Time Series Analysis with R

Yanchang Zhao
http://www.RDataMining.com

R and Data Mining Course

Beijing University of Posts and Telecommunications,
Beijing, China

July 2019

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Contents

Introduction

Time Series Decomposition

Time Series Forecasting

Time Series Clustering

Time Series Classification

Online Resources

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 ∗
Time Series Analysis with R

I time series data in R

I time series decomposition, forecasting, clustering and
classification
I autoregressive integrated moving average (ARIMA) model
I Dynamic Time Warping (DTW)
I Discrete Wavelet Transform (DWT)
I k-NN classification

∗
Chapter 8: Time Series Analysis and Mining, in book
R and Data Mining: Examples and Case Studies.
http://www.rdatamining.com/docs/RDataMining-book.pdf
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Time Series Data in R

I class ts
I represents data which has been sampled at equispaced points
in time
I frequency=7: a weekly series
I frequency=12: a monthly series
I frequency=4: a quarterly series

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Time Series Data in R

## an example of time series data

a <- ts(1:20, frequency = 12, start = c(2011, 3))
print(a)
## Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec
## 2011 1 2 3 4 5 6 7 8 9 10
## 2012 11 12 13 14 15 16 17 18 19 20

str(a)
## Time-Series [1:20] from 2011 to 2013: 1 2 3 4 5 6 7 8 9 10...

attributes(a)
## $tsp
## [1] 2011.167 2012.750 12.000
##
## $class
## [1] "ts"

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Contents

Introduction

Time Series Decomposition

Time Series Forecasting

Time Series Clustering

Time Series Classification

Online Resources

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What is Time Series Decomposition

To decompose a time series into

components [Brockwell and Davis, 2016]:
I Trend component: long term trend
I Seasonal component: seasonal variation
I Cyclical component: repeated but non-periodic fluctuations
I Irregular component: the residuals

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Data AirPassengers
Data AirPassengers: monthly totals of Box Jenkins international
airline passengers, 1949 to 1960. It has 144(=12×12) values.
## load time series data
plot(AirPassengers)
600
500
AirPassengers

400
300
200
100

1950 1952 1954 1956 1958 1960

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Decomposition
## time series decomposation
apts <- ts(AirPassengers, frequency = 12)
f <- decompose(apts)
plot(f$figure, type = "b") # seasonal figures
60
40
20
f$figure

0
−20
−40

2 4 6 8 10 12
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Decomposition
plot(f)

Decomposition of additive time series

500
observed
300
450100
350
trend
250
20 40 60 150
seasonal
0
60 −40
40
random
20
0
−40

2 4 6 8 10 12

Time 10 / 40
Contents

Introduction

Time Series Decomposition

Time Series Forecasting

Time Series Clustering

Time Series Classification

Online Resources

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Time Series Forecasting

I To forecast future events based on known past data

I For example, to predict the price of a stock based on its past
performance
I Popular models
I Autoregressive moving average (ARMA)
I Autoregressive integrated moving average (ARIMA)

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Forecasting

## build an ARIMA model

fit <- arima(AirPassengers, order=c(1,0,0),
list(order=c(2,1,0), period=12))
## make forecast
fore <- predict(fit, n.ahead=24)
## error bounds at 95% confidence level
upper.bound <- fore$pred + 2*fore$se
lower.bound <- fore$pred - 2*fore$se

## plot forecast results

ts.plot(AirPassengers, fore$pred, upper.bound, lower.bound,
col = c(1, 2, 4, 4), lty = c(1, 1, 2, 2))
legend("topleft", col = c(1, 2, 4), lty = c(1, 1, 2),
c("Actual", "Forecast", "Error Bounds (95% Confidence)"))

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Forecasting

700 Actual
Forecast
Error Bounds (95% Confidence)
600
500
400
300
200
100

1950 1952 1954 1956 1958 1960 1962

Time

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Contents

Introduction

Time Series Decomposition

Time Series Forecasting

Time Series Clustering

Time Series Classification

Online Resources

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Time Series Clustering

I To partition time series data into groups based on similarity or

distance, so that time series in the same cluster are similar
I Measure of distance/dissimilarity
I Euclidean distance
I Manhattan distance
I Maximum norm
I Hamming distance
I The angle between two vectors (inner product)
I Dynamic Time Warping (DTW) distance
I ...

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Dynamic Time Warping (DTW)
DTW finds optimal alignment between two time
series [Keogh and Pazzani, 2001].
## Dynamic Time Warping (DTW)
library(dtw)
idx <- seq(0, 2 * pi, len = 100)
a <- sin(idx) + runif(100)/10
b <- cos(idx)
align <- dtw(a, b, step = asymmetricP1, keep = T)
dtwPlotTwoWay(align)
1.0
0.5
Query value

0.0
−0.5
−1.0

0 20 40 60 80 100 17 / 40
Synthetic Control Chart Time Series

I The dataset contains 600 examples of control charts

synthetically generated by the process in Alcock and
Manolopoulos (1999).
I Each control chart is a time series with 60 values.
I Six classes:
I 1-100 Normal
I 101-200 Cyclic
I 201-300 Increasing trend
I 301-400 Decreasing trend
I 401-500 Upward shift
I 501-600 Downward shift
I http://kdd.ics.uci.edu/databases/synthetic_control/synthetic_
control.html

