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R programming notes

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Remember that if you have questions about a particular R function, you can access its

documentation with a question mark followed by the function name:

?function_name_here.

However, in the case of an operator like the colon used above,you must enclose the

symbol in backticks like this: ?`:`.

(NOTE: The backtick (`)

key is generally located in the top left corner of a keyboard, above the Tab key.If you

don't have a backtick key, you can use regular quotes.)

Length() operator gives the length of the list.

of length of my_Seq

If we're interested in creating a vector that contains 40 zeros, we can use rep(0,

times = 40).

Two join two vector c(y) and c(z) -> c(y,z)

There are multiple classes that are grouped together as "numeric" classes, the 2 most

common of which are double (for double precision floating point numbers) and integer. R

will automatically convert between the numeric classes when needed, so for the most

part it does not matter to the casual user whether the number 3 is currently stored as an

integer or as a double. Most math is done using double precision, so that is often the

default storage.

Sometimes you may want to specifically store a vector as integers if you know that they

will never be converted to doubles (used as ID values or indexing) since integers require

less storage space. But if they are going to be used in any math that will convert them to

double, then it will probably be quickest to just store them as doubles to begin with.

Vectors:

Atomic Vectors :

Contains exactly one data type.

Logical Operators : The `<` and `>=` symbols in these examples are

called 'logical operators'. Otherlogical operators include `>`, `<=`, `==` for

exact equality, and `!=` for inequality

quotes are used to distinguish character objects.

my_char<-c("My","name","is")

1. Paste() join two strings together

2. The `collapse` argument to the paste() function tells R that when we join together

the elements of the my_char character vector, we'd like to separate them with

single spaces

3. To add or contcaneate use the c() function

a <- "apple"

b <- "banana"

# Put a and b together, with a space in between:

paste(a, b)

#> [1] "apple banana"

# With no space, use sep="", or use paste0():

paste(a, b, sep="")

#> [1] "applebanana"

paste0(a, b)

#> [1] "applebanana"

# With a comma and space:

paste(a, b, sep=", ")

#> [1] "apple, banana"

# With a vector

d <- c("fig", "grapefruit", "honeydew")

# If the input is a vector, use collapse to put the elements together:

paste(d, collapse=", ")

#> [1] "fig, grapefruit, honeydew"

# If the input is a scalar and a vector, it puts the scalar with each

# element of the vector, and returns a vector:

paste(a, d)

#> [1] "apple fig"

"apple grapefruit" "apple honeydew"

# Use sep and collapse:

paste(a, d, sep="-", collapse=", ")

#> [1] "apple-fig, apple-grapefruit, apple-honeydew"

[collapse for vectors , sep for scalars)

Lists:

Contains multiple data types.

Dimensions are extra attributes applied to a vector to turn it into a matrix or a higher

dimensional array: so a dim(int_list) is NULL

Length()

> mylist <- list (1:10)

> length (mylist)

[1] 1

In such a case you are not looking for the length of the list, but of its first element :

> length (mylist[[1]])

[1] 10

> mylist <- list(1:10, rnorm(25), letters[1:3])

> length (mylist)

[1] 3

> df <- data.frame (matrix(0, ncol = 30, nrow = 2))

> typeof (df)

[1] "list"

In such a case you may be interested in ncol() and nrow() rather than length() :

> ncol (df)

[1] 30

> nrow (df)

[1] 2

Though length() will also work (but it's a trick when your data.frame has only one

column) :

> length (df)

[1] 30

> length (df[[1]])

[1] 2

NA

Is.variablename checks the variable[is.na checks if NA is there]

NA is a placeholder for something that does not exist ,it is not a value.

NAN:

When 1/0 or inf-inf etc

elements form vectors

The way you tell R that you want to select some particular elements (i.e.

a'subset') from a vector is by placing an 'index vector' in

square bracketsimmediately following the name of the vector , x[1:10], picks the

first 10 elements

Index vectors come in four different flavors -- logical vectors, vectors of positive

integers, vectors of negative integers,

Logical vectors-subsetting

Combing multiple conditions in subsetting : x[!is.na(x)&x>0]

Many programming languages use what's called 'zero-based indexing', which

means that the first element of a vector is considered element 0. R uses 'onebasedindexing', which (you guessed it!) means the first element of a vector is 1.

