Overview

  • Why use R?

  • Use RStudio to write and run R programmes

  • Create and start an R project

  • Use install.packages() to install packages

  • How to get help in R

  • See examples of data wrangling and visualisation

Why use R?

What can R do?

  • Data import

  • Data management and wrangling

  • Exploratory data analysis

  • Statistical modelling

  • Advanced statistics

  • Machine learning

  • Data visualisation

  • Reports, articles

  • Dashboards, web apps

  • Integrates well with other languages

  • Packages: share your code and use others

The R Ecosystem

Base R

15 base packages

  • Create R objects
  • Summaries
  • Maths functions
  • Statistics
  • Graphics
  • Datasets
  • Statistics methodology
  • More maths
  • More graphics

The R Ecosystem

Contributed packages

CRAN

Bioconductor

GitHub

  • Packages in development
  • GitHub-only packages

The tidyverse

The tidyverse is an opinionated collection of R packages designed for data science. All packages share an underlying design philosophy, grammar and data structures.

From https://education.rstudio.com/blog/2020/07/teaching-the-tidyverse-in-2020-part-1-getting-started/

tidyverse 2.0.0. includes lubridate for date-times as well (not shown in image).

penguins data

  • Available in R >= 4.5.0

  • Originally popularised in the palmerpenguins package, as a great dataset for learning data exploration, visualisation and on which to practice statistical methodology.

  • It contains measurement data for 344 penguins, from three different species, collected from three islands in the Palmer Archipelago, Antarctica.

Penguin artwork by Allison Horst https://allisonhorst.github.io/palmerpenguins/articles/art.html

The R community

Another reason to love R is the community around it.

It prides itself on being friendly, diverse, helpful, and supportive.

Introducing RStudio

At first

With script

RStudio cheatsheet

Best practice: use R projects

An RStudio project is a contect for working on a specific project

  • Keeps files well-organised

  • Automatically sets working directory to project root

  • Has separate workspace and command history

  • Works well with version control via git or svn

Getting started with projects

  • Create a project from a new or existing directory via the file menu or new project button

  • Switch project, or open a different project in a new RStudio instance via the project menu

RStudio project demo

  • Create R-Foundations project

  • Create first script

Using the console

  • For things that only need doing once, e.g. installing packages

  • For doing things you don’t need to track, e.g. requesting help files

  • To quickly explore new ideas before adding them to a script

Using the console: shortcuts

RStudio provides a few shortcuts to help write code in the R console

  • ↑/↓ go back/forward through history one command at a time
  • Ctrl/⌘ + ↑ review recent history and select command
  • Tab view possible completions for part-written expression

Code completion (using Tab) is also provided in the source editor

Using the console: demo

1 + 1
?log
log(10)
exp(-4 * 4 / 2) / sqrt(2 * pi)
install.packages("tidyverse")
install.packages("palmerpenguins") # Only if using R < 4.5.0

Using scripts

Text files saved with an .R suffix are recognised as R code

Code can be sent directly from a script to the console as follows:

  • Ctrl/⌘ + ↵ or Run button run current line
    • Run multiple lines by selecting first
  • Ctrl/⌘ + Shift + ↵ or Source button
    • Run the script from start to finish.

Why R scripts?

Writing an R script for an analysis has several advantages over a graphical user interface (GUI)

  • It provides a record of the exact approach used in an analysis
  • It enables the analysis to be easily reproduced and modified
  • It allows greater control

Good practice for R Scripts

Organising your R script well will help you and others understand and use it.

  • Add comment or two at start to describe purpose of script
    • Use one or more # to start a comment
  • Load required data and packages at the start
  • Avoid hard-coding: define variables such as file paths early on
  • Give functions and variable meaningful names
  • use ### or #--- to separate sections (in RStudio Code > Insert Section)

Installing packages

In console

  • Install a package with install.packages("package_name")

    • Watch out for the plural!

