horst" width="60%" />
<img src="img/202303-rladies-dashboard.png" alt="RUG and RLadies chapter stats" width="80%" /><img src="img/202303-rugs-dashboard.png" alt="RUG and RLadies chapter stats" width="80%" />
]
---
# We all go through the 'stages of R'
.center[
<img src="https://github.com/allisonhorst/stats-illustrations/raw/main/rstats-artwork/r_rollercoaster.png" alt="R Knowledge Rollercoaster: An illustrated cartoon graph with 'How much I think I know about R' on the y-axis, with axis labels at 'I know nothing' and 'I know lots', versus 'time' on the x-axis. The line varies widely between the two. Above the line are emoji-like faces, showing uncertainty and hope early on. At a second peak is the label 'join R community on twitter', with a 'mind-blown' emoji face. The line quickly descends, but with a happy looking emoji character sliding down it." width="70%" />
]
---
# What can you do with R?
#### Data wrangling | knowing about your data
#### Data analysis & summarization | including RStats
#### Data visualization & graphical summaries
#### Reproducible research
#### Manuscripts, books, thesis
#### Interactive web apps
#### Webpages, blogs
#### and more...
_We've shared a few examples for each towards the end._
---
class: inverse, center, middle
# Getting Started
---
# First steps...
### Install R/RStudio
You are recommended to use the [RStudio IDE](https://www.rstudio.com/products/rstudio/), but you do not have to.
--
### Install tidyverse and gapminder (data) and other required packages
```r
install.packages("tidyverse") # for data wrangling
install.packages("gapminder") # sample dataset
install.packages("rmarkdown", # Convert R Markdown documents into various formats
"knitr", # for dynamic report generation
"gganimate", # for animation
"gifski") # gganimate's dependency
```
<img src="https://d33wubrfki0l68.cloudfront.net/57299a1dcd979c623325f11bf5e5ce60f3d4eb00/e4602/wp-content/uploads/2018/10/black.png" alt="R programming logo in blue" width="20%" />
<img src="https://www.rstudio.com/wp-content/uploads/2014/04/tidyverse.png" alt="tidyverse package hex from RStudio" width="10%" />
<img src="https://www.gapminder.org/wp-content/themes/gapminder2/images/gapminder-logo.svg" alt="gapminder logo from website (yellow bordered text) for gapminder package" width="30%" />
---
# Importing your data
```r
library(tidyverse)
read_csv(file="my_data.csv",
col_names=T) # comma-separated values, as exported from excel/spreadsheets
read_delim(file="my_data.txt", col_names=T,
delim="//") # any delimitter
# Other useful packages
# readxl by Jenny Bryan
read_excel(path="path/to/excel.xls",
sheet=1,
range="A1:D50",
col_names=T)
```
---
# The Gapminder data
.center[
<img src="https://s3-eu-west-1.amazonaws.com/static.gapminder.org/GapminderMedia/wp-uploads/20161007154225/countries_health_wealth_2016_v71.png" alt="Snapshot of the gapminder data health vs wealth in 2015" width="60%" />
]
---
# Viewing your data
```r
library(tidyverse)