R accepts negative integer indexes. Whereas x[c(2, 10)] gives us ONLY the 2nd

and 10th elements of x, x[c(-2, -10)] gives us all elements of x EXCEPT for the 2nd

and 10 elements. Try x[c(-2, -10)] now to see this

For named Vectors : subsetting slightly different

vect

foo bar norf

11 2 NA

Vect[bar] gives the elemen: bar 2

Vect[2] gives the 2nd element: bar 2

Matrices contain only one type of data

Matrices are vectors with dimension attribute

To represent tabular data with rows and columns

Dim(vector)= Null unlike Matrixes

To assign dim attribute of a vector , dim(vec)<-c(3,4) : creates a matrix of

3x4

Classes in R

Class(of numeric vector ) gives numeric

DATA frames

Data frames are represented as a special type of list where every element of

the list has to have the same length. Each element of the list can be thought of

as a column and the length of each element of the list is the number of rows.

Unlike matrices, data frames can store different classes of objects in each

column. Matrices must have every element be the same class (e.g. all integers or

Each represent a

all numeric).

colum

Len of foo= no of rows of foo

Belongs to class data.frame

To assign colnames

> colnames(my_data)<-cnames

Logic in R

There are two logical values in R, also called Roolean values. They are TRUE and FALSE.

In R you can construct logical expressions which will evaluate to either TRUE or FALSE.

In order to negate Roolean expressions you can use the NOT operator. An

exclamation point `!` will cause !TRUE (say: not true) to evaluate to FALSE and !

FALSE (say: not false) to evaluate to TRUE.

You can use the `&` operator to evaluate AND across a vector. The `&&` version

of AND only evaluates the first member of a vector. Lets test both for practice.

Type the expression TRUE & c(TRUE, FALSE, FALSE).

The OR operator follows a similar set of rules. The `|` version of OR evaluates OR

across an entire vector, while the `||` version of OR only evaluates the first

member of a vector

Precednece of Operators

AND operators are evaluated before OR operators

Is.true() : If that argument evaluates to TRUE, the

function will return TRUE. Otherwise, the function will return FALSE.

1

The function identical() will return TRUE if the two R objects passed to it as

arguments are identical

Xor function: the xor() function, which takes two arguments. The xor() function

stands for exclusive OR. If one argument evaluates to TRUE and one argument

evaluates to FALSE, then this function will return TRUE, otherwise it will return

FALSE.(if both arguments true -> False)

true or true = true

true xor true = false

the indices of the vector that are TRUE. For example which(c(TRUE, FALSE, TRUE))

would return the

vector c(1, 3).

the functions any() and all() take logical vectors as their argument. The any()

function will return TRUE if one or more of the elements

in the logical vector is TRUE. The all() function will return TRUE if every element in the

logical vector is TRUE

Functions

Functions are one of the fundamental building blocks of the R language. They are

small pieces of reusable code that can be treated like any other R object. Function

name followed by parantheses.

console to run)

function_name <- function(arg1, arg2){

Manipulate arguments in some way

Return a value

}

parantheses)

If arguments specified explicitly , can be used whichever order

func_name(x,y) same as func name(y=,x=)

Args(func_name) returns arguments of the function.

evaluate <- function(func, dat){

func(dat)

}

Method of the

function

Passing functions into functions , without the argument function being defined.

Anonymised fucntions :

> evaluate(function(x){x+1},6)

[1] 7

element

lapply(unique_vals, function(elem) elem[2])

mad_libs <- function(...){

# Do your argument unpack

args<-list(...)

place<-args[[place]]

adjective<-args[[adjective]]

paste(News from, place, today where, adjective, students took to the

streets in protest of the new, noun, being installed on campus.)

}

want:

%p% <- function(a,b){ # Remember to add arguments!

Paste(a,b)

Loops

For loop

Create a place

holder for the

results

These powerful functions, along with their close relatives (vapply() and tapply(), among

others) offer a concise and convenient means of implementing the Split-Apply-Combine

strategy for data analysis.

Each of the *apply functions will SPLIT up some data into smaller pieces, APPLY afunction

to each piece, then COMBINE the results. A more detailed discussion of this strategy is

found in Hadley Wickhams Journal of Statistical Software paper titled The Split-ApplyCombine Strategy for Data Analysis.

Lapply()

The lapply() function takes a list as input, applies a function to each element ofthe list,

then returns a list of the same length as the original one.

Data frame is a list of vectors.

Since a data frame is really just a list of vectors (you can see this with as.list(flags)), we

can use lapply() to apply the class() function to each column of the flags dataset.

