Statistical Models

Lecture 4

Dr. Silvio Fanzon
S.Fanzon@hull.ac.uk

University of Hull

Dr. John Fry
J.M.Fry@hull.ac.uk

University of Hull

Lecture 4:
Hypothesis tests in R
Part 1

Outline of Lecture 4

  1. t-test
  2. The basics of R
  3. Vectors
  4. t-test in R
  5. Graphics

Part 1:
t-test

One-sample Two-sided t-test

Goal: estimate the mean \mu of a normal population N(\mu,\sigma^2). If \mu_0 is guess for \mu H_0 \colon \mu = \mu_0 \qquad H_1 \colon \mu \neq \mu_0

  • One-sample means we sample only from one population
  • The variance \sigma is unknown
  • Suppose the sample size is n, with sample X_1 ,\ldots,X_n
  • We consider the t-statistics T = \frac{\overline{X}-\mu_0}{S/\sqrt{n}}
  • Recall: T \sim t_{n-1} Student’s t-distribution with n-1 degrees of freedom

One-sample Two-sided t-test

Procedure for all tests

  1. Calculation
  2. Reference statistical tables or numerical values
  3. Interpretation

One-sample Two-sided t-test

Calculation

  • We have n samples available x_1,\ldots,x_n
  • Compute sample mean \overline{x} = \frac{1}{n} \sum_{i=1}^n x_i
  • Compute the sample standard deviation s = \sqrt{\frac{\sum_{i=1}^n x_i^2 - n \overline{x}^2}{n-1}}

One-sample Two-sided t-test

Calculation

  • Compute the estimated standard error \mathop{\mathrm{e.s.e.}}= \frac{s}{\sqrt{n}}

  • Compute the t-statistic t = \frac{\text{estimate } - \text{ hypothesised value}}{\mathop{\mathrm{e.s.e.}}} = \frac{\overline x - \mu_0}{s/\sqrt{n}}

  • \mu_0 is the value of the null hypothesis H_0

One-sample Two-sided t-test

p-value

  • After computing t-statistic we need to compute p-value

  • p-value is a measure of how strange the data is in relation to the null hypothesis

  • We have 2 options:

    • LOW p-value \quad \implies \quad reject H_0
    • HIGH p-value \quad \implies \quad do not reject H_0

  • In this course we reject H_0 for p-values p<0.05

One-sample Two-sided t-test

p-value

  • For two-sided t-test the p-value is defined as p := 2P(t_{n-1}> |t|) where t_{n-1} is the t-distribution with n-1 degrees of freedom

  • Therefore the p-value is p = 2P(\text{Observing t }| \, \mu=\mu_0)

One-sample Two-sided t-test

p-value

  • p<0.05 means that the test statistic t is extreme: \,\, P(t_{n-1}> |t|)<0.025

  • t falls in the grey areas in the t_{n-1} plot below: Each grey area measures 0.025

One-sample Two-sided t-test

p-value

  • How to compute p?
    • Use statistical tables – Available here
    • Use R – Next sections

One-sample Two-sided t-test

Reference statistical tables

Find Table 13.1 in this file

  • Look at the row with Degree of Freedom n-1 (or its closest value)
  • Find critical value t^* := t_{n-1}(0.025) in column 0.025
  • Example: n=10, DF =9, t^*=t_{9}(0.025)=2.262

One-sample Two-sided t-test

Reference statistical tables

  • The critical value t^* = t_{n-1}(0.025) found in the table satisfies P(t_{n-1}>t^*) = 0.025

  • By definition of p-value for two-sided t-test we have p := 2P(t_{n-1}>|t|)

  • Therefore, for |t|>t^* \begin{align*} p & := 2P(t_{n-1}>|t|) \\ & < 2P(t_{n-1}>t^*) = 2 \cdot (0.025) = 0.05 \end{align*}

  • Conclusion: \qquad |t|>t^* \quad \iff \quad p<0.05

One-sample Two-sided t-test

Interpretation

Recall that p = 2P ( \text{Observing t } | \mu = \mu_0). We have two possibilities:

  • |t|>t^*
    • In this case p<0.05
    • The observed statistic t is very unlikely under H_0
    • We reject H_0
  • |t| \leq t^*
    • In this case p>0.05
    • The observed statistic t is not unlikely under H_0
    • We do not reject H_0

Example: 2008 crisis

  • Data: Monthly Consumer Confidence Index (CCI) in 2007 and 2009
  • Question: Did the crash of 2008 have lasting impact upon CCI?
  • Observation: Data shows a massive drop in CCI between 2009 and 2007
  • Method: Use t-test to see if data is sufficient to prove that CCI actually dropped
Month J F M A M J J A S O N D
CCI 2007 86 86 88 90 99 97 97 96 99 97 90 90
CCI 2009 24 22 21 21 19 18 17 18 21 23 22 21
Difference 62 64 67 69 80 79 80 78 78 74 68 69

Example: 2008 crisis

  • This is really a two-sample problem – CCI data in 2 populations: 2007 and 2009
  • It reduces to a one-sample problem because we have directly comparable units
  • If units cannot be compared, then we must use a two-sample approach
  • Two-sample approach will be discussed later
Month J F M A M J J A S O N D
CCI 2007 86 86 88 90 99 97 97 96 99 97 90 90
CCI 2009 24 22 21 21 19 18 17 18 21 23 22 21
Difference 62 64 67 69 80 79 80 78 78 74 68 69

Example: 2008 crisis

Setting up the test

  • We want to test if there was a change in CCI from 2007 to 2009
  • We are really only interested in the difference in CCI
  • Let \mu be the (unknown) average difference in CCI
  • The null hypothesis is that there was (on average) no change in CCI H_0 \colon \mu = 0
  • The alternative hypothesis is that there was some change: H_1 \colon \mu \neq 0
  • Note that this is a two-sided test

Example: 2008 crisis

Calculation

Using the available data, we need to compute:

  • Sample mean and standard deviation \overline{x} = \frac{1}{n} \sum_{i=1}^n x_i \qquad s = \sqrt{\frac{\sum_{i=1}^n x_i^2 - n \overline{x}^2}{n-1}}

  • Test statistic t = \frac{\overline x - \mu_0}{s/\sqrt{n}}

Example: 2008 crisis

Calculation


CCI J F M A M J J A S O N D
Difference 62 64 67 69 80 79 80 78 78 74 68 69

\begin{align*} \overline{x} & =\frac{1}{n} \sum_{i=1}^{n} x_i=\frac{1}{12} \left(62+64+67+{\ldots}+68+69\right)=\frac{868}{12}=72.33 \\ \sum_{i=1}^{n} x_i^2 & = 62^2+64^2+67^2+{\ldots}+68^2+69^2 = 63260 \\ s & = \sqrt{ \frac{\sum_{i=1}^n x_i^2 - n \overline{x}^2}{n-1} } = \sqrt{\frac{63260-12\left(\frac{868}{12}\right)^2}{11}} = \sqrt{\frac{474.666}{11}} = 6.5689 \end{align*}

Example: 2008 crisis

Calculation

  • The sample size is n=12
  • The sample mean is \overline{x}=72.33
  • The sample standard deviation is s = 6.5689
  • The hypothesized mean is \mu_0 = 0
  • The t-statistic is t = \frac{\overline{x} - \mu_0}{s/\sqrt{n}} = \frac{72.33 - 0}{6.5689/\sqrt{12}} = 38.145

Example: 2008 crisis

Reference statistical tables

Find Table 13.1 in this file

  • Find row with DF = n-1 (or closest). Find critical value t^* in column 0.025
  • In our case: n=12, DF =11, t^*= t_{11}(0.025) =2.201

Example: 2008 crisis

Reference statistical tables

  • Plot of t_{11} distribution. White area is 0.95, total shaded area is 0.05
  • Probability of observing |t|>t^* = 2.201 is p with p<0.025

Example: 2008 crisis

Interpretation

  • We have computed:

    • Test statistic t = 38.145
    • Critical value t^* = 2.201

  • Therefore |t| = 38.145 > 2.201 = t^*

  • This implies rejecting the null hypothesis H_0 \colon \mu = 0

Example: 2008 crisis

Interpretation

  • t-test implies that mean difference in CCI is \mu \neq 0

  • The sample mean difference is positive (\bar{x}=72.33)

  • Conclusions:

    • CCI has changed from 2007 to 2009 (backed by t-test)
    • CCI seems higher in 2007 than in 2009 (backed by sample mean)
    • The 2008 crash seems to have reduced consumer confidence

Part 2:
The basics of R

What is R?