gapminder::gapminder # Data is in a cleaned up 'tibble' format by default
```
```
## # A tibble: 1,704 × 6
## country continent year lifeExp pop gdpPercap
## <fct> <fct> <int> <dbl> <int> <dbl>
## 1 Afghanistan Asia 1952 28.8 8425333 779.
## 2 Afghanistan Asia 1957 30.3 9240934 821.
## 3 Afghanistan Asia 1962 32.0 10267083 853.
## 4 Afghanistan Asia 1967 34.0 11537966 836.
## 5 Afghanistan Asia 1972 36.1 13079460 740.
## 6 Afghanistan Asia 1977 38.4 14880372 786.
## 7 Afghanistan Asia 1982 39.9 12881816 978.
## 8 Afghanistan Asia 1987 40.8 13867957 852.
## 9 Afghanistan Asia 1992 41.7 16317921 649.
## 10 Afghanistan Asia 1997 41.8 22227415 635.
## # … with 1,694 more rows
```
--
```r
str(gapminder) # Structure of the dataframe
head(gapminder) # Shows the top few observations (rows) of your data frame
glimpse(gapminder) # Info-dense summary of the data
```
---
# Viewing your data
**A quick tabulated snapshot**
```r
library(knitr)
kable(head(gapminder::gapminder), format = 'html')
```
<table>
<thead>
<tr>
<th style="text-align:left;"> country </th>
<th style="text-align:left;"> continent </th>
<th style="text-align:right;"> year </th>
<th style="text-align:right;"> lifeExp </th>
<th style="text-align:right;"> pop </th>
<th style="text-align:right;"> gdpPercap </th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align:left;"> Afghanistan </td>
<td style="text-align:left;"> Asia </td>
<td style="text-align:right;"> 1952 </td>
<td style="text-align:right;"> 28.801 </td>
<td style="text-align:right;"> 8425333 </td>
<td style="text-align:right;"> 779.4453 </td>
</tr>
<tr>
<td style="text-align:left;"> Afghanistan </td>
<td style="text-align:left;"> Asia </td>
<td style="text-align:right;"> 1957 </td>
<td style="text-align:right;"> 30.332 </td>
<td style="text-align:right;"> 9240934 </td>
<td style="text-align:right;"> 820.8530 </td>
</tr>
<tr>
<td style="text-align:left;"> Afghanistan </td>
<td style="text-align:left;"> Asia </td>
<td style="text-align:right;"> 1962 </td>
<td style="text-align:right;"> 31.997 </td>
<td style="text-align:right;"> 10267083 </td>
<td style="text-align:right;"> 853.1007 </td>
</tr>
<tr>
<td style="text-align:left;"> Afghanistan </td>
<td style="text-align:left;"> Asia </td>
<td style="text-align:right;"> 1967 </td>
<td style="text-align:right;"> 34.020 </td>
<td style="text-align:right;"> 11537966 </td>
<td style="text-align:right;"> 836.1971 </td>
</tr>
<tr>
<td style="text-align:left;"> Afghanistan </td>
<td style="text-align:left;"> Asia </td>
<td style="text-align:right;"> 1972 </td>
<td style="text-align:right;"> 36.088 </td>
<td style="text-align:right;"> 13079460 </td>
<td style="text-align:right;"> 739.9811 </td>
</tr>
<tr>
<td style="text-align:left;"> Afghanistan </td>
<td style="text-align:left;"> Asia </td>
<td style="text-align:right;"> 1977 </td>
<td style="text-align:right;"> 38.438 </td>
<td style="text-align:right;"> 14880372 </td>
<td style="text-align:right;"> 786.1134 </td>
</tr>
</tbody>
</table>
---
# Viewing your data
**Your full data!**
```r
library(rmarkdown)
paged_table(gapminder::gapminder)
```
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<script data-pagedtable-source type="application/json">
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</script>
</div>
---
# Viewing your data
**w/ dynamic filtering**
```r
library(gapminder)
DT::datatable(head(gapminder, 1000),
fillContainer = FALSE, options = list(pageLength = 5))
```
<div class="datatables html-widget html-fill-item-overflow-hidden html-fill-item" id="htmlwidget-14a1c3ff1cef8c8bd80a" style="width:100%;height:auto;"></div>
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class=\"display\">\n <thead>\n <tr>\n <th> <\/th>\n <th>country<\/th>\n <th>continent<\/th>\n <th>year<\/th>\n <th>lifeExp<\/th>\n <th>pop<\/th>\n <th>gdpPercap<\/th>\n <\/tr>\n <\/thead>\n<\/table>","options":{"pageLength":5,"columnDefs":[{"className":"dt-right","targets":[3,4,5,6]},{"orderable":false,"targets":0}],"order":[],"autoWidth":false,"orderClasses":false,"lengthMenu":[5,10,25,50,100]}},"evals":[],"jsHooks":[]}</script>