Sapply():

sapply() allows you to automate this process by calling lapply() behind the scenes,but

then attempting to simplify (hence the s in sapply) the result for you. Use sapply()

opposed to lapply.

It simplifies , classes to matrix, vectors etc .

When Sapply cannot simplify works the same way as lapply (i.e when lengths of the

elements are not equal , if len=1 returns 1 , if len>1 matrix.

use flag_colors <- flags[, 11:17] to extract the columns containing the color data and

store them in a new data frame called flag_colors. (Note the commabefore 11:17. This

subsetting command tells R that we want all rows, but only

| columns 11 through 17

vapply() allows you to specify it explicitly. If the result doesnt match the format

you specify,vapply() will throw an error, causing the operation to stop. This can

prevent significant problems in your code that might be caused by getting

unexpected return values from sapply().

expect the class function to return a character vector of length 1 when applied to

EACH column of the flags dataset.

Tapply

As a data analyst, youll often wish to split your data up into groups based on thevalue of

some variable, then apply a function to the members of each group. Thenext function

well look at, tapply(), does exactly that.

interpreted as a categorical variable (called a factor in R). and counts the

instances of the variable in the dataset

Factors

Factors are used to represent categorical data and can be unordered or ordered.

One can think of a factor as an integer vector where each integer has a label.

Use tapply(flags$animate, flags$landmass, mean) to apply the mean function to the

'animate' variable separately for each of the six landmass groups, thus giving

| us the proportion of flags containing an animate image WITHIN each landmass group.

> tapply(flags$animate, flags$landmass, mean)

1

2

3

4

5

6

0.4193548 0.1764706 0.1142857 0.1346154 0.1538462 0.3000000

Numerical

variable or

vetor

Categorical

variablle or

factor

Type ls() to list the variables in your workspace or ls(dataname) to get data

specific variables.

You can see nrow()_-> for number of columns and ncolumns()-> for

number of columns

Names() -> attribute of objects(vectors,lists , matrices etc) , which gives

the variables of the data as a character vector.

Summary(data_name) to get summary ..

Depending on the class , R creates a summary

statistics. :summary() provides different output for each

variable, depending on its class. For numeric data such as

Precip_Min, summary() displays the minimum, 1st quartile,

median, mean, 3rd quartile, and maximum. These values

help us understand how the data are distributed

summary() displays the number of times each value (or 'level')

occurs in the data. For example, each value of Scientific_Name

only appears once, since it is unique to a specific plant. In

contrast, the summary for Duration (also a factorvariable) tells

us that our dataset contains 3031 Perennial plants, 682 Annual

plants, etc.

Str(),

The beauty of str() is that it combines many of the features of the other functions you've

already seen, all in a concise and readable format. At the very top, it tells us that the

class of plants is 'data.frame' and that it has 5166 observations and 10 variables. It then

gives us the name and

objects in R.

applied to most

Simulation in R

simulate rolling four six-sided dice: sample(1:6, 4, replace = TRUE).

> sample(1:6, 4, replace = TRUE)

A vector ,

from which

to choose

to choose

means that each number is

"replaced" after it is selected, so

that the same number can show up

more than once.

Binomial random variable represent the no of successes (heads) in a given

number of independent trials (COIN FLIPS).

Therefore, we can generate a single random variable thatrepresents the number of heads

in 100 flips of our unfair coin using rbinom(1, size = 100, prob = 0.7).

Normal Distribution

Dates are represented by the 'Date' class and times are represented by the 'POSIXct'

(large integer) and 'POSIXlt'(list) classes. Internally, dates are stored as the number of

days since 1970-01-01 and times are stored as either the number of seconds since 197001-01 (for 'POSIXct') or a list of seconds, minutes,hours, etc.

it is similar to as.POSIXlt(), except that the input doesn't have to

be in a particular format (YYYY-MM-DD)

R Data Frames :

Besides storing a single number in a variable, you can also store text, vectors, matrices,

and

| even whole data sets, which R users call DATA FRAMES.

Continious Variables :

A CONTINUOUS VARIABLE is one that can assume any value within the scope of the

problem. For the

'cars' data set:

price, city MPG, and weight are all continuous variables, as there is no

inherent restriction on the possible values of each of the three variables (except for

negative numbers, of course!