  • R is a high-level programming language (like Python)
  • This means R deals automatically with some details of computer execution:
    • Memory allocation
    • Resources allocation
  • R is focused on manipulating and analyzing data

References

Slides are based on

  • [1] Dalgaard, P.
    Introductory statistics with R
    Second Edition, Springer, 2008

  • [2] Davies, T.M.
    The book of R
    No Starch Press, 2016

Concise Statistics with R


Comprehensive R manual

Installing R

  • R is freely available on Windows, Mac OS and Linux
  • To install:
    • Download R from CRAN https://cran.r-project.org
    • Make sure you choose the right version for your system
    • Follow the instructions to install

How to use R?

  • We have installed R. What now?

  • Launch the R Console. There are two ways:

    • Find the R application on your machine
    • Open a terminal, type R, exectute

R application

This is how the R Console looks on the Mac OS app

R from terminal

This is how the R Console looks on the Mac Terminal

What can R do?

  • R Console is waiting for commands
  • You can use the R Console interactively:
    • Type a command after the symbol >
    • Press Enter to execute
    • R will respond

Warning

  • The following slides might look like a lot of information
  • However you do not have to remember all the material
  • It is enough to:
    • Try to understand the examples
    • Know that certain commands exist and what they do
  • Combining commands to create complex codes comes with experience

Example

Few lines of code can lead to impressive results

Example: Plotting 1000 values randomly generated from normal distribution

plot(rnorm(1000))

R as a calculator

R can perform basic mathematical operations

Below you can see R code and the corresponding answer

2 + 2
[1] 4
2 * 3 - 1 + 2 ^ 7
[1] 133
exp(-10)
[1] 4.539993e-05
log(2)
[1] 0.6931472
pi
[1] 3.141593
sin(pi/2)
[1] 1

R Scripts

  • The interactive R Console is OK for short codes

  • For longer code use R scripts

    • Write your code in a text editor
    • Save your code to a plain text file with .txt or .R extension
    • Execute your code in the R Console with source("file_name.R")

  • Examples of text editors

RStudio

  • RStudio is an alternative to R Console and text editors: Download here
    • RStudio is an Integrated Development Environment (IDE)
    • It is the R version of Spyder for Python
  • RStudio includes:
    • Direct-submission code editor
    • Separate point-and-click panes for files, objects, and project management
    • Creation of markup documents incorporating R code

Working Directory

  • R session has a working directory associated with it

  • Unless specified, R will use a default working directory

  • To check the location of the working directory, use the getwd function

  • On my MacOS system I get \qquad

  • File paths are always enclosed in double quotation marks

  • Note that R uses forward slashes (not backslashes) for paths

  • You can change the default working directory using the function setwd

setwd("/folder1/folder2/folder3/")
  • File path can be relative to current working directory or full (system root drive)

Working Directory

RStudio

In RStudio you can set the working directory from the menu bar:

  • Session -> Set Working Directory -> Choose Directory

Comments

  • Good practice to document your code
  • This means adding comments directly in the code
  • Comments should be brief and explain what a chunk of code does
  • To insert a comment preface the line with a hash mark #
# This is a comment in R
# Comments are ignored by R

1 + 1   # This works out the result of one plus one!
[1] 2

R Packages

  • The base installation of R comes ready with:
    • Commands for numeric calculations
    • Common statistical analyses
    • Plotting and visualization
  • More specialized techniques and data sets are contained in packages (libraries)
# To install a package run
install.packages("package_name")

# To load a package into your code type
library("package_name")

# To update all the packages intalled type
update.packages()

Help!

