#r basics

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R Basics - R Programming Language Introduction

R Basics – R Programming Language Introduction

R Basics – R Programming Language Introduction

Learn the essentials of R Programming – R Beginner Level! What you’ll learn

You will learn how to navigate in the RStudio interface

You will learn how to make basic graphs

You will learn about the basic structure of R including packages

You will learn how to perform basic commands in the R programming language

You will also learn how to…

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[yeoldeeccentric-blog]

Count NAs in a data frame

I've got a data frame called "in_da_club". I want to count the NAs for a variable called, let's say, "Dicks_on_Dancefloor". 

table(is.na(in_da_club$Dicks_on_Dancefloor)) 

and voila.

[yeoldeeccentric-blog]

Indexing data frames!

Another thing! Shit!

Say we have a data frame we'll call, uh, fuck, I dunno, "data". 

data[1:2] prints the first two columns of the data frame.

data[,1:2] also prints the first two cols of the data frame. 

data[1:2,] prints the first two rows. 

Location, location, location. 

[yeoldeeccentric-blog]

R - How to set my fucking working directory

I use getwd() to see my current working directory. 

Then...Christ I'm hungover...

I use setwd("directory") to set a new working directory. 

Example:

setwd("/Users/Desktop/R Programming")

Just like that, motherfucker.

[sasrandme]

R graphics plot types

scatter plot types

we use the tree data set as example data set

head(trees)

Girth Height Volume 1 8.3 70 10.3 2 8.6 65 10.3 3 8.8 63 10.2 4 10.5 72 16.4 5 10.7 81 18.8 6 10.8 83 19.7

par(mfrow=c(3,3)) plot(trees$Girth,trees$Height,type="p",main="type='p'") ## points plot(trees$Girth,trees$Height,type="l",main="type='l'") ## a line plot(trees$Girth,trees$Height,type="b",main="type='b'") ## both plot(trees$Girth,trees$Height,type="o",main="type='o'") ## both overplotted plot(trees$Girth,trees$Height,type="c",main="type='c'") ## lines like in "b" plot(trees$Girth,trees$Height,type="h",main="type='h'") ## vertical lines plot(trees$Girth,trees$Height,type="s",main="type='s'") ## stair steps (first horizontal) plot(trees$Girth,trees$Height,type="S",main="type='S'") ## stair steps (first vertical) plot(trees$Girth,trees$Height,type="n",main="type='n'") ## none

[sasrandme]

R - subscripting 3

subscripting with positive and negative indices

character subscripting (vectors and lists)

logical subscripting

subsetting with logical indices

elements corresponding to a TRUE in the subscript vector are selected, those corresponding to a FALSE are excluded, NAs in the the logical subscript vector produce NAs

my.vector <- letters[1:10] # vector of a...j my.vector

[1] "a" "b" "c" "d" "e" "f" "g" "h" "i" "j"

my.index <- rep(c(TRUE,FALSE),5) # the subscript vector (of length 10) my.index

[1] TRUE FALSE TRUE FALSE TRUE FALSE TRUE FALSE TRUE FALSE

my.vector[my.index]

[1] "a" "c" "e" "g" "i"

if the subscript vector consists of less elements than the subscripted vector, it is repeated as many times as necessary (warning if the the vector length is not a multiple of the length of the subscript vector)

short.index <- c(T,F) # T is the same as TRUE, F as FALSE short.index

[1] TRUE FALSE

my.vector[short.index] # has the same result as above

[1] "a" "c" "e" "g" "i"

if the subscript vector is longer than the vector for every TRUE or NA entry without target a NA is produced

short.vector <- letters[1:3] short.vector

[1] "a" "b" "c"

my.index <- rep(c(T,F,NA),2) my.index

[1] TRUE FALSE NA TRUE FALSE NA

short.vector[my.index]

[1] "a" NA NA NA

[sasrandme]