---
# Tidying your data
.center[
<img src="https://github.com/allisonhorst/stats-illustrations/raw/main/rstats-artwork/tidydata_2.jpg" alt="There are two sets of anthropomorphized data tables. The top group of three tables are all rectangular and smiling, with a shared speech bubble reading 'our columns are variables and our rows are observations!'. Text to the left of that group reads 'The standard structure of tidy data means that 'tidy datasets are all alike...' The lower group of four tables are all different shapes, look ragged and concerned, and have different speech bubbles reading (from left to right) 'my column are values and my rows are variables', 'I have variables in columns AND in rows', 'I have multiple variables in a single column', and 'I don’t even KNOW what my deal is.' Next to the frazzled data tables is text '...but every messy dataset is messy in its own way. -Hadley Wickham.'" width="70%" />
]
---
# Tidying your data
```r
pivot_longer() # wide -> long
pivot_wider() # long -> wide
separate() # Separate 1 COLUMN -> many COLUMNS
unite() # Unite several COLUMNS -> 1 COLUMN
```
---
# Tidying your data
.center[
<img src="https://github.com/gadenbuie/tidyexplain/raw/main/images/tidyr-pivoting.gif" alt="GAdenBuie Tidyexplain gif for long to wide data transformation" width="40%" />
]
---
# Wrangling your data
```r
filter() # PICK observations by their values | ROWS
select() # PICK variables by their names | COLUMNS
mutate() # CREATE new variables w/ functions of existing variables | COLUMNS
transmute() # COMPUTE 1 or more COLUMNS but drop original columns
arrange() # REORDER the ROWS
summarize() # COLLAPSE many values to a single SUMMARY
group_by() # GROUP data into rows with the same value of variable (COLUMN)
```
---
# Wrangling your data
**w/ filter**
.center[
<img src="https://github.com/allisonhorst/stats-illustrations/raw/main/rstats-artwork/dplyr_filter.jpg" alt="Allison Horst dply::filter. Cartoon showing three fuzzy monsters either selecting or crossing out rows of a data table. If the type of animal in the table is 'otter' and the site is 'bay', a monster is drawing a purple rectangle around the row. If those conditions are not met, another monster is putting a line through the column indicating it will be excluded. Stylized text reads 'dplyr::filter() - keep rows that satisfy your conditions.'" width="70%" />
]
---
# Wrangling your data
```r
head(gapminder) # Snapshot of the dataframe
# Now, filter by year and look at only the data from the year 1962
filter(gapminder, year==1962)
# Can be rewritten using "Piping" %>%
gapminder %>% # Pipe ('then') operator to serially connect operations
filter(year==1962)
# Filter for China in 2002
gapminder %>%
filter(year==2002, country=="China")
```
---
# Wrangling your data
```
## # A tibble: 142 × 6
## country continent year lifeExp pop gdpPercap
## <fct> <fct> <int> <dbl> <int> <dbl>
## 1 Afghanistan Asia 1962 32.0 10267083 853.
## 2 Albania Europe 1962 64.8 1728137 2313.
## 3 Algeria Africa 1962 48.3 11000948 2551.
## 4 Angola Africa 1962 34 4826015 4269.
## 5 Argentina Americas 1962 65.1 21283783 7133.
## 6 Australia Oceania 1962 70.9 10794968 12217.
## 7 Austria Europe 1962 69.5 7129864 10751.
## 8 Bahrain Asia 1962 56.9 171863 12753.
## 9 Bangladesh Asia 1962 41.2 56839289 686.
## 10 Belgium Europe 1962 70.2 9218400 10991.
## # … with 132 more rows
```
```
## # A tibble: 1 × 6
## country continent year lifeExp pop gdpPercap
## <fct> <fct> <int> <dbl> <int> <dbl>
## 1 China Asia 2002 72.0 1280400000 3119.
```
---
# Math Expressions
You can write LaTeX math expressions inside a pair of dollar signs, <br>
_e.g.,_ `$\alpha+\beta$` renders `\(\alpha+\beta\)`.