  • R comes with help files that you can use to search for particular functionality
  • For example you can check out how to precisely use a given function
  • To call for help type help(object_name)
help(mean)     # Mean is R function to compute average of some values

Further Help

  • Sometimes the output of help() can be cryptic
  • Seek help through Google
    • Qualify the search with R or the name of an R package
    • Paste an error message – chances are it is common error
  • Even better: Internet search sites specialized for R searches

Plotting random numbers

Let us go back to the example of the command plot(rnorm(1000))

The function rnorm(n) outputs n randomly generated numbers from N(0,1)

rnorm(5)
[1]  1.0786565 -0.0823201 -1.4221775 -0.3084164 -0.5282035

These can then be plotted by concatenating the plot command

plot(rnorm(5))

Note:

  • The values plotted (next slide) are, for sure, different from the ones listed above

  • This is because every time you call rnorm(5) new values are generated

  • We need to store the generated values if we want to re-use them

Plotting random numbers

Variables and Assignments

  • Values can be stored in symbolic variables or objects
  • To store values into variables we use assignments
  • The assignment operator in R is denoted by <-
  • <- denotes an arrow pointing to the variable to which the value is assigned

Variables and Assignments

Example

  • To assign the value 2 to the variable x enter x <- 2
  • To recover the value in x just type x
x <- 2
x
[1] 2

Variables and Assignments

Example

  • From now on, x has the value 2
  • The variable x can be used in subsequent operations
  • Such operations do not alter the value of x
x <- 2
x + x
[1] 4
x
[1] 2

Example - Your first R code

  1. Open a text editor and copy paste the below code
# This codes sums two numbers and prints result on screen
x <- 1
y <- 2

result <- x + y

# Print the result on screen
cat("Code run successfully!")
cat("The sum of", x , "and", y, "is", result)

Example - Your first R code

  1. Save to a plain text file named either

    • my_first_code.R
    • my_first_code.txt

  2. Move this file to Desktop

  3. Open the R Console and change working directory to Desktop

# In MacOS type
setwd("~/Desktop")

# In Windows type
setwd("C:/Users/YourUsername/Desktop")

Example - Your first R code

  1. Run your code in the R Console by typying either
source("my_first_code.R")
source("my_first_code.txt")
  1. You should get the following output
Code run successfully!
The sum of 1 and 2 is 3

The workspace

  • Variables created in a session are stored in a Workspace
  • To display stored variables use
    • ls()
# Create 3 variables x, y, z
x <- 2
y <- "Dog"
z <- pi

# Workspace contains variables x, y, z
# This can be displayed by using ls()
ls()
[1] "x" "y" "z"

The workspace

You can remove variables from workspace by using

  • rm()
# Create 3 variables x, y, z
x <- 2
y <- "Dog"
z <- pi

# Remove x from workspace
rm(x)

# Now the workspace contains only y and z
ls( )
[1] "y" "z"

The workspace

To completely clear the workspace use

  • rm(list = ls())
# Create 3 variables x, y, z
x <- 2
y <- "Dog"
z <- pi

# Remove all variables from workspace
rm(list = ls())

# Let us check that the workspace is empty
ls( )
character(0)

Saving the Workspace

  • You can save the workspace using the command
    • save.image("file_name.RData")
  • The file file_name.RData
    • Is saved in the working directory
    • Contains all the objects currently in the workspace
  • You can load a saved workspace in a new R session with the command
    • load("file_name.RData")

Project Management

  • Recommended: keep all the files related to a project in a single folder

  • Such folder will have to be set as working directory in R Console

  • Saving the workspace could be dangerous

    • This is because R Console automatically loads existing saved workspaces
    • You might forget that this happens, and have undesired objects in workspace
    • This might lead to unintended results

  • Always store your code in R Scripts

Exiting R and Saving

To quit the R Console type q()

  • You will be asked if you want to save your session
  • If you say YES, the session will be saved in a .RData file in the working directory
  • Such file will be automatically loaded when you re-open the R Console
  • I recommend you DO NOT save your session

Exiting R and Saving

Summary

  • Write your code in R Scripts
  • These are .txt or .R text files
  • For later: Data should be stored in .txt files
  • DO NOT save your session when prompted

Part 3:
Vectors

Vectors

  • We saw how to store a single value in a variable
  • Series of values can be stored in vectors
  • Vectors can be constructed via the command c()
# Constuct a vector and store it in variable "vector"
vector <- c(60, 72, 57, 90, 95, 72)