Discrete Variables :

A DISCRETE VARIABLE is a variable that may take on one of a limited, and

usually fixed, number of possible values. A CATEGORICAL VARIABLE is similar to a

discrete variable, however, instead of assuming a fixed value, the variable is ascribed a

fixed categorical description.

In our 'cars' data set, the number of passengers is a discrete variable, while the type and

drive train are examples of categorical variables.

Notice that the number of passengers is a discrete variable since the capacity of each car

may only be described in whole numbers.

Descriptive statistics:

Before a statistician engages in a thorough analysis of the data set, it

is useful to first visualize the data.

By organizing the data into a PLOT or GRAPH, a statistician is able to

explore and summarize some basic properties of the data set. The discipline of

quantitatively describing the main properties of a data set is known as DESCRIPTIVE

STATISTICS.

Central Tendency :

One of the most common descriptive statistics is a MEASURE OF CENTRAL

TENDENCY. For a specific data set, CENTRAL TENDENCY seeks to locate a central value or

a typical value for a certain variable.

It may also be referred to as the AVERAGE or the CENTER of the data.

The most common measures of central tendency are the MEAN, MEDIAN, and MODE of a

set of data.

AVERAGE, is the most common measurement of the center of the data. To

calculate the mean, you must first sum all of the values of interest, and

| then divide that sum by the total number of values used in the sum.

x 1 + x 2+ .. x n

n

R command : mean(cars$price)

Median (middle number): When the total number of values is odd, finding the

median, or 'middle' value, is quite easy. However, if the total number of values is

even, there is no middle value amongst the

Actual data. In this case, you must calculate the average of the two middle values

amongst the data points. In other words, in the case of an even number of values, the

MEDIAN is reported as the MEAN of the two middle values of the data set.

>> R command :

summary(cars$mpgCity)

Min. 1st Qu. Median Mean 3rd Qu. Max.

16.00 19.00 21.00 23.31 28.00 46.00

Types of Plots:

Dot Plots(good for smaller data sets):

The simplest type of plot is the DOT PLOT, which is used to visually convey the values of

one variable. In a dot plot, there is only a horizontal x-axis, and the data points are

represented as dots above this axis.

Since dot plots effectively display the specific numerical value of one

variable for each individual in the data set, it is a particularly useful tool for smaller data

sets.

Range :

This discussion of the dot plot brings me to our first descriptive statistic, the RANGE of

adata set. Just as the name would seem to imply, the range is the difference between the

maximum and minimum values of the data set. Range = Max-Min

R command : range(cars$price)

Data Analysis

The purpose of analyzing a sample is to draw conclusions about the population from

which the sample was selected. This is called INFERENCE and is the primary goal of

INFERENTIAL STATISTICS

In order to make any inferences about the population, we first need to describe the

sample. This is the primary goal of DESCRIPTIVE STATISTICS.

Central Tendency

Arithmetic Mean

The ARITHMETIC MEAN, or simply the MEAN or AVERAGE, is the most common

measurement of central tendency. To calculate the mean of a dataset, you first sum all of

the values and then divide that sum by the total number of values in the dataset

Arithmetic median

An alternative to the mean, which is not influenced at all by extreme values, is the

MEDIAN. The median is computed by sorting all values from least to greatest and then

selecting the middlevalue. If there is an even number of values, then there are actually 2

middle values. In this case, the MEDIAN is equal to the MEAN of the 2 middle values

MODE

Finally, we may be most interested in finding the value that shows up the most in our

dataset.In other words, what is the most common value in our dataset? This is called the

MODE and it is found by counting the number of times that each value appears in the

dataset and selecting the

| most frequent value.

-Use table function

Dispersion

While measures of central tendency are used to estimate the middle values of a dataset,

measuresof dispersion are important for describing thespread of the data.

The term dispersion refers to degree to which the data values are scattered around an

average value. Dispersion is synonymous with other words such as variability and

spread.

Range

The first descriptive statistic that can describe the variability of a data set is known as

the

RANGE. The range is the difference between the maximum and minimum values of the

data set

Range=max_value-min_value

Variance

The second important measure of variability is known as VARIANCE. Mathematically,

VARIANCE is

The average of the squared differences from the mean. More simply, variance represents

the total distance of the data from the mean

Standard deviation

SD= var

The standard deviation is very important when analyzing our data set. A small standard

deviation indicates that the data points tend to be located near the mean value, while a

large standard deviation indicates that the data points are spread further from the mean.

