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Time Series Analysis (TSA) - Tutorial

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Tutorial: Time series analysis in R

D G Rossiter
Cornell University, Section of Soil & Crop Sciences
ISRIC–World Soil Information
W¬ 'f0 ffb

March 3, 2020

è ï ôå
“Take time to sharpen your axe before you start to chop
firewood.”

Contents

1 Introduction 1

2 Loading and examining a time series 2

2.1 Example 1: Groundwater level . . . . . . . . . . . . . . . . . . 2
2.2 Example 2: Daily rainfall . . . . . . . . . . . . . . . . . . . . . . 11
2.3 Answers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21

3 Analysis of a single time series 24

3.1 Summaries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
3.1.1 Numerical summaries . . . . . . . . . . . . . . . . . . . 24
3.1.2 Graphical summaries . . . . . . . . . . . . . . . . . . . . 25
3.2 Smoothing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
3.2.1 Aggregation . . . . . . . . . . . . . . . . . . . . . . . . . . 28
3.2.2 Smoothing by filtering . . . . . . . . . . . . . . . . . . . 29
3.2.3 Smoothing by local polynomial regression . . . . . . . 32
3.3 Decomposition . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
3.4 Serial autocorrelation . . . . . . . . . . . . . . . . . . . . . . . . 39
3.5 Partial autocorrelation . . . . . . . . . . . . . . . . . . . . . . . 45
3.6 Spectral analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
3.7 Answers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54

Version 2.1 Copyright © 2009–2012, 2018–2020 D G Rossiter

All rights reserved. Reproduction and dissemination of the work as a
whole (not parts) freely permitted if this original copyright notice is in-
cluded. Sale or placement on a web site where payment must be made to
access this document is strictly prohibited. To adapt or translate please
contact the author ([email protected]).
4 Modelling a time series 57
4.1 Modelling by decomposition . . . . . . . . . . . . . . . . . . . . 57
4.2 Modelling by OLS linear regression . . . . . . . . . . . . . . . . 59
4.3 Modelling by GLS linear regression . . . . . . . . . . . . . . . . 62
4.3.1 Modelling a decomposed series . . . . . . . . . . . . . 69
4.3.2 Non-parametric tests for trend . . . . . . . . . . . . . . 71
4.3.3 A more difficult example . . . . . . . . . . . . . . . . . . 74
4.4 Autoregressive integrated moving-average (ARIMA) models 76
4.4.1 Autoregressive (AR) models . . . . . . . . . . . . . . . . 76
4.4.2 Moving average (MA) models . . . . . . . . . . . . . . . 82
4.4.3 ARMA models . . . . . . . . . . . . . . . . . . . . . . . . 83
4.4.4 ARIMA models . . . . . . . . . . . . . . . . . . . . . . . . 83
4.4.5 Periodic autoregressive (PAR) models . . . . . . . . . . 84
4.5 Modelling with ARIMA models . . . . . . . . . . . . . . . . . . 86
4.5.1 Checking for stationarity . . . . . . . . . . . . . . . . . 87
4.5.2 Determining the AR degress . . . . . . . . . . . . . . . 90
4.6 Predicting with ARIMA models . . . . . . . . . . . . . . . . . . 94
4.7 Answers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95

5 Intervention analysis 98
5.1 A known intervention . . . . . . . . . . . . . . . . . . . . . . . . 98
5.2 Answers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100

6 Comparing two time series 100

6.1 Answers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106

7 Gap filling 107

7.1 Simulating short gaps in a time series . . . . . . . . . . . . . . 108
7.2 Gap filling by interpolation . . . . . . . . . . . . . . . . . . . . 110
7.2.1 Linear interpolation . . . . . . . . . . . . . . . . . . . . . 110
7.2.2 Spline interpolation . . . . . . . . . . . . . . . . . . . . . 112
7.3 Simulating longer gaps in time series . . . . . . . . . . . . . . 114
7.3.1 Non-systematic gaps . . . . . . . . . . . . . . . . . . . . 114
7.3.2 Systematic gaps . . . . . . . . . . . . . . . . . . . . . . . 117
7.4 Estimation from other series . . . . . . . . . . . . . . . . . . . 119
7.5 Answers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 124