# Print vector
print(vector)
[1] 60 72 57 90 95 72

Vectorized arithmetic

  • A vector is handled by R as a single object
  • You can do calculations with vectors, as long as they are of the same length
  • Important: Operations are exectuted component-wise
# Constuct two vectors of radius and height of 6 cylinders
radius <- c(6, 7, 5, 9, 9, 7)
height <- c(1.7, 1.8, 1.6, 2, 1, 1.9)

# Compute the volume of each cylinder and store it in "volume"
volume <- pi * radius^2 * height

# Print volume
print(volume)
[1] 192.2655 277.0885 125.6637 508.9380 254.4690 292.4823

Vectorized arithmetic

  • If 2 vectors do not have the same length then the shorter vector is cycled
  • This is called broadcasting
a <- c(1, 2, 3, 4, 5, 6, 7)
b <- c(0, 1)

a + b
[1] 1 3 3 5 5 7 7
  • In the example the vector a has 7 components while b has 2 components
  • The operation a + b is executed as follows:
    • b is copied 4 times to match the length of a
    • a + b is then obtained by a + \tilde{b} = (1, 2, 3, 4, 5, 6, 7) + (0, 1, 0, 1, 0, 1, 0) = (1, 3, 3, 5, 5, 7, 7)

Vectorized arithmetic

Useful applications of broadcasting are:

  • Multiplying a vector by a scalar
  • Adding a scalar to each component of a vector
vector <- c(1, 2, 3, 4, 5, 6)
scalar <- 2

# Multiplication of vector by a scalar
vector * scalar
[1]  2  4  6  8 10 12
# Summing a scalar to each component of a vector
vector + scalar
[1] 3 4 5 6 7 8

Sum and length

Two very useful vector operators are:

  • sum(x) which returns the sum of the components of x
  • length(x) which returns the length of x
x <- c(1, 2, 3, 4, 5)

sum <- sum(x)
length <- length(x)

cat("Here is the vector x:", x)
cat("The components of vector x sum to", sum)
cat("The length of vector x is", length)
Here is the vector x: ( 1 2 3 4 5 )
The components of vector x sum to 15
The length of vector x is 5

Computing sample mean and variance

Using vectorized operations

Given a vector \mathbf{x}= (x_1,\ldots,x_n) we want to compute sample mean and variance \overline{x} = \frac{1}{n} \sum_{i=1}^n x_i \,, \qquad s^2 = \frac{\sum_{i=1}^n (x_i - \overline{x})^2 }{n-1} 

# Computing sample mean of vector x
xbar = sum(x) / length(x)


# Computing sample variance of vector x
n = length(x)
s2 = sum( (x - barx)^2 ) / (n - 1)

Computing sample mean and variance

Using built in functions

  • R is a statistical language
  • There are built in functions to compute sample mean and variance:
    • mean(x) computes the sample mean of x
    • sd(x) computes the sample standard deviation of x
    • var(x) computes the sample variance of x

Computing sample mean and variance

Example

  • Let us go back to an Example we saw in Lecure 3
  • Below is the Wage data on 10 Advertising Professionals Accountants
Professional x_1 x_2 x_3 x_4 x_5 x_6 x_7 x_8 x_9 x_{10}
Wage 36 40 46 54 57 58 59 60 62 63
  • In Lecture 3 we have computed \overline{x} and s^2 by hand
  • Let us compute them using R

Computing sample mean and variance

Example

# First store the wage data into a vector
x <- c(36, 40, 46, 54, 57, 58, 59, 60, 62, 63)

# Compute the sample mean using formula
xbar = sum(x) / length(x)

# Compute the sample mean using built in R function
xbar_check = mean(x)

# We now print both results to screen
cat("Sample mean computed with formula is", xbar)
cat("Sample mean computed by R is", xbar_check)
cat("They coincide!")
Sample mean computed with formula is 53.5
Sample mean computed by R is 53.5
They coincide!