  • Install multiple packages with install.packages(c("package1", "package2"))

    • The c() function creates a vector

  • Or use install button in packages pane:

Loading packages

In script

  • Load packages with library(package_name)

Your turn

  • Create an R project called “r-foundations”

  • Install the tidyverse package, and palmerpenguins if using R < 4.5.0

  • Find the help page for the penguins dataset

  • Find the help page for the filter function in the dplyr package

  • Experiment typing commands into the console or in an R script.

link to slides

R script demo

### load packages
library(tidyverse)
library(palmerpenguins) # Only if R < 4.5

### Inspect data (base R functions)
View(penguins)
head(penguins)
summary(penguins)

### tidyverse functions
glimpse(penguins)

The data

penguins
      species    island bill_len bill_dep flipper_len body_mass    sex year
1      Adelie Torgersen     39.1     18.7         181      3750   male 2007
2      Adelie Torgersen     39.5     17.4         186      3800 female 2007
3      Adelie Torgersen     40.3     18.0         195      3250 female 2007
4      Adelie Torgersen       NA       NA          NA        NA   <NA> 2007
5      Adelie Torgersen     36.7     19.3         193      3450 female 2007
6      Adelie Torgersen     39.3     20.6         190      3650   male 2007
7      Adelie Torgersen     38.9     17.8         181      3625 female 2007
8      Adelie Torgersen     39.2     19.6         195      4675   male 2007
9      Adelie Torgersen     34.1     18.1         193      3475   <NA> 2007
10     Adelie Torgersen     42.0     20.2         190      4250   <NA> 2007
11     Adelie Torgersen     37.8     17.1         186      3300   <NA> 2007
12     Adelie Torgersen     37.8     17.3         180      3700   <NA> 2007
13     Adelie Torgersen     41.1     17.6         182      3200 female 2007
14     Adelie Torgersen     38.6     21.2         191      3800   male 2007
15     Adelie Torgersen     34.6     21.1         198      4400   male 2007
16     Adelie Torgersen     36.6     17.8         185      3700 female 2007
17     Adelie Torgersen     38.7     19.0         195      3450 female 2007
18     Adelie Torgersen     42.5     20.7         197      4500   male 2007
19     Adelie Torgersen     34.4     18.4         184      3325 female 2007
20     Adelie Torgersen     46.0     21.5         194      4200   male 2007
21     Adelie    Biscoe     37.8     18.3         174      3400 female 2007
22     Adelie    Biscoe     37.7     18.7         180      3600   male 2007
23     Adelie    Biscoe     35.9     19.2         189      3800 female 2007
24     Adelie    Biscoe     38.2     18.1         185      3950   male 2007
25     Adelie    Biscoe     38.8     17.2         180      3800   male 2007
26     Adelie    Biscoe     35.3     18.9         187      3800 female 2007
27     Adelie    Biscoe     40.6     18.6         183      3550   male 2007
28     Adelie    Biscoe     40.5     17.9         187      3200 female 2007
29     Adelie    Biscoe     37.9     18.6         172      3150 female 2007
30     Adelie    Biscoe     40.5     18.9         180      3950   male 2007
31     Adelie     Dream     39.5     16.7         178      3250 female 2007
32     Adelie     Dream     37.2     18.1         178      3900   male 2007
33     Adelie     Dream     39.5     17.8         188      3300 female 2007
34     Adelie     Dream     40.9     18.9         184      3900   male 2007
35     Adelie     Dream     36.4     17.0         195      3325 female 2007
36     Adelie     Dream     39.2     21.1         196      4150   male 2007
37     Adelie     Dream     38.8     20.0         190      3950   male 2007
38     Adelie     Dream     42.2     18.5         180      3550 female 2007
39     Adelie     Dream     37.6     19.3         181      3300 female 2007
40     Adelie     Dream     39.8     19.1         184      4650   male 2007
41     Adelie     Dream     36.5     18.0         182      3150 female 2007
42     Adelie     Dream     40.8     18.4         195      3900   male 2007
43     Adelie     Dream     36.0     18.5         186      3100 female 2007
44     Adelie     Dream     44.1     19.7         196      4400   male 2007
45     Adelie     Dream     37.0     16.9         185      3000 female 2007
46     Adelie     Dream     39.6     18.8         190      4600   male 2007
47     Adelie     Dream     41.1     19.0         182      3425   male 2007
48     Adelie     Dream     37.5     18.9         179      2975   <NA> 2007