A BOX PLOT, also called a BOX-AND-WHISKER PLOT, is used to summarize the main

descriptive statistics of a particular data set and this type of plot helps illustrate the

concept of variability.

A box plot is used to visually represent the MINIMUM, FIRST QUARTILE (Q1),

MEDIAN,THIRD QUARTILE (Q3), and MAXIMUM of a data set.

The height of each box is referred to as the INTERQUARTILE RANGE (IQR). The more

variability within the data, the larger the IQR. On the other hand, less variability within

the data means a smaller IQR. The bottom of the box in the box plot corresponds to the

value of the first quartile (Q1), and the top of the box corresponds to the value of the

third quartile (Q3).

Whiskers are approx. 25% above and below the data

and discrete data)

Dot Plots

Histogram

Here I have created a histogram using the miles per gallon data for all of our cars. As you

may notice, the values of the MPG along the x-axis are partitioned into bins with a range

of 5.

The second bin, for example, groups together all of the cars that get 21-25 MPG in the

city, and so forth.

Note that the bin to the left of this contains those cars with 20 MPG since this value

cannot be counted in both bins. The frequency of values in each bin,or the number of

cars in each of the intervals, is reported along the y-axis.

Significance of Histograms

Data Density

Taller bars signify the range of values in which the majority of the data is located,

whereas shorter bars represent a range of values in which only a little bit of the data is

located. In other words, histograms provide a view of the DATA DENSITY.

Skewness

Histograms are particularly useful in viewing and describing the shape of the distribution

of the data. A distribution of data may have a left skew, a right skew, or no skew at all.

SKEWNESS is a measure of the extent to which the distribution of the data 'leans' to one

side or the other.

A distribution that has a left skew is one in which the left TAIL of the plot is longer. In

other words, on a histogram the majority of the distribution is located to the right of the

mean.

A special type of histogram is known as a STEM-AND-LEAF PLOT. This plot organizes

numerical data in order of decimal place value. The left-hand column of the plot contains

the STEMS, or the numerical values of the tens digit for each of the data points,

organized vertically in increasing order.

The LEAVES are located in the right-hand column of the plot and are the values of the

ones digit for each data point of the corresponding stem,

organized horizontally in

increasing order

Statistical Interference

Introduction

Regression Models

Introduction

plot(jitter(child,4)~parent,galton)

by using R's function "jitter" on the children's heights, we can spread out the data

to simulate the measurement errors and make high

frequency heights more visible.

Needs to be added and loaded each time working with data.. library(dpylr)

package..

The first step of working with data in dplyr is to load the data into what the

package authors call a 'data frame tbl' or 'tbl_df'.Use the following code to create

a new tbl_df called cran: cran <- tbl_df(mydf).

The dplyr philosophy is to have small functions that each do one thing well."

Specifically, dplyr supplies five 'verbs' that cover most fundamental data

manipulation tasks: select(),filter(), arrange(), mutate(), and summarize().

Vectorization in R:

R is a high-level, interpreted computer language. This means that R takes care

of a lot of basic computer tasks for you. For instance, when you type

i <- 5.0

questions s itself.Compare

this to a compiled language :

like C

Comparision with C

int i

i = 5

This tells the computer the i will store data of the type int (integers), and

assign the value 5 to it. If I try to assign 5.5 to it, something will go wrong.

But C doesnt have to figure out what type of data is is represented by i and

this is part of what makes it faster

Internal functions like fft created with C wrap , hence faster processing time.

However , R still has to work out argument inputs costing time

If you need to run a function over all the values in a vector, you could pass a

whole vector through the R function to the compiled code, or you could call

the R function repeatedly for each value. If you do the latter, R has to do the

figuring out stuff, as well as the translation, each time. But if you call it once,

with a vector, the figuring out part happens just once.

With just a few function calls that are actually calling compiled code, itll

be more efficient than if you write long program, with the added

overhead of many function calls.

BLAS is generally designed to be highly efficient and has things like

built-in parallel processing, hardware-specific implementation, and a

host of other tricks. So if your calculations can be expressed in actual

linear algebra terms, such as matrix multiplication

Apply functions:

Another thing that ply functions help with is avoiding what are known

as side effects. When you run aply function, everything happens inside that

function, and nothing changes in your working environment (this is known as

functional programming). In a for loop, on the other hand, when you do

something like for(i in 1:10), you get the leftover i in your environment.

This is considered bad practice sometimes.

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