You can use the display style with double dollar signs (`$$`):
```{}
$$EWCos_{j} = Cos(v_{dis}(S),EWlogFC_{j})$$
```
`$$EWCos_{j} = Cos(v_{dis}(S),EWlogFC_{j})$$`
--
Check out a math-riddled manuscript written with RMarkdown:
[jravilab.github.io/connectivity_scores](//jravilab.github.io/connectivity_scores)
---
# Visualizing your data
```r
ggplot(gapminder) +
aes(x=gdpPercap, y=lifeExp, size=pop, color=country) +
geom_point(show.legend=FALSE)
```
--
<img src="index_files/figure-html/unnamed-chunk-20-1.png" width="60%" />
---
# Visualizing your data
```r
ggplot(gapminder) +
aes(x=gdpPercap, y=lifeExp, size=pop, color=country) +
geom_point(show.legend=FALSE) +
* facet_wrap(~year)
```
<img src="index_files/figure-html/unnamed-chunk-22-1.png" width="60%" />
---
# Visualizing your data
**The code**
```r
library(tidyverse)
library(gapminder)
static_plot <- ggplot(gapminder,
aes(gdpPercap, lifeExp,
size = pop, colour = country)) +
geom_point(alpha = 0.7, show.legend = FALSE) +
scale_colour_manual(values = country_colors) +
scale_size(range = c(2, 12)) +
scale_x_log10() + theme_minimal() +
facet_wrap(~continent)
static_plot
```
---
# Visualizing your data
**The plot**
<img src="index_files/figure-html/gapminder-static2-1.png" width="60%" />
---
# Visualizing your data
**The code**
```r
library(gganimate)
ggplot(gapminder,
aes(gdpPercap, lifeExp,
size = pop, colour = country)) +
geom_point(alpha = 0.7, show.legend = FALSE) +
scale_colour_manual(values = country_colors) +
scale_size(range = c(2, 12)) +
scale_x_log10() + theme_minimal() +
facet_wrap(~continent) +
* # Here comes the gganimate specific bits
* labs(title = 'Year: {frame_time}', # labels
* x = 'GDP per capita', y = 'life expectancy') +
* transition_time(year) + # the dynamic variable
* ease_aes('linear')
```
---
# Visualizing your data
[**The plot**](https://jananiravi.github.io/workshop-tidyverse/gapminder/workshop-tidyverse-gapminder#gganimate)
<img src="index_files/figure-html/gapminder-gganimate2-1.gif" width="80%" />
---
```r
library(leaflet)
leaflet() %>% addTiles() %>% setView(-93.65, 42.0285, zoom = 17)
```
<div class="leaflet html-widget html-fill-item-overflow-hidden html-fill-item" id="htmlwidget-37291ca3a1c970dd1d2d" style="width:100%;height:432px;"></div>
<script type="application/json" data-for="htmlwidget-37291ca3a1c970dd1d2d">{"x":{"options":{"crs":{"crsClass":"L.CRS.EPSG3857","code":null,"proj4def":null,"projectedBounds":null,"options":{}}},"calls":[{"method":"addTiles","args":["https://{s}.tile.openstreetmap.org/{z}/{x}/{y}.png",null,null,{"minZoom":0,"maxZoom":18,"tileSize":256,"subdomains":"abc","errorTileUrl":"","tms":false,"noWrap":false,"zoomOffset":0,"zoomReverse":false,"opacity":1,"zIndex":1,"detectRetina":false,"attribution":"© <a href=\"https://openstreetmap.org\">OpenStreetMap<\/a> contributors, <a href=\"https://creativecommons.org/licenses/by-sa/2.0/\">CC-BY-SA<\/a>"}]}],"setView":[[42.0285,-93.65],17,[]]},"evals":[],"jsHooks":[]}</script>
---
# Saving your data
```r
library(tidyverse)
# Save your file name
plot1 <- "gapminder_static_plot.png"
# Save your absolute/relative path
my_full_path <- here("gapminder")