49     Adelie     Dream     36.0     17.9         190      3450 female 2007
50     Adelie     Dream     42.3     21.2         191      4150   male 2007
51     Adelie    Biscoe     39.6     17.7         186      3500 female 2008
52     Adelie    Biscoe     40.1     18.9         188      4300   male 2008
53     Adelie    Biscoe     35.0     17.9         190      3450 female 2008
54     Adelie    Biscoe     42.0     19.5         200      4050   male 2008
55     Adelie    Biscoe     34.5     18.1         187      2900 female 2008
56     Adelie    Biscoe     41.4     18.6         191      3700   male 2008
57     Adelie    Biscoe     39.0     17.5         186      3550 female 2008
58     Adelie    Biscoe     40.6     18.8         193      3800   male 2008
59     Adelie    Biscoe     36.5     16.6         181      2850 female 2008
60     Adelie    Biscoe     37.6     19.1         194      3750   male 2008
61     Adelie    Biscoe     35.7     16.9         185      3150 female 2008
62     Adelie    Biscoe     41.3     21.1         195      4400   male 2008
63     Adelie    Biscoe     37.6     17.0         185      3600 female 2008
64     Adelie    Biscoe     41.1     18.2         192      4050   male 2008
65     Adelie    Biscoe     36.4     17.1         184      2850 female 2008
66     Adelie    Biscoe     41.6     18.0         192      3950   male 2008
67     Adelie    Biscoe     35.5     16.2         195      3350 female 2008
68     Adelie    Biscoe     41.1     19.1         188      4100   male 2008
69     Adelie Torgersen     35.9     16.6         190      3050 female 2008
70     Adelie Torgersen     41.8     19.4         198      4450   male 2008
71     Adelie Torgersen     33.5     19.0         190      3600 female 2008
72     Adelie Torgersen     39.7     18.4         190      3900   male 2008
73     Adelie Torgersen     39.6     17.2         196      3550 female 2008
74     Adelie Torgersen     45.8     18.9         197      4150   male 2008
75     Adelie Torgersen     35.5     17.5         190      3700 female 2008
76     Adelie Torgersen     42.8     18.5         195      4250   male 2008
77     Adelie Torgersen     40.9     16.8         191      3700 female 2008
78     Adelie Torgersen     37.2     19.4         184      3900   male 2008
79     Adelie Torgersen     36.2     16.1         187      3550 female 2008
80     Adelie Torgersen     42.1     19.1         195      4000   male 2008
81     Adelie Torgersen     34.6     17.2         189      3200 female 2008
82     Adelie Torgersen     42.9     17.6         196      4700   male 2008
83     Adelie Torgersen     36.7     18.8         187      3800 female 2008
84     Adelie Torgersen     35.1     19.4         193      4200   male 2008
85     Adelie     Dream     37.3     17.8         191      3350 female 2008
86     Adelie     Dream     41.3     20.3         194      3550   male 2008
87     Adelie     Dream     36.3     19.5         190      3800   male 2008
88     Adelie     Dream     36.9     18.6         189      3500 female 2008
89     Adelie     Dream     38.3     19.2         189      3950   male 2008
90     Adelie     Dream     38.9     18.8         190      3600 female 2008
91     Adelie     Dream     35.7     18.0         202      3550 female 2008
92     Adelie     Dream     41.1     18.1         205      4300   male 2008
93     Adelie     Dream     34.0     17.1         185      3400 female 2008
94     Adelie     Dream     39.6     18.1         186      4450   male 2008
95     Adelie     Dream     36.2     17.3         187      3300 female 2008
96     Adelie     Dream     40.8     18.9         208      4300   male 2008
97     Adelie     Dream     38.1     18.6         190      3700 female 2008
98     Adelie     Dream     40.3     18.5         196      4350   male 2008
99     Adelie     Dream     33.1     16.1         178      2900 female 2008
100    Adelie     Dream     43.2     18.5         192      4100   male 2008
101    Adelie    Biscoe     35.0     17.9         192      3725 female 2009
102    Adelie    Biscoe     41.0     20.0         203      4725   male 2009
103    Adelie    Biscoe     37.7     16.0         183      3075 female 2009
104    Adelie    Biscoe     37.8     20.0         190      4250   male 2009
105    Adelie    Biscoe     37.9     18.6         193      2925 female 2009
106    Adelie    Biscoe     39.7     18.9         184      3550   male 2009
107    Adelie    Biscoe     38.6     17.2         199      3750 female 2009
