Eᔕᖇs ᗯIᑎTEᖇ ᗯOᖇKᔕᕼOᑭ ☔

The basics

Introduction

• R
• R markdown, R notebook

Vectors:

• subsetting, recycling
• Vector types: numeric, logical, character, complex
• Some operations : +,-, /, *, %/%, %%, ==, !=
• Some functions: any, all, example, help, ?, ??, sum, sd, mean, factorial, abs

Matrices:

• subsetting, basic operations

Functions:

• Basic function format, environments, return, recursions

Flow control in R:

• if, if-else, ifelse, for, while, break, next

Lists:

• basic operations; accessing elements, list structure
• lapply, sapply, tapply, by, do.call
• … as parameter

Factors:

• structure, addition of elements, addition of new levels
• Conversion to numeric

Data manipulation

Data frames

• read in: read.table, read.csv, read.tsv
• basics - subset() and []
• merge, order, unique

Package: dplyr

• filter, slice, select
• %>%, grouping
• summarise, arrange, lead, lag, n, count
• mutate, mutate_all, transmute

Package: data.table

• i: selecting rows
• j: selecting columns, returning list list() / .()
• by: by
• operations on columns
• Adding new columns
• .N, .I, .GRP
• keys
• .SD, .SDcols
• {}: supressing intermediate output
• merge
• roll
• foverlaps

Regular expressions

• grep
• Special characters: ^$ \ . + * ?
• Special brackets: [], (), {}. \1
• stringr package

Package: tidyr

What is clean data?

• rows = observations
• columns = attributes

How to clean up messy data:

• Spread: Each column single attribute
• Gather: Column headers are variable names
• Sepatrate: Busy columns
• Merge multiple tables (baseR, dplyr, data.table)

Data visualization

• Plots in base R VS ggplot examples

Some useful graphs:

• Scatter plot
• Q-Q plot
• Histograms
• Density plots
• correlation matrix (package:corrplot)
• Heatmap (package: pheatmap)

Package: ggplot2

• Basics: ggplot(dataframe, aes(x,y))
• Different layer examples: geom_point(), geom_histogram(), geom_smooth(), geom_bar(), geom_boxplot(), geom_density(), …
• Groupings: group, fill, facets
• Other: titles, axes, legends, colors, themes

Interactive graphs

• Interactive graphs examples with ggplotly
• shiny