# To save as a tab-delimited text file ...
{{ggsave(filename=plot1,
plot=static_plot,
device="png",
path=my_full_path,
dpi=300) }}
```
---
# Have fun w/ programming
.center[
<img src="https://github.com/allisonhorst/stats-illustrations/raw/main/other-stats-artwork/debugging.jpg" alt="Allison Horst's image on the phases of debugging!" width="70%" />
]
---
# Do more with R
.pull-left[
- Draft a **Manuscript** | [jravilab.github.io/connectivity_scores](//jravilab.github.io/connectivity_scores)
- Create a **Website** | [jravilab.github.io](//jravilab.github.io)
- **Present** your data | e.g., [jravilab.github.io/R_intro](//jravilab.github.io/R_intro)
- Create a **Web application** | [jravilab.org/molevolvr](http://jravilab.org/molevolvr)
- Write your **Thesis** or an **e-Book** | [jravilab.github.io/lab_docs](https://jravilab.github.io/lab_docs)
- Material: [github.com/rladies-eastlansing](www.github.com/rladies-eastlansing)
<img src="https://github.com/allisonhorst/stats-illustrations/raw/main/rstats-artwork/code_hero.jpg" alt="RStats community by Allison Horst: A person in a cape that reads 'code hero' who looks like they are flying through the air while typing on a computer while saying 'I’m doing a think all on my own!' The coder’s arms and legs have ropes attached to two hot air balloons lifting them up, with labels on the balloons including 'teachers', 'bloggers', 'friends', 'developers'. Below the code hero, several people carry a trampoline with labels 'support' and 'community' that will catch them if they fall" width="40%" />
]
.pull-right[
<img src="https://github.com/allisonhorst/stats-illustrations/raw/main/rstats-artwork/r_first_then.png" alt="A digital cartoon by Allison Horst with two illustrations: the top shows the R-logo with a scary face, and a small scared little fuzzy monster holding up a white flag in surrender while under a dark stormcloud. The text above says: at first I was like... The lower cartoon is a friendly, smiling R-logo jumping up to give a happy fuzzy monster a high-five under a smiling sun and next to colorful flowers. The text above the bottom illustration reads: but now it's like..." width="80%" />
]
---
# Acknowledgments
- GARD 2023 | Chelsie Boodoo
- Content by Dr. Janani Ravi | Janani.Ravi@cuanschutz.edu | [@janani137](//twitter.com/janani137) | [jravilab.github.io](//jravilab.github.io)
- Slides created via the R package [xaringan](https://github.com/yihui/xaringan) built with [remark.js](https://remarkjs.com), [knitr](https://yihui.org/knitr/), and [R Markdown](https://rmarkdown.rstudio.com).
- Cartoons from Allison Horst; Tidyverse GIFs by Garrick Aden-Buie.
- [JRaviLab](https://jravilab.github.io) | [Krishnan Lab](https://thekrishnanlab.org)
- [R-Ladies East Lansing](https://github.com/rladies-eastlansing) | [Women+ Data Science](https://github.com/women-plus-datascience) | [AsiaR](//github.com/AsiaR-community)
.pull-left[
### How to reach us
Jill.Bilodeaux@cuanschutz.edu <br>
Kewalin.Samart@cuanschutz.edu | [@KewalinSamart](//twitter.com/KewalinSamart) <br>
JRaviLab on [Twitter](//twitter.com/JRaviLab) | [GitHub](//github.com/JRaviLab) | [Mastodon](https://genomic.social/@jravilab)
]
.pull-right[
<img src="https://octodex.github.com/images/baracktocat.jpg" alt="Baracktocat, GitHub Octocat with 'Yes we code' election themed poster" width="40%" style="display: block; margin: auto 0 auto auto;" />
]
You can access all relevant material pertaining to this workshop [here](https://github.com/jravilab/R_intro).
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