108    Adelie    Biscoe     38.2     20.0         190      3900   male 2009
109    Adelie    Biscoe     38.1     17.0         181      3175 female 2009
110    Adelie    Biscoe     43.2     19.0         197      4775   male 2009
111    Adelie    Biscoe     38.1     16.5         198      3825 female 2009
112    Adelie    Biscoe     45.6     20.3         191      4600   male 2009
113    Adelie    Biscoe     39.7     17.7         193      3200 female 2009
114    Adelie    Biscoe     42.2     19.5         197      4275   male 2009
115    Adelie    Biscoe     39.6     20.7         191      3900 female 2009
116    Adelie    Biscoe     42.7     18.3         196      4075   male 2009
117    Adelie Torgersen     38.6     17.0         188      2900 female 2009
118    Adelie Torgersen     37.3     20.5         199      3775   male 2009
119    Adelie Torgersen     35.7     17.0         189      3350 female 2009
120    Adelie Torgersen     41.1     18.6         189      3325   male 2009
121    Adelie Torgersen     36.2     17.2         187      3150 female 2009
122    Adelie Torgersen     37.7     19.8         198      3500   male 2009
123    Adelie Torgersen     40.2     17.0         176      3450 female 2009
124    Adelie Torgersen     41.4     18.5         202      3875   male 2009
125    Adelie Torgersen     35.2     15.9         186      3050 female 2009
126    Adelie Torgersen     40.6     19.0         199      4000   male 2009
127    Adelie Torgersen     38.8     17.6         191      3275 female 2009
128    Adelie Torgersen     41.5     18.3         195      4300   male 2009
129    Adelie Torgersen     39.0     17.1         191      3050 female 2009
130    Adelie Torgersen     44.1     18.0         210      4000   male 2009
131    Adelie Torgersen     38.5     17.9         190      3325 female 2009
132    Adelie Torgersen     43.1     19.2         197      3500   male 2009
133    Adelie     Dream     36.8     18.5         193      3500 female 2009
134    Adelie     Dream     37.5     18.5         199      4475   male 2009
135    Adelie     Dream     38.1     17.6         187      3425 female 2009
136    Adelie     Dream     41.1     17.5         190      3900   male 2009
137    Adelie     Dream     35.6     17.5         191      3175 female 2009
138    Adelie     Dream     40.2     20.1         200      3975   male 2009
139    Adelie     Dream     37.0     16.5         185      3400 female 2009
140    Adelie     Dream     39.7     17.9         193      4250   male 2009
141    Adelie     Dream     40.2     17.1         193      3400 female 2009
142    Adelie     Dream     40.6     17.2         187      3475   male 2009
143    Adelie     Dream     32.1     15.5         188      3050 female 2009
144    Adelie     Dream     40.7     17.0         190      3725   male 2009
145    Adelie     Dream     37.3     16.8         192      3000 female 2009
146    Adelie     Dream     39.0     18.7         185      3650   male 2009
147    Adelie     Dream     39.2     18.6         190      4250   male 2009
148    Adelie     Dream     36.6     18.4         184      3475 female 2009
149    Adelie     Dream     36.0     17.8         195      3450 female 2009
150    Adelie     Dream     37.8     18.1         193      3750   male 2009
151    Adelie     Dream     36.0     17.1         187      3700 female 2009
152    Adelie     Dream     41.5     18.5         201      4000   male 2009
153    Gentoo    Biscoe     46.1     13.2         211      4500 female 2007
154    Gentoo    Biscoe     50.0     16.3         230      5700   male 2007
155    Gentoo    Biscoe     48.7     14.1         210      4450 female 2007
156    Gentoo    Biscoe     50.0     15.2         218      5700   male 2007
157    Gentoo    Biscoe     47.6     14.5         215      5400   male 2007
158    Gentoo    Biscoe     46.5     13.5         210      4550 female 2007
159    Gentoo    Biscoe     45.4     14.6         211      4800 female 2007
160    Gentoo    Biscoe     46.7     15.3         219      5200   male 2007
161    Gentoo    Biscoe     43.3     13.4         209      4400 female 2007
162    Gentoo    Biscoe     46.8     15.4         215      5150   male 2007
163    Gentoo    Biscoe     40.9     13.7         214      4650 female 2007
164    Gentoo    Biscoe     49.0     16.1         216      5550   male 2007
165    Gentoo    Biscoe     45.5     13.7         214      4650 female 2007
166    Gentoo    Biscoe     48.4     14.6         213      5850   male 2007
