Introduction to R

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# Introduction to R
### Sara Mortara & Andrea Sánchez-Tapia
### re.green | ¡liibre!
### 2022-07-05

---

## welcome | bienvenidas | bem-vindas

Andrea Sánchez-Tapia (she/her)

]

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<center>
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<img src="figs/sara.jpg" width="300" />

Sara Mortara (she/her)
]

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### Graduate course _Data analysis' projects using R_

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__Good practices__ in data analysis

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---

## overview of the course

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---
# today

- overview of R and RStudio

- run a script from a specific location (pwd)

- read an external file in R

---

## why learn `R`?

+ the language of choice for academic statisticians

+ **_libre_ software**: free and free-to-be-used-and-modified for any means -> one of the pillars of open science

+ __script-based__: reproducibility, easier to scale up your analyses, transparency (track errors), great way to learn about methods

+ __interdisciplinary and modular__: lots of code written by area specialists. At the core of its philosophy is a smooth transition from user to programmer

+ __communication__ with other tools: manuscripts, presentations, apps and dashboards

---
## why learn `R`?

+ communication with __other programming languages__ (ex. __reticulate__ to run python scripts)

+ great __graphic capabilities__!

+ __official support__: help in documentation, mailing lists

+ __an active and welcoming community__:  email lists, Stack Overflow, [RStudio community](community.rstudio.com/), useR groups, .purple[R-Ladies+] chapters, Slack communities, <svg viewBox="0 0 512 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <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"></path></svg> `#rstats`

---
## `R` has a modular structure: __packages__

+ `R` __base__ installation includes base packages developed and maintained by the __`R` Core Development Team__

+ other packages are created by the community and hosted in __CRAN__ (The Comprehensive `R` Archive Network) or Bioconductor, GitHub, rOpenSci.org

+ to install packages from CRAN: `install.packages("tidyverse")`

---
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# Running R in RStudio

---
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# Setup and project organization

---
## working directory

+ you have to tell R where you will be working, so that it understands where to read tables, where to save outputs etc: __working directory__

+ `getwd()` in the console

+ the default is __"home"__: check general options and the "File" tab

+ you can tell R and RStudio where you want to work with `setwd()`

+ even better: instead of opening RStudio open an __R script__ or a __RStudio project__ (just as you would in MS Word   <svg viewBox="0 0 384 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M369.9 97.9L286 14C277 5 264.8-.1 252.1-.1H48C21.5 0 0 21.5 0 48v416c0 26.5 21.5 48 48 48h288c26.5 0 48-21.5 48-48V131.9c0-12.7-5.1-25-14.1-34zM332.1 128H256V51.9l76.1 76.1zM48 464V48h160v104c0 13.3 10.7 24 24 24h104v288H48zm220.1-208c-5.7 0-10.6 4-11.7 9.5-20.6 97.7-20.4 95.4-21 103.5-.2-1.2-.4-2.6-.7-4.3-.8-5.1.3.2-23.6-99.5-1.3-5.4-6.1-9.2-11.7-9.2h-13.3c-5.5 0-10.3 3.8-11.7 9.1-24.4 99-24 96.2-24.8 103.7-.1-1.1-.2-2.5-.5-4.2-.7-5.2-14.1-73.3-19.1-99-1.1-5.6-6-9.7-11.8-9.7h-16.8c-7.8 0-13.5 7.3-11.7 14.8 8 32.6 26.7 109.5 33.2 136 1.3 5.4 6.1 9.1 11.7 9.1h25.2c5.5 0 10.3-3.7 11.6-9.1l17.9-71.4c1.5-6.2 2.5-12 3-17.3l2.9 17.3c.1.4 12.6 50.5 17.9 71.4 1.3 5.3 6.1 9.1 11.6 9.1h24.7c5.5 0 10.3-3.7 11.6-9.1 20.8-81.9 30.2-119 34.5-136 1.9-7.6-3.8-14.9-11.6-14.9h-15.8z"></path></svg>)

---
## project organization and best practices

+ projects are better organized if we use __one folder per project__ and  __subfolders__ within our working directory

+ we shouldn't modify __raw data files__ but __save processed data__ (and the corresponding scripts)

+ instead of __absolute paths__ we should use __relative paths__:
  + `.` "here"
  + `./figs` a subfolder called `figs`
  + the upper level `..`
  
--

+ avoid `C:users/your_name/your_file_structure/your_working_directory`

---
## In this and the following sessions

```

project/
*    ├── data/
*    │   ├── raw
*    │   └── processed
     ├── docs/
*    ├── figs/
     ├── R/
*    ├── output/
*    └── README.md
```

---
## RStudio projects

RStudio projects create a __.Rproj__ file in your folder that acts as a shortcut for your projects

+ unzip the .zip file into a folder of your preference

+ open the .Rproj file and run `getwd()`

---
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# introduction to R

---
## introduction to R

+ `<-` is the assignment operation in R and it does not return output it __creates objects__ that are saved in the workspace
(`Alt + -`)

+ overwriting objects __does not affect other objects__

+  __naming object tips__: 
 + don't begin with a number or symbol.
 + there are forbidden words 
 + be consistent with your __coding style__! 
 + avoid dots
 + __name functions as verbs and objects as nouns__