8 Simulation 125
8.1 AR models . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 125
8.2 Answers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 130

References 131

Index of R concepts 133

ii
1 Introduction

Time series are repeated measurements of one or more variables over

time. They arise in many applications in earth, natural and water re-
source studies, including ground and surface water monitoring (quality
and quantity), climate monitoring and modelling, agricultural or other
production statistics. Time series have several characteristics that make
their analysis different from that of non-temporal variables:
1. The variable may have a trend over time;
2. The variable may exhibit one or more cycles of different period;
3. There will almost always be serial correlation between subsequent
observations;
4. The variable will almost always have a “white noise” component,
i.e. random variation not explained by any of the above.
This tutorial presents some aspects of time series analysis (shorthand
“TSA”1 ), using the R environment for statistical computing and visu-
alisation [12, 14] and its dialect of the S language. R users seriously
interested in this topic are well-advised to refer to the text of Metcalfe
and Cowpertwait [13]2 , part of the excellent UseR! series from Springer3 .
The Comprehensive R Action Network (CRAN) has a “Task View” on time
series analysis4 . This lists all the R packages applicable to TSA, catego-
rized and with a brief description of each. In addition, Shumway and
Stoffer [16] is an advanced text which uses R for its examples. Venables
and Ripley [18] include a chapter on time series analysis in S (both R and
S-PLUS dialects), mostly using examples from Diggle [8].
Good introductions to the concepts of time series analysis are Diggle
[8] for biological applications, Box [4] for forecasting and control, Hipel
and McLeod [10] (available on the web) for water resources and environ-
mental modelling, and Salas [15] from the Handbook of Hydrology for
hydrological applications. Davis [7] includes a brief introduction to time
series for geologists. Wilks [20, Ch. 8] discusses time series for climate
analysis, with emphasis on simulation.
The tutorial is organized as a set of tasks followed by questions to check
your understanding; answers are at the end of each section. If you are
ambitious, there are also some challenges: tasks and questions with no
solution provided, that require the integration of skills learned in the
section.
1
Not to be confused with a bureaucratic monster with the same initials
2
http://link.springer.com/book/10.1007/978-0-387-88698-5
3
http://link.springer.com/bookseries/6991
4
http://cran.r-project.org/web/views/TimeSeries.html

1
2 Loading and examining a time series

We use two datasets5 to illustrate different research questions and oper-

ations of time series analysis:

1. Monthly groundwater levels (§2.1);

2. Daily rainfall amounts (§2.2).

These also illustrate some of the problems with importing external datasets
into R and putting data into a form suitable for time-series analysis.
All the datasets in this exercise are assumed to be stored in the ds_tsa
“datasets” subdirectory, under the directory where this tutorial is stored.

2.1 Example 1: Groundwater level

The first example dataset is a series of measurements of the depth to

groundwater (in meters) in two wells used for irrigation in the Anatolian
plateau, Turkey, from January 1975 through December 2004 CE. These
are provided as text files anatolia_hati.txt and anatolia_alibe.txt.

Q1 : What are some things that a water manager would want to know
about this time series? Jump to A1 •

Task 1 : Start R and switch to the directory where the example datasets
are stored. •

Task 2 : Examine the file for the first well. •

You could review the file in a plain-text editor; here we use the file.show
function:
file.show("./ds_tsa/anatolia_hati.txt")

Here are the first and last lines of the file:

34.36
34.45
34.7
...
55.96
55.55
54.83

Q2 : Can you tell from this file that it is a time series? Jump to A2 •
5
kindly provided by colleagues in the University of Twente/faculty ITC’s Water Re-
sources department, https://www.itc.nl/WRS

2
Task 3 : Read this file into R and examine its structure. •
Using the scan function to read a file into a vector:
gw <- scan("./ds_tsa/anatolia_hati.txt")
str(gw)

## num [1:360] 34.4 34.5 34.7 34.8 34.9 ...

Q3 : What is the structure? Jump to A3 •

Task 4 : Convert the vector of measurements for this well into a time
series and examine its structure and attributes. •
The ts function converts a vector into a time series; it has several argu-
ments, of which enough must be given to specify the series:

• start : starting date of the series;

• end : ending date of the series;
• frequency : number of observations in the series per unit of time;
• deltat : fraction of the sampling period between successive ob-
servations.