167    Gentoo    Biscoe     45.8     14.6         210      4200 female 2007
168    Gentoo    Biscoe     49.3     15.7         217      5850   male 2007
169    Gentoo    Biscoe     42.0     13.5         210      4150 female 2007
170    Gentoo    Biscoe     49.2     15.2         221      6300   male 2007
171    Gentoo    Biscoe     46.2     14.5         209      4800 female 2007
172    Gentoo    Biscoe     48.7     15.1         222      5350   male 2007
173    Gentoo    Biscoe     50.2     14.3         218      5700   male 2007
174    Gentoo    Biscoe     45.1     14.5         215      5000 female 2007
175    Gentoo    Biscoe     46.5     14.5         213      4400 female 2007
176    Gentoo    Biscoe     46.3     15.8         215      5050   male 2007
177    Gentoo    Biscoe     42.9     13.1         215      5000 female 2007
178    Gentoo    Biscoe     46.1     15.1         215      5100   male 2007
179    Gentoo    Biscoe     44.5     14.3         216      4100   <NA> 2007
180    Gentoo    Biscoe     47.8     15.0         215      5650   male 2007
181    Gentoo    Biscoe     48.2     14.3         210      4600 female 2007
182    Gentoo    Biscoe     50.0     15.3         220      5550   male 2007
183    Gentoo    Biscoe     47.3     15.3         222      5250   male 2007
184    Gentoo    Biscoe     42.8     14.2         209      4700 female 2007
185    Gentoo    Biscoe     45.1     14.5         207      5050 female 2007
186    Gentoo    Biscoe     59.6     17.0         230      6050   male 2007
187    Gentoo    Biscoe     49.1     14.8         220      5150 female 2008
188    Gentoo    Biscoe     48.4     16.3         220      5400   male 2008
189    Gentoo    Biscoe     42.6     13.7         213      4950 female 2008
190    Gentoo    Biscoe     44.4     17.3         219      5250   male 2008
191    Gentoo    Biscoe     44.0     13.6         208      4350 female 2008
192    Gentoo    Biscoe     48.7     15.7         208      5350   male 2008
193    Gentoo    Biscoe     42.7     13.7         208      3950 female 2008
194    Gentoo    Biscoe     49.6     16.0         225      5700   male 2008
195    Gentoo    Biscoe     45.3     13.7         210      4300 female 2008
196    Gentoo    Biscoe     49.6     15.0         216      4750   male 2008
197    Gentoo    Biscoe     50.5     15.9         222      5550   male 2008
198    Gentoo    Biscoe     43.6     13.9         217      4900 female 2008
199    Gentoo    Biscoe     45.5     13.9         210      4200 female 2008
200    Gentoo    Biscoe     50.5     15.9         225      5400   male 2008
201    Gentoo    Biscoe     44.9     13.3         213      5100 female 2008
202    Gentoo    Biscoe     45.2     15.8         215      5300   male 2008
203    Gentoo    Biscoe     46.6     14.2         210      4850 female 2008
204    Gentoo    Biscoe     48.5     14.1         220      5300   male 2008
205    Gentoo    Biscoe     45.1     14.4         210      4400 female 2008
206    Gentoo    Biscoe     50.1     15.0         225      5000   male 2008
207    Gentoo    Biscoe     46.5     14.4         217      4900 female 2008
208    Gentoo    Biscoe     45.0     15.4         220      5050   male 2008
209    Gentoo    Biscoe     43.8     13.9         208      4300 female 2008
210    Gentoo    Biscoe     45.5     15.0         220      5000   male 2008
211    Gentoo    Biscoe     43.2     14.5         208      4450 female 2008
212    Gentoo    Biscoe     50.4     15.3         224      5550   male 2008
213    Gentoo    Biscoe     45.3     13.8         208      4200 female 2008
214    Gentoo    Biscoe     46.2     14.9         221      5300   male 2008
215    Gentoo    Biscoe     45.7     13.9         214      4400 female 2008
216    Gentoo    Biscoe     54.3     15.7         231      5650   male 2008
217    Gentoo    Biscoe     45.8     14.2         219      4700 female 2008
218    Gentoo    Biscoe     49.8     16.8         230      5700   male 2008
219    Gentoo    Biscoe     46.2     14.4         214      4650   <NA> 2008
220    Gentoo    Biscoe     49.5     16.2         229      5800   male 2008
221    Gentoo    Biscoe     43.5     14.2         220      4700 female 2008
222    Gentoo    Biscoe     50.7     15.0         223      5550   male 2008
223    Gentoo    Biscoe     47.7     15.0         216      4750 female 2008
224    Gentoo    Biscoe     46.4     15.6         221      5000   male 2008
225    Gentoo    Biscoe     48.2     15.6         221      5100   male 2008
