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The Epidemiologist R Handbook
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Welcome
About this book
1
Editorial and technical notes
2
Download handbook and data
Basics
3
R Basics
4
Transition to R
5
Suggested packages
6
R projects
7
Import and export
Data Management
8
Cleaning data and core functions
9
Working with dates
10
Characters and strings
11
Factors
12
Pivoting data
13
Grouping data
14
Joining data
15
De-duplication
16
Iteration, loops, and lists
Analysis
17
Descriptive tables
18
Simple statistical tests
19
Univariate and multivariable regression
20
Missing data
21
Standardised rates
22
Moving averages
23
Time series and outbreak detection
24
Epidemic modeling
25
Contact tracing
26
Survey analysis
27
Survival analysis
28
GIS basics
Data Visualization
29
Tables for presentation
30
ggplot basics
31
ggplot tips
32
Epidemic curves
33
Demographic pyramids and Likert-scales
34
Heat plots
35
Diagrams and charts
36
Combinations analysis
37
Transmission chains
38
Phylogenetic trees
39
Interactive plots
Reports and dashboards
40
Reports with R Markdown
41
Organizing routine reports
42
Dashboards with R Markdown
43
Dashboards with Shiny
Miscellaneous
44
Writing functions
45
Directory interactions
46
Version control and collaboration with Git and Github
47
Common errors
48
Getting help
49
R on network drives
50
Data Table
Table of contents
2.1
Download offline handbook
Use download link
Use our R package
2.2
Download data to follow along
Use our R package
Download one-by-one
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Introduction
1
Editorial and technical notes
3
R Basics