R - subscripting 2

subscripting with positive and negative indices

character subscripting (vectors and lists)

logical subscripting

subsetting with character indices - vectors and lists

extract elements of named vectors, lists

named.x <- 1:10 # produce a vector containing the numbers 1...10 named.x # has no names yet

[1] 1 2 3 4 5 6 7 8 9 10

if the object has no names, NAs are produced

named.x["one"]

[1] NA

name the vector:

names(named.x) <- c("one","two","three","four","five","six","seven","eight","nine","ten") named.x

one two three four five six seven eight nine ten 1 2 3 4 5 6 7 8 9 10

now it works

named.x["one"]

one 1

if names are duplicated only the first match is returned (the value with the lowest index)

names(named.x)<-rep(c("one","two","three","four","five"),rep(2,5)) named.x

one one two two three three four four five five 1 2 3 4 5 6 7 8 9 10

named.x[c("one","two","three")]

one two three 1 3 5

NA is returned if a name do not match any element

named.x["twenty"]

NA

NA is returned if a subscript is character NA

named.x[c("one",NA,"three")]

one three 1 NA 5

to find all occurences one can use %in% and then subset with the logical vector (you can do this in one step)

named.x[names(named.x) %in% c("one","two")]

one one two two 1 2 3 4

[sasrandme]

R - subscripting

subscripting with positive and negative indices

character subscripting (vectors and lists)

logical subscripting

subsetting

creating a list for examples

myl <- list(one=10,two=20,three=30) myi <- "one"

one

subsetting is carried out with three different operators:

dollar: $

square bracket: [

double square bracket: [[

these are generic functions

there are four basic types of subscript indices

positive integers

negative integers

logical vectors

character vectors

the first (left-most) index moves the fastest, the right-most index is the slowest (so a matrix is filled column by column)

the square bracket

the returned value is of the same type of the value it is applied to

myl[c(1,2)]

10 20

evaluate its second argument

myl[myi]

10

does not use partial matching when extracting named elements

myl["on"]

cannot be used for subscripting environments

the double square bracket

extract a single value

myl[[1]]

10

evaluate its second argument

myl[[myi]]

10

does not use partial matching when extracting named elements

myl[["on"]]

the dollar

extract a single value

myl$two

20

does not evaluate its second argument

myl$myi

uses partial matching extracting named elements

myl$on

10

cannot be used for subscripting atomic vectors

subsetting with positive indices

vector of positive integer values to indicate the set to be extracted

myv <- 1:10 myi <- c(2,4,7) myv[myi] myv[c(2,4,7)]

[1] 2 4 7 [1] 2 4 7

if the subscript is larger than the length of the vector, NAs are produce

myv[c(1,11,3)]

[1] 1 NA 3

NA as subscript produces also a NA

myv[c(1,11,NA)]

[1] 1 NA NA

zero as subscript will be ignored

myv[c(1,2,0,3)]

[1] 1 2 3

if the subscript vector has the length zero, the result is also of length zero

myi <- numeric() myv[myi]

integer(0)

example: select elements which have even numbered subscripts

v <- rnorm(20) myi <- seq(2,length(v),by=2) myi v[myi]

[1] 2 4 6 8 10 12 14 16 18 20 [1] 0.35380115 -0.02156840 -1.51804278 0.38278037 0.03867578 -1.25803279 [7] 0.62863255 0.07111270 -0.73416837 0.18966622

subsetting with negative indices

subscript vector consists of negative integer values indicating the indices not to be extracted

zero as subscript will be ignored

myv[-c(1,2,0,3)]

[1] 4 5 6 7 8 9 10

NAs are not allowed

myv[-c(1,NA,3)]

Error in myv[-c(1, NA, 3)] : nur Nullen dürfen mit negativen Indizes gemischt werden

zero length subscript produces zero length result

myv <- 1:10 myi <- numeric() myv[-myi]

integer(0)

positive and negatives subscripts cannot be mixed

to be continued... (most parts taken from Gentleman, R Programming for Bioinformatics) …