Computing sample mean and variance

Example

# Compute the sample variance using formula
xbar = mean(x)
n = length(x)
s2 = sum( (x - xbar)^2 ) / (n - 1) 

# Compute the sample variance using built in R function
s2_check = var(x)

# We now print both results to screen
cat("Sample variance computed with formula is", s2)
cat("Sample variance computed by R is", s2_check)
cat("They coincide!")
Sample variance computed with formula is 90.27778
Sample variance computed by R is 90.27778
They coincide!

Part 4:
t-test in R

t-test in R

  • We are now ready to do some statistics in R
  • We start by looking at the t-test
  • Specifically, to the One-sample Two-sided t-test

Goal of t-test: Estimate mean \mu of normal population N(\mu,\sigma^2). If \mu_0 is guess for \mu H_0 \colon \mu = \mu_0 \qquad H_1 \colon \mu \neq \mu_0

Method: Given sample X_1 ,\ldots,X_n we look at the statistics T = \frac{\overline{X}-\mu_0}{S/\sqrt{n}} \sim t_{n-1}

t-test by hand

  1. Given the data x_1,\ldots,x_n, compute the t-statistic t = \frac{\text{estimate } - \text{ hypothesised value}}{\mathop{\mathrm{e.s.e.}}} = \frac{\overline x - \mu_0}{s/\sqrt{n}} with sample mean and sample standard deviation \overline{x} = \frac{1}{n} \sum_{i=1}^n x_i \,, \qquad s = \sqrt{\frac{\sum_{i=1}^n x_i^2 - n \overline{x}^2}{n-1}}

  2. Find the critical value t^* = t_{n-1}(0.025) in Statistical Table 13.1

  • If |t|>t^* reject H_0. The mean is not \mu_0
  • If |t| \leq t^* do not reject H_0. There is not enough evidence

t-test

  1. Given the sample x_1,\ldots,x_n, R can compute the t-statistic t = \frac{\text{estimate } - \text{ hypothesised value}}{\mathop{\mathrm{e.s.e.}}} = \frac{\overline x - \mu_0}{s/\sqrt{n}}

  2. R can compute the precise p-value (no need for Statistical Tables) p = 2P(|t_{n-1}|>t)

  • If p < 0.05 reject H_0. The mean is not \mu_0
  • If p \geq 0.05 do not reject H_0. There is not enough evidence

Note: The above operations can be done at the same time by command t.test

t-test code in R

  1. Store the sample x_1,\ldots,x_n in an R vector using
    • data_vector <- c(x1, ..., xn)
  2. Perform a two-sided t-test on data_vector with null hypothesis mu0 using
    • t.test(data_vector, mu = mu0)
  3. Read output. R will tell you
    • t-statistic
    • degrees of freedom
    • p-value
    • alternative hypothesis
    • confidence interval (where true mean is likely to be)
    • sample mean

t-test command

Relevant options of t.test are

  1. mu = mu0 tells R to test null hypothesis H_0 \colon \mu = \mu_0

  2. If mu = mu0 is not specified, R assumes \mu_0 = 0

  3. alternative = "greater" tells R to perform one-sided t-test H_0 \colon \mu > \mu_0

t-test command

  1. alternative = "smaller" tells R to perform one-sided t-test H_0 \colon \mu < \mu_0

  2. conf.level = n changes the confidence interval level to n (default is 0.95)

Example: 2008 crisis

Let us go back to the 2008 Crisis example

  • Data: Monthly Consumer Confidence Index (CCI) in 2007 and 2009
  • Question: Did the crash of 2008 have lasting impact upon CCI?
  • Observation: Data shows a massive drop in CCI between 2009 and 2007
  • Method: Use t-test to see if data is sufficient to prove that CCI actually dropped
Month J F M A M J J A S O N D
CCI 2007 86 86 88 90 99 97 97 96 99 97 90 90
CCI 2009 24 22 21 21 19 18 17 18 21 23 22 21
Difference 62 64 67 69 80 79 80 78 78 74 68 69

Example: 2008 crisis

Setting up the test

  • We want to test if there was a change in CCI from 2007 to 2009

  • We interested in the difference in CCI

  • The null hypothesis is that there was (on average) no change in CCI H_0 \colon \mu = 0

  • The alternative hypothesis is that there was some change: H_1 \colon \mu \neq 0