226    Gentoo    Biscoe     46.5     14.8         217      5200 female 2008
227    Gentoo    Biscoe     46.4     15.0         216      4700 female 2008
228    Gentoo    Biscoe     48.6     16.0         230      5800   male 2008
229    Gentoo    Biscoe     47.5     14.2         209      4600 female 2008
230    Gentoo    Biscoe     51.1     16.3         220      6000   male 2008
231    Gentoo    Biscoe     45.2     13.8         215      4750 female 2008
232    Gentoo    Biscoe     45.2     16.4         223      5950   male 2008
233    Gentoo    Biscoe     49.1     14.5         212      4625 female 2009
234    Gentoo    Biscoe     52.5     15.6         221      5450   male 2009
235    Gentoo    Biscoe     47.4     14.6         212      4725 female 2009
236    Gentoo    Biscoe     50.0     15.9         224      5350   male 2009
237    Gentoo    Biscoe     44.9     13.8         212      4750 female 2009
238    Gentoo    Biscoe     50.8     17.3         228      5600   male 2009
239    Gentoo    Biscoe     43.4     14.4         218      4600 female 2009
240    Gentoo    Biscoe     51.3     14.2         218      5300   male 2009
241    Gentoo    Biscoe     47.5     14.0         212      4875 female 2009
242    Gentoo    Biscoe     52.1     17.0         230      5550   male 2009
243    Gentoo    Biscoe     47.5     15.0         218      4950 female 2009
244    Gentoo    Biscoe     52.2     17.1         228      5400   male 2009
245    Gentoo    Biscoe     45.5     14.5         212      4750 female 2009
246    Gentoo    Biscoe     49.5     16.1         224      5650   male 2009
247    Gentoo    Biscoe     44.5     14.7         214      4850 female 2009
248    Gentoo    Biscoe     50.8     15.7         226      5200   male 2009
249    Gentoo    Biscoe     49.4     15.8         216      4925   male 2009
250    Gentoo    Biscoe     46.9     14.6         222      4875 female 2009
251    Gentoo    Biscoe     48.4     14.4         203      4625 female 2009
252    Gentoo    Biscoe     51.1     16.5         225      5250   male 2009
253    Gentoo    Biscoe     48.5     15.0         219      4850 female 2009
254    Gentoo    Biscoe     55.9     17.0         228      5600   male 2009
255    Gentoo    Biscoe     47.2     15.5         215      4975 female 2009
256    Gentoo    Biscoe     49.1     15.0         228      5500   male 2009
257    Gentoo    Biscoe     47.3     13.8         216      4725   <NA> 2009
258    Gentoo    Biscoe     46.8     16.1         215      5500   male 2009
259    Gentoo    Biscoe     41.7     14.7         210      4700 female 2009
260    Gentoo    Biscoe     53.4     15.8         219      5500   male 2009
261    Gentoo    Biscoe     43.3     14.0         208      4575 female 2009
262    Gentoo    Biscoe     48.1     15.1         209      5500   male 2009
263    Gentoo    Biscoe     50.5     15.2         216      5000 female 2009
264    Gentoo    Biscoe     49.8     15.9         229      5950   male 2009
265    Gentoo    Biscoe     43.5     15.2         213      4650 female 2009
266    Gentoo    Biscoe     51.5     16.3         230      5500   male 2009
267    Gentoo    Biscoe     46.2     14.1         217      4375 female 2009
268    Gentoo    Biscoe     55.1     16.0         230      5850   male 2009
269    Gentoo    Biscoe     44.5     15.7         217      4875   <NA> 2009
270    Gentoo    Biscoe     48.8     16.2         222      6000   male 2009
271    Gentoo    Biscoe     47.2     13.7         214      4925 female 2009
272    Gentoo    Biscoe       NA       NA          NA        NA   <NA> 2009
273    Gentoo    Biscoe     46.8     14.3         215      4850 female 2009
274    Gentoo    Biscoe     50.4     15.7         222      5750   male 2009
275    Gentoo    Biscoe     45.2     14.8         212      5200 female 2009
276    Gentoo    Biscoe     49.9     16.1         213      5400   male 2009
277 Chinstrap     Dream     46.5     17.9         192      3500 female 2007
278 Chinstrap     Dream     50.0     19.5         196      3900   male 2007
279 Chinstrap     Dream     51.3     19.2         193      3650   male 2007
280 Chinstrap     Dream     45.4     18.7         188      3525 female 2007
281 Chinstrap     Dream     52.7     19.8         197      3725   male 2007
282 Chinstrap     Dream     45.2     17.8         198      3950 female 2007
283 Chinstrap     Dream     46.1     18.2         178      3250 female 2007
284 Chinstrap     Dream     51.3     18.2         197      3750   male 2007
285 Chinstrap     Dream     46.0     18.9         195      4150 female 2007