Only one of frequency or deltat should be provided, they are two ways
to specify the same information. The ending date end is optional if either
frequency or deltat are given, because the end will just be when the
vector ends.
In this example we know from the metadata that the series begins in
January 1975 and ends in December 2004; it is a monthly series. The
simplest way to specify it is by starting date and frequency.
After the series is established, we examine its structure with str and
attributes with attributes.
gw <- ts(gw, start=1975, frequency=12)
str(gw)

## Time-Series [1:360] from 1975 to 2005: 34.4 34.5 34.7 34.8 34.9 ...

attributes(gw)

## $tsp
## [1] 1975.000 2004.917 12.000
##
## $class
## [1] "ts"

start(gw)

## [1] 1975 1

end(gw)

## [1] 2004 12

3
In the above example we also show the start and end functions to show
the starting and ending dates in a time series.

Task 5 : Print the time series; also show the the time associated with
each measurement, and the position of each observation in the cycle. •
The generic print method specializes into print.ts to show the actual
values; time shows the time associated with each measurement, and
cycle shows the position of each observation in the cycle.
print(gw)

Here we just show the first and last two years.

Jan Feb Mar Apr May Jun Jul Aug Sep Oct
1975 34.36 34.45 34.70 34.80 34.88 35.16 35.60 35.86 35.86 35.70
1976 35.22 35.18 34.98 35.20 35.51 35.32 34.45 34.54 34.39 34.18
...
2003 53.32 52.48 51.37 51.07 50.71 52.78 54.35 55.46 56.52 55.70
2004 53.08 52.41 51.71 51.66 52.84 54.11 55.28 56.11 57.02 55.96
Nov Dec
1975 35.48 35.28
1976 33.92 33.73
...
2003 54.47 54.21
2004 55.55 54.83

Note how the month names are automatically assigned. From the ts doc-
umentation: “Values of 4 and 12 are assumed in print methods to imply a
quarterly and monthly series respectively.” Specifically print.ts makes
this assumption.
time(gw)

Again, only the beginning and end of the full series:

Jan Feb Mar Apr May Jun Jul

1975 1975.000 1975.083 1975.167 1975.250 1975.333 1975.417 1975.500
1976 1976.000 1976.083 1976.167 1976.250 1976.333 1976.417 1976.500
...
2003 2003.000 2003.083 2003.167 2003.250 2003.333 2003.417 2003.500
2004 2004.000 2004.083 2004.167 2004.250 2004.333 2004.417 2004.500
Aug Sep Oct Nov Dec
1975 1975.583 1975.667 1975.750 1975.833 1975.917
1976 1976.583 1976.667 1976.750 1976.833 1976.917
...
2003 2003.583 2003.667 2003.750 2003.833 2003.917
2004 2004.583 2004.667 2004.750 2004.833 2004.917
cycle(gw)

Again, only the beginning and end of the full series:

Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec
1975 1 2 3 4 5 6 7 8 9 10 11 12
1976 1 2 3 4 5 6 7 8 9 10 11 12
...
2003 1 2 3 4 5 6 7 8 9 10 11 12
2004 1 2 3 4 5 6 7 8 9 10 11 12

4
Q4 : What are the units of each of these? Jump to A4 •

Task 6 : Determine the series’ frequency and interval between observa-

tions. •
Of course we know this from the metadata, but this information can
also be extracted from the series object with the frequency and deltat,
methods, as in the arguments to ts.
frequency(gw)

## [1] 12

deltat(gw)