Example: 2008 crisis

R code

# Enter CCI data in 2 vectors using function c()
score_2007 <- c(86, 86, 88, 90, 99, 97, 97, 96, 99, 97, 90, 90)
score_2009 <- c(24, 22, 21, 21, 19, 18, 17, 18, 21, 23, 22, 21)

# Compute vector of differences in CCI
difference <- score_2007 - score_2009

# Perform t-test on difference with null hypothesis mu = 0
# Store answer in "answer"
answer -> t.test(difference, mu = 0)

# Print the answer
print(answer)

Example: 2008 crisis

Output of t.test


    One Sample t-test

data:  difference
t = 38.144, df = 11, p-value = 4.861e-13
alternative hypothesis: true mean is not equal to 0
95 percent confidence interval:
 68.15960 76.50706
sample estimates:
mean of x 
 72.33333

Example: 2008 crisis

Analysis of Output


    One Sample t-test


  • Description of the test that we have asked for
  • Note: t.test has automatically assumed that a one-sample test is desired

Example: 2008 crisis

Analysis of Output


data:  difference


  • This says which data are being tested
  • In our case we test the data in difference

Example: 2008 crisis

Analysis of Output


t = 38.144, df = 11, p-value = 4.861e-13


This is the best part:

  • \texttt{t} = \, t-statistic from data
  • \texttt{df} = \, degrees of freedom
  • \texttt{p-value} = \, the exact p-value

Note:

  • You do not need Statistical Tables!
  • You see that p < 0.05
  • Therefore we reject null hypothesis that the mean difference is 0

Example: 2008 crisis

Analysis of Output


alternative hypothesis: true mean is not equal to 0


  • R tells us the alternative hypothesis is \mu \neq 0

  • Hence the Null hypothesis tested is H_0 \colon \mu = 0

  • Warning:

    • This message is not telling you to accept to alternative hypothesis
    • This message is only stating the alternative hypothesis

Example: 2008 crisis

Analysis of Output


95 percent confidence interval:
 68.15960 76.50706


This is a 95 \% confidence interval for the true mean:

  • Confidence interval: is the set of (hypothetical) mean values from which the data do not deviate significantly
  • It is based on inverting the t-test by solving for the values of \mu that cause t to lie within its acceptance region

Example: 2008 crisis

Analysis of Output


95 percent confidence interval:
 68.15960 76.50706


  • For 95 \% confidence interval this means solving P( |t_{n-1}| < t) = 0.95 \,, \qquad t = \frac{\overline{x}-\mu}{\mathop{\mathrm{e.s.e.}}}
  • Solving wrt \mu yields \overline{x} - t_{n-1}(0.025) \times \mathop{\mathrm{e.s.e.}}< \mu < \overline{x} + t_{n-1}(0.025) \times \mathop{\mathrm{e.s.e.}}

Example: 2008 crisis

Analysis of Output


95 percent confidence interval:
 68.15960 76.50706


  • R calculated the quantities \overline{x} \pm t_{n-1}(0.025) \times \mathop{\mathrm{e.s.e.}}

  • Based on the data, we conclude that the set of (hypothetical) mean values is \mu \in [68.15960, 76.50706]

Example: 2008 crisis

Analysis of Output


sample estimates:
mean of x 
 72.33333


  • This is the sample mean
  • You could have easily computed this with the code
    • mean(difference)

Example: 2008 crisis

Conclusion

The key information is:

  • We conducted a two-sided t-test for the mean difference \mu \neq 0
  • Results give significant evidence p<0.05 that \mu \neq 0
  • The sample mean difference \overline{x} = 72.33333 \gg 0
  • This suggest CCI mean difference \mu \gg 0
  • Hence consumer confidence is higher in 2007 than in 2009

Part 5:
Graphics

Graphics

R has extensive built in graphing functions:

  • Fancier graphing functions are contained in the library ggplot2 (see link)

  • However we will be using the basic built in R graphing functions

Graphics

Scatter plot

  • Suppose given 2 vectors x and y of same length
  • The scatter plot of pairs (x_i,y_i) can be generated with plot(x, y)