286 Chinstrap     Dream     51.3     19.9         198      3700   male 2007
287 Chinstrap     Dream     46.6     17.8         193      3800 female 2007
288 Chinstrap     Dream     51.7     20.3         194      3775   male 2007
289 Chinstrap     Dream     47.0     17.3         185      3700 female 2007
290 Chinstrap     Dream     52.0     18.1         201      4050   male 2007
291 Chinstrap     Dream     45.9     17.1         190      3575 female 2007
292 Chinstrap     Dream     50.5     19.6         201      4050   male 2007
293 Chinstrap     Dream     50.3     20.0         197      3300   male 2007
294 Chinstrap     Dream     58.0     17.8         181      3700 female 2007
295 Chinstrap     Dream     46.4     18.6         190      3450 female 2007
296 Chinstrap     Dream     49.2     18.2         195      4400   male 2007
297 Chinstrap     Dream     42.4     17.3         181      3600 female 2007
298 Chinstrap     Dream     48.5     17.5         191      3400   male 2007
299 Chinstrap     Dream     43.2     16.6         187      2900 female 2007
300 Chinstrap     Dream     50.6     19.4         193      3800   male 2007
301 Chinstrap     Dream     46.7     17.9         195      3300 female 2007
302 Chinstrap     Dream     52.0     19.0         197      4150   male 2007
303 Chinstrap     Dream     50.5     18.4         200      3400 female 2008
304 Chinstrap     Dream     49.5     19.0         200      3800   male 2008
305 Chinstrap     Dream     46.4     17.8         191      3700 female 2008
306 Chinstrap     Dream     52.8     20.0         205      4550   male 2008
307 Chinstrap     Dream     40.9     16.6         187      3200 female 2008
308 Chinstrap     Dream     54.2     20.8         201      4300   male 2008
309 Chinstrap     Dream     42.5     16.7         187      3350 female 2008
310 Chinstrap     Dream     51.0     18.8         203      4100   male 2008
311 Chinstrap     Dream     49.7     18.6         195      3600   male 2008
312 Chinstrap     Dream     47.5     16.8         199      3900 female 2008
313 Chinstrap     Dream     47.6     18.3         195      3850 female 2008
314 Chinstrap     Dream     52.0     20.7         210      4800   male 2008
315 Chinstrap     Dream     46.9     16.6         192      2700 female 2008
316 Chinstrap     Dream     53.5     19.9         205      4500   male 2008
317 Chinstrap     Dream     49.0     19.5         210      3950   male 2008
318 Chinstrap     Dream     46.2     17.5         187      3650 female 2008
319 Chinstrap     Dream     50.9     19.1         196      3550   male 2008
320 Chinstrap     Dream     45.5     17.0         196      3500 female 2008
321 Chinstrap     Dream     50.9     17.9         196      3675 female 2009
322 Chinstrap     Dream     50.8     18.5         201      4450   male 2009
323 Chinstrap     Dream     50.1     17.9         190      3400 female 2009
324 Chinstrap     Dream     49.0     19.6         212      4300   male 2009
325 Chinstrap     Dream     51.5     18.7         187      3250   male 2009
326 Chinstrap     Dream     49.8     17.3         198      3675 female 2009
327 Chinstrap     Dream     48.1     16.4         199      3325 female 2009
328 Chinstrap     Dream     51.4     19.0         201      3950   male 2009
329 Chinstrap     Dream     45.7     17.3         193      3600 female 2009
330 Chinstrap     Dream     50.7     19.7         203      4050   male 2009
331 Chinstrap     Dream     42.5     17.3         187      3350 female 2009
332 Chinstrap     Dream     52.2     18.8         197      3450   male 2009
333 Chinstrap     Dream     45.2     16.6         191      3250 female 2009
334 Chinstrap     Dream     49.3     19.9         203      4050   male 2009
335 Chinstrap     Dream     50.2     18.8         202      3800   male 2009
336 Chinstrap     Dream     45.6     19.4         194      3525 female 2009
337 Chinstrap     Dream     51.9     19.5         206      3950   male 2009
338 Chinstrap     Dream     46.8     16.5         189      3650 female 2009
339 Chinstrap     Dream     45.7     17.0         195      3650 female 2009
340 Chinstrap     Dream     55.8     19.8         207      4000   male 2009
341 Chinstrap     Dream     43.5     18.1         202      3400 female 2009
342 Chinstrap     Dream     49.6     18.2         193      3775   male 2009
343 Chinstrap     Dream     50.8     19.0         210      4100   male 2009
344 Chinstrap     Dream     50.2     18.7         198      3775 female 2009