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Synthetic Control Chart Time Series

# read data into R

# sep="": the separator is white space, i.e., one
# or more spaces, tabs, newlines or carriage returns
sc <- read.table("../data/synthetic_control.data", header=F, sep="")
# show one sample from each class
idx <- c(1, 101, 201, 301, 401, 501)
sample1 <- t(sc[idx,])
plot.ts(sample1, main="")

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 201 101 1
25 30 35 40 45 15 20 25 30 35 40 45 24 26 28 30 32 34 36

0
Six Classes

10
20
30

Time
40
50
60
501 401 301
10 15 20 25 30 35 25 30 35 40 45 0 10 20 30

0
10
20
30

Time
40
50
60

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Hierarchical Clustering with Euclidean distance

# sample n cases from every class

n <- 10
s <- sample(1:100, n)
idx <- c(s, 100 + s, 200 + s, 300 + s, 400 + s, 500 + s)
sample2 <- sc[idx, ]
observedLabels <- rep(1:6, each = n)
## hierarchical clustering with Euclidean distance
hc <- hclust(dist(sample2), method = "ave")
plot(hc, labels = observedLabels, main = "")

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Hierarchical Clustering with Euclidean distance

140
120
100
Height

80
60

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6

2
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1
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dist(sample2)
hclust (*, "average")

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Hierarchical Clustering with Euclidean distance

# cut tree to get 8 clusters

memb <- cutree(hc, k = 8)
table(observedLabels, memb)
## memb
## observedLabels 1 2 3 4 5 6 7 8
## 1 10 0 0 0 0 0 0 0
## 2 0 3 1 1 3 2 0 0
## 3 0 0 0 0 0 0 10 0
## 4 0 0 0 0 0 0 0 10
## 5 0 0 0 0 0 0 10 0
## 6 0 0 0 0 0 0 0 10

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Hierarchical Clustering with DTW Distance

# hierarchical clustering with DTW distance

myDist <- dist(sample2, method = "DTW")
hc <- hclust(myDist, method = "average")
plot(hc, labels = observedLabels, main = "")
# cut tree to get 8 clusters
memb <- cutree(hc, k = 8)
table(observedLabels, memb)
## memb
## observedLabels 1 2 3 4 5 6 7 8
## 1 10 0 0 0 0 0 0 0
## 2 0 4 3 2 1 0 0 0
## 3 0 0 0 0 0 6 4 0
## 4 0 0 0 0 0 0 0 10
## 5 0 0 0 0 0 0 10 0
## 6 0 0 0 0 0 0 0 10

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 Height

0 200 400 600 800 1000

3
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myDist
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hclust (*, "average") 6
6
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Hierarchical Clustering with DTW Distance

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Contents

Introduction

Time Series Decomposition

Time Series Forecasting

Time Series Clustering

Time Series Classification

Online Resources

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Time Series Classification

Time Series Classification

I To build a classification model based on labelled time series
I and then use the model to predict the lable of unlabelled time
series
Feature Extraction
I Singular Value Decomposition (SVD)
I Discrete Fourier Transform (DFT)
I Discrete Wavelet Transform (DWT)
I Piecewise Aggregate Approximation (PAA)
I Perpetually Important Points (PIP)
I Piecewise Linear Representation
I Symbolic Representation

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Decision Tree (ctree)

ctree from package party

## build a decision tree

classId <- rep(as.character(1:6), each = 100)
newSc <- data.frame(cbind(classId, sc))
library(party)
ct <- ctree(classId ~ ., data = newSc,
controls = ctree_control(minsplit = 20,
minbucket = 5, maxdepth = 5))

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Decision Tree

pClassId <- predict(ct)

table(classId, pClassId)
## pClassId
## classId 1 2 3 4 5 6
## 1 100 0 0 0 0 0
## 2 1 97 2 0 0 0
## 3 0 0 99 0 1 0
## 4 0 0 0 100 0 0
## 5 4 0 8 0 88 0
## 6 0 3 0 90 0 7

# accuracy
(sum(classId == pClassId))/nrow(sc)
## [1] 0.8183333

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DWT (Discrete Wavelet Transform)
I Wavelet transform provides a multi-resolution representation
using wavelets [Burrus et al., 1998].
I Haar Wavelet Transform – the simplest DWT
http://dmr.ath.cx/gfx/haar/

I DFT (Discrete Fourier Transform): another popular feature

extraction technique

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DWT (Discrete Wavelet Transform)

# extract DWT (with Haar filter) coefficients

library(wavelets)
wtData <- NULL
for (i in 1:nrow(sc)) {
a <- t(sc[i, ])
wt <- dwt(a, filter = "haar", boundary = "periodic")
wtData <- rbind(wtData, unlist(c(wt@W, wt@V[[wt@level]])))
}
wtData <- as.data.frame(wtData)
wtSc <- data.frame(cbind(classId, wtData))