+ you can see which objects are saved in the workspace by using `ls()`

---

## about the workspace

+ R creates __objects__ that occupy RAM memory: the __workspace__

+ the __workspace__ can be saved and loaded between sessions BUT

+ __you can lose track of how you created the objects in the workspace__

+ `#goodpractices` don't save the workspace

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.pull-left[in the general options]

---
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# functions, arguments and understanding the  help

---
## functions and arguments

```
weight_kg <- sqrt(10)
round(3.14159)
args(round)
```

---
## if you know the name of the function
```
help(function)
?function
args(function)
```

+ select the name of the function and click __F1__

Check the structure of the help file:

+ Description
+ Usage
+ Arguments
+ Details

---
## if you don't know the name of the function

```
??kruskal
```

(or search it - google it - duckduckgo it)

---
## the structure of a function help

`args(function)`

+ The arguments of a function are coded:
  + in order
  + with or without default settings
  
--

You can either
+ use the arguments in order, without naming them
+ use the first arguments without naming them and then some optional arguments, with name

---
## data types in R

<small>

```r
animals  <- c("mouse", "rat", "dog")
weight_g <- c(50, 60, 65, 82)
```

```r
class(animals)
```

```
## [1] "character"
```

```r
class(weight_g)
```

```
## [1] "numeric"
```
</small>

`character` and `numeric` but also `logical` and `integer` ("whole" numbers, with no decimal component, in N), `complex`, and others.

---
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---
## subsetting vectors

+ R is __1-indexed__ and intervals are closed (not half-open)

```r
animals <- c("mouse", "rat", "dog", "cat")
animals[2]
```

```
## [1] "rat"
```

+ Subsetting is done with brackets `[]`

```r
animals[c(3, 2)]
```

```
## [1] "dog" "rat"
```

---
## conditional subsetting

```r
weight_g <- c(21, 34, 39, 54, 55)
weight_g[c(TRUE, FALSE, FALSE, TRUE, TRUE)]
```

```
## [1] 21 54 55
```

Nobody works like this, instead we use __logical clauses__ to __generate__ these logical vectors

---

## logical clauses

+ equality or not: `==`, `!=`
+ inequalities: `<`. `>`, `<=`, `>=`
+ union (OR) `|`
+ intersection (AND) `&`
+ belonging `%in%`
+ differences between sets: `setdiff()`
+ negation works `!`: "not in" `!a %in% b`

---
## comparing vectors

<small>

```r
animals      <- c("mouse", "rat", "dog", "cat")
more_animals <- c("rat", "cat", "dog", "duck", "goat")
animals %in% more_animals
```

```
## [1] FALSE  TRUE  TRUE  TRUE
```

---
##comparing vectors

<small>

```r
animals      <- c("mouse", "rat", "dog", "cat")
more_animals <- c("rat", "cat", "dog", "duck", "goat")
animals == more_animals
```

```
## Warning in animals == more_animals: comprimento do objeto maior não é múltiplo
## do comprimento do objeto menor
```

```
## [1] FALSE FALSE  TRUE FALSE FALSE
```

+ Vectors are compared __one by one AND recycled__ when one of them is shorter, so use `%in%` when you want to check __belonging to a set__

---
## missing data

<small>

```r
heights <- c(2, 4, 4, NA, 6)
mean(heights)
```

```
## [1] NA
```

```r
max(heights)
```

```
## [1] NA
```

```r
mean(heights, na.rm = TRUE)
```

```
## [1] 4
```

```r
max(heights, na.rm = TRUE)
```

```
## [1] 6
```

---

## data structures

+ __vector__: lineal arrays (one dimension: only length)

+ __factors__: vectors (one-dimensional) representing __categorical variables__ and thus having __levels__

+ __matrices__: arrays of vectors -> the same type (all numeric or all character, for instance) (two dimensions: width and length)

+ __data frames__: two-dimensional arrays but might be of combined types (i.e., column 1 with names, column 2 with numbers)

+ __arrays__ are similar to matrices and dataframes but may be three-dimensional ("layered" data frames)

+ __list__: literally a list of anything (a list of data frames, or different objects)

---
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# Getting help in R

---
## Getting help

+ `help()` and `vignette()`
+ community forums
+ comminity slack (R-Ladies+, LatinR...)
+ stack overflow

---
## Other sources of help

+ Taskviews

[https://cran.r-project.org/web/views/](https://cran.r-project.org/web/views/)

---
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# ¡Thanks!

<center>
<svg viewBox="0 0 512 512" style="position:relative;display:inline-block;top:.1em;fill:#A70000;height:1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M476 3.2L12.5 270.6c-18.1 10.4-15.8 35.6 2.2 43.2L121 358.4l287.3-253.2c5.5-4.9 13.3 2.6 8.6 8.3L176 407v80.5c0 23.6 28.5 32.9 42.5 15.8L282 426l124.6 52.2c14.2 6 30.4-2.9 33-18.2l72-432C515 7.8 493.3-6.8 476 3.2z"></path></svg> [saramortara@gmail.com](mailto:saramortara@gmail.com) | [andreasancheztapia@gmail.com](mailto:andreasancheztapia@gmail.com)