Example: Suppose to have data of weights and heights of 6 people

  • To plot weight against height code is as follows
  • When you run plot() in R Console the plot will appear in a pop-up window
# Store weight and height data in 2 vectors
weight <- c(60, 72, 57, 90, 95, 72)
height <- c(1.75, 1.80, 1.65, 1.90, 1.74, 1.91)

# Plot weight against height
plot(weight, height)

Graphics

Graphics

Scatter plot – Options

  • You can customize your plot in many ways
  • Example: you can represent points (x_i,y_i) with triangles instead of circles
  • This can be done by including the command
    • pch = 2
  • pch stands for plotting character
# Store weight and height data in 2 vectors
weight <- c(60, 72, 57, 90, 95, 72)
height <- c(1.75, 1.80, 1.65, 1.90, 1.74, 1.91)

# Plot weight against height using little triangles
plot(weight, height, pch = 2)

Graphics

Graphics

Plotting 1D function f(x)

  • Create a grid of x values x = (x_1, \ldots, x_n)
  • Evaluate f on such grid. This yields a vector y = (f(x_1), \ldots, f(x_n))
  • Generate a scatter plot with
    • plot(x, y)
  • Use the function lines to linearly interpolate the scatter plot:
    • lines(x, y)

Graphics

Plotting functions - Example

Let us plot the parabola y = x^2 \,, \qquad x \in [-1,1] 

# Input vector for grid of x coordinates
x <- c(-1, -0.5, 0, 0.5, 1)

# Compute the function y=x^2 on the grid
y <- x^2

# Generate scatter plot of (x,y)
plot(x, y)

# Add linear interpolation
lines(x, y)

Graphics

Graphics

Plotting functions - Example

  • The previous plot was quite rough

  • This is because we only computed y=x^2 on the grid x = (-1, -0.5, 0, 0.5, 1)

  • We could refine the grid by hand, but this is not practical

  • To generate a finer grid we can use the built in R function

    • seq()

Seq function

seq(from, to, by, length.out) generates a vector containing a sequence:

  • from – The beginning number of the sequence
  • to – The ending number of the sequence
  • by – The step-size of the sequence (the increment)
  • length.out – The total length of the sequence

Example: Generate the vector of even numbers from 2 to 20

x <- seq(from = 2, to = 20, by = 2)
print(x)
 [1]  2  4  6  8 10 12 14 16 18 20

Seq function

Note: The following commands are equivalent:

  • seq(from = x1, to = x2, by = s)
  • seq(x1, x2, s)

Example: Generate the vector of odd numbers from 1 to 11

x <- seq(from = 1, to = 11, by = 2)
y <- seq(1, 11, 2)

cat("Vector x is: (", x, ")")
cat("Vector y is: (", y, ")")
cat("They are the same!")
Vector x is: ( 1 3 5 7 9 11 )
Vector y is: ( 1 3 5 7 9 11 )
They are the same!

Graphics

Plotting functions - Example

  • We go back to plotting y = x^2 \,, \qquad x \in [-1, 1]
  • We want to generate a grid, or sequece:
    • Starting at 0
    • Ending at 1
    • With increments of 0.2
x <- seq(from = -1, to = 1, by = 0.2)
print(x)
 [1] -1.0 -0.8 -0.6 -0.4 -0.2  0.0  0.2  0.4  0.6  0.8  1.0

Graphics

Plotting functions - Example

# Use seq() to generate x grid
x <- seq(from = -1, to = 1, by = 0.2)

# Plot the function y=x^2
plot(x, x^2)
lines(x, x^2)

Graphics

Scatter plot - Example

Let us go back to the example of plotting random normal values

  • First we generate a vector x with 1000 random normal values
  • Then we plot x via plot(x)
  • The command plot(x) implicitly assumes that:
    • x is the second argument: Values to plot on y-axis
    • The first argument is the vector seq(1, 1000)
    • Note that seq(1, 1000) is the vector of components numbers of x
x <- rnorm(1000)

plot(x)

Graphics

References

Homepage      License      Contact

[1]
Dalgaard, Peter, Introductory statistics with R, Second Edition, Springer, 2008.
[2]
Davies, Tilman M., The book of R, No Starch Press, 2016.