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Decision Tree with DWT

## build a decision tree

ct <- ctree(classId ~ ., data = wtSc,
controls = ctree_control(minsplit=20, minbucket=5,
maxdepth=5))
pClassId <- predict(ct)
table(classId, pClassId)
## pClassId
## classId 1 2 3 4 5 6
## 1 98 2 0 0 0 0
## 2 1 99 0 0 0 0
## 3 0 0 81 0 19 0
## 4 0 0 0 74 0 26
## 5 0 0 16 0 84 0
## 6 0 0 0 3 0 97

(sum(classId==pClassId)) / nrow(wtSc)
## [1] 0.8883333

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plot(ct, ip_args = list(pval = F), ep_args = list(digits = 0))

1
V57

≤ 117 > 117

2 9
W43 V57

≤ −4 > −4 ≤ 140 > 140

3 6 11
W5 W31 V57

≤ 178 > 178

12 17
W22 W31

≤ −8 > −8 ≤ −6 > −6 ≤ −6 > −6 ≤ −15 > −15

14 19
W31 W43

≤ −13 > −13 ≤3 >3

Node 4 (n = 68) Node 5 (n = 6) Node 7 (n = 9) Node 8 (n = 86) Node 10 (n = 31) Node 13 (n = 80) Node 15 (n = 9) Node 16 (n = 99) Node 18 (n = 12) Node 20 (n = 103) Node 21 (n = 97)
1 1 1 1 1 1 1 1 1 1 1
0.8 0.8 0.8 0.8 0.8 0.8 0.8 0.8 0.8 0.8 0.8
0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.6
0.4 0.4 0.4 0.4 0.4 0.4 0.4 0.4 0.4 0.4 0.4
0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2
0 0 0 0 0 0 0 0 0 0 0
123456 123456 123456 123456 123456 123456 123456 123456 123456 123456 123456

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k-NN Classification

I find the k nearest neighbours of a new instance

I label it by majority voting
I needs an efficient indexing structure for large datasets

## k-NN classification
k <- 20
newTS <- sc[501, ] + runif(100) * 15
distances <- dist(newTS, sc, method = "DTW")
s <- sort(as.vector(distances), index.return = TRUE)
# class IDs of k nearest neighbours
table(classId[s$ix[1:k]])
##
## 4 6
## 3 17

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k-NN Classification

I find the k nearest neighbours of a new instance

I label it by majority voting
I needs an efficient indexing structure for large datasets

## k-NN classification
k <- 20
newTS <- sc[501, ] + runif(100) * 15
distances <- dist(newTS, sc, method = "DTW")
s <- sort(as.vector(distances), index.return = TRUE)
# class IDs of k nearest neighbours
table(classId[s$ix[1:k]])
##
## 4 6
## 3 17

Results of majority voting: class 6

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The TSclust Package

I TSclust: a package for time seriesclustering †

I measures of dissimilarity between time series to perform time
series clustering.
I metrics based on raw data, on generating models and on the
forecast behavior
I time series clustering algorithms and cluster evaluation metrics

†
http://cran.r-project.org/web/packages/TSclust/
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Contents

Introduction

Time Series Decomposition

Time Series Forecasting

Time Series Clustering

Time Series Classification

Online Resources

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Online Resources

I Book titled R and Data Mining: Examples and Case

Studies [Zhao, 2012]
http://www.rdatamining.com/docs/RDataMining-book.pdf
I R Reference Card for Data Mining
http://www.rdatamining.com/docs/RDataMining-reference-card.pdf
I Free online courses and documents
http://www.rdatamining.com/resources/
I RDataMining Group on LinkedIn (27,000+ members)
http://group.rdatamining.com
I Twitter (3,300+ followers)
@RDataMining

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The End

Thanks!
Email: yanchang(at)RDataMining.com
Twitter: @RDataMining
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How to Cite This Work

I Citation
Yanchang Zhao. R and Data Mining: Examples and Case Studies. ISBN
978-0-12-396963-7, December 2012. Academic Press, Elsevier. 256
pages. URL: http://www.rdatamining.com/docs/RDataMining-book.pdf.
I BibTex
@BOOK{Zhao2012R,
title = {R and Data Mining: Examples and Case Studies},
publisher = {Academic Press, Elsevier},
year = {2012},
author = {Yanchang Zhao},
pages = {256},
month = {December},
isbn = {978-0-123-96963-7},
keywords = {R, data mining},
url = {http://www.rdatamining.com/docs/RDataMining-book.pdf}
}

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References I

Brockwell, P. J. and Davis, R. A. (2016).

Introduction to Time Series and Forecasting, ISBN 9783319298528.
Springer.

Burrus, C. S., Gopinath, R. A., and Guo, H. (1998).

Introduction to Wavelets and Wavelet Transforms: A Primer.
Prentice-Hall, Inc.

Keogh, E. J. and Pazzani, M. J. (2001).

Derivative dynamic time warping.
In the 1st SIAM Int. Conf. on Data Mining (SDM-2001), Chicago, IL, USA.

Zhao, Y. (2012).
R and Data Mining: Examples and Case Studies, ISBN 978-0-12-396963-7.
Academic Press, Elsevier.

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