datasets::penguins vs palmerpenguins::penguins

colnames(penguins)
[1] "species"     "island"      "bill_len"    "bill_dep"    "flipper_len"
[6] "body_mass"   "sex"         "year"       
colnames(palmerpenguins::penguins)
[1] "species"           "island"            "bill_length_mm"   
[4] "bill_depth_mm"     "flipper_length_mm" "body_mass_g"      
[7] "sex"               "year"
datasets palmerpenguins
bill_len bill_length_mm
bill_dep bill_depth_mm
flipper_len flipper_length_mm
body_mass body_mass_g

How many of each species?

library(tidyverse)
count(penguins, species)
    species   n
1    Adelie 152
2 Chinstrap  68
3    Gentoo 124

How many of each species on each island?

count(penguins, species, island, .drop = FALSE)
    species    island   n
1    Adelie    Biscoe  44
2    Adelie     Dream  56
3    Adelie Torgersen  52
4 Chinstrap    Biscoe   0
5 Chinstrap     Dream  68
6 Chinstrap Torgersen   0
7    Gentoo    Biscoe 124
8    Gentoo     Dream   0
9    Gentoo Torgersen   0

Show me the bill dimensions of the 5 heaviest female Gentoo penguins

penguins |>
  filter(sex == "female",
         species == "Gentoo") |>
  slice_max(body_mass, n = 5) |>
  select(contains("bill"))
  bill_len bill_dep
1     46.5     14.8
2     45.2     14.8
3     49.1     14.8
4     44.9     13.3
5     45.1     14.5

The native pipe

|> is a pipe.

It passes what comes before into the first argument of what comes after.

Pipes are a powerful tool for clearly expressing a sequence of multiple operations.

We’ll talk more about pipes in the data wrangling session.

What’s the mean bill length, by species?

penguins |>
  summarise(mean_bill_length = mean(bill_len, na.rm = TRUE),
            .by = species)
    species mean_bill_length
1    Adelie         38.79139
2    Gentoo         47.50488
3 Chinstrap         48.83382

What’s the relationship between bill length and depth?

ggplot(data = penguins,
       aes(x = bill_len,
           y = bill_dep)) +
  geom_point() +
  geom_smooth(method = "lm", se = FALSE, color = "gray50") +
  labs(title = "Penguin bill dimensions",
       subtitle = "Negative correlation between bill length and depth for Penguins at Palmer Station LTER",
       x = "Bill length (mm)",
       y = "Bill depth (mm)") +
  theme_minimal() + 
  theme(plot.title.position = "plot")

ggplot(data = penguins,
       aes(x = bill_len,
           y = bill_dep,
           group = species)) +
  geom_point(aes(color = species, 
                 shape = species),
             size = 3,
             alpha = 0.8) +
  geom_smooth(method = "lm", se = FALSE, aes(color = species)) +
  scale_color_manual(values = c("darkorange","purple","cyan4")) +
  labs(title = "Penguin bill dimensions",
       subtitle = "Positive correlation between bill length and depth for Adelie, Chinstrap and Gentoo Penguins at Palmer Station LTER",
       x = "Bill length (mm)",
       y = "Bill depth (mm)",
       color = "Penguin species",
       shape = "Penguin species") +
  theme_minimal() +
  theme(plot.title.position = "plot",
        plot.subtitle = element_text(size = rel(0.95)))

This is an illustration of Simpson’s Paradox.

Simpson’s paradox is a phenomenon in probability and statistics in which a trend appears in several groups of data but disappears or reverses when the groups are combined.

Example adapted from https://allisonhorst.github.io/palmerpenguins/articles/examples.html

Getting help in R

Within R: Help with functions

# help with a specific function
help(function_name)
?function_name

# quick reminder of the function arguments
arg(function_name)

# see an example
example(function_name)

# see the source code
## in console
function_name
## in View pane (easier to read, syntax highlighting)
View(function_name)

Within R: help.search

# when ?function_name fails (e.g. don't have package loaded)
help.search("function_name") # note quotation marks
??function_name

# for when you can't quite remember the function name
??something_like_function_name

# R help start page
help.start()
## note that using the RStudio Help home button gives even more resources

Within R: Help with package

# `help`
help(package = "package_name")
# Help panel in RStudio will give links to all documentation
# and help pages for that package

# find/browse vignettes for installed (or specific) packages
browseVignettes()
browseVignettes("package_name")

# use auto-completion in RStudio to see what functions 
# are in a package
?package::

dplyr demo

RStudio Help home demo

Getting help at Warwick

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License

Licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License (CC BY-NC-SA 4.0).