## [1] 0.08333333

Q5 : What are the units of each of these? Jump to A5 •

Task 7 : Plot the time series. •

The generic plot method specializes to plot.ts for time-series objects.
There are several ways to visualise this, we show a few possibilities here:

par(mfrow=c(1,3))
# pdf("AnatoliaWell1.pdf", width=10, height=5)
plot(gw, ylab="Depth to water table (m)", main="Anatolia Well 1")
# dev.off()
plot(gw, type="o", pch=20, cex=0.6, col="blue",
ylab="Depth to water table (m)", main="Anatolia Well 1")
plot(gw, type="h", col="blue", ylab="Depth to water table (m)",
main="Anatolia Well 1")
par(mfrow=c(1,1))

Anatolia Well 1 Anatolia Well 1 Anatolia Well 1

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1975 1980 1985 1990 1995 2000 2005 1975 1980 1985 1990 1995 2000 2005 1975 1980 1985 1990 1995 2000 2005

Time Time Time

Q6 : What are the outstanding features of this time series? Jump to A6

•

5
Task 8 : Plot three cycles of the time series, from the shallowest depth
at the end of the winter rains (April) beginning in 1990, to see annual
behaviour. •
We use the window function to extract just part of the series. The start
and end can have both a cycle (here, year) and position in cycle (here,
month), connected with the c ‘catentate’ function:
window(gw, start=c(1990,4), end=c(1993,3))

## Jan Feb Mar Apr May Jun Jul Aug Sep Oct
## 1990 39.07 40.16 42.50 43.20 44.11 43.79 43.34
## 1991 41.44 40.85 40.74 40.52 41.27 42.11 43.88 45.09 45.06 44.22
## 1992 42.42 41.46 40.82 40.82 41.73 42.19 43.26 44.49 44.28 43.54
## 1993 42.13 41.66 41.28
## Nov Dec
## 1990 42.61 41.92
## 1991 43.16 42.48
## 1992 42.05 42.48
## 1993

plot(window(gw, start=c(1990,4), end=c(1993,3)), type="o",

ylab="Depth to water table (m)", main="Anatolia Well 1")

Anatolia Well 1

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45

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1990.5 1991.0 1991.5 1992.0 1992.5 1993.0

Time

Q7 : What is the annual cycle? Jump to A7 •

This region of Turkey has a typical Mediterranean climate: hot and dry
in the summer, cool and moist in the winter. These wells are used for
irrigation in the summer months.
The window function may also be used to extract a single element, by
specifying the same start and end date:
window(gw, start=c(1990,1), end=c(1990,1))

6
## Jan
## 1990 39.95

Another way to view a time series is as the differences between succes-

sive measurements.

Task 9 : Compute and view the difference for lag 1 (one month), lag 2
(two months), and lag 12 (one year), for the period 1990 – 1992. •
The diff function computes differences, by default for successive mea-
surements; the lag argument specifies different lags (intervals between
measurements):
window(gw, 1990, c(1992,12))

## Jan Feb Mar Apr May Jun Jul Aug Sep Oct
## 1990 39.95 39.89 39.38 39.07 40.16 42.50 43.20 44.11 43.79 43.34
## 1991 41.44 40.85 40.74 40.52 41.27 42.11 43.88 45.09 45.06 44.22
## 1992 42.42 41.46 40.82 40.82 41.73 42.19 43.26 44.49 44.28 43.54
## Nov Dec
## 1990 42.61 41.92
## 1991 43.16 42.48
## 1992 42.05 42.48

diff(window(gw, 1990, c(1992,12)))

## Jan Feb Mar Apr May Jun Jul Aug Sep Oct
## 1990 -0.06 -0.51 -0.31 1.09 2.34 0.70 0.91 -0.32 -0.45
## 1991 -0.48 -0.59 -0.11 -0.22 0.75 0.84 1.77 1.21 -0.03 -0.84
## 1992 -0.06 -0.96 -0.64 0.00 0.91 0.46 1.07 1.23 -0.21 -0.74
## Nov Dec
## 1990 -0.73 -0.69
## 1991 -1.06 -0.68
## 1992 -1.49 0.43

diff(window(gw, 1990, c(1992,12)), lag=2)

## Jan Feb Mar Apr May Jun Jul Aug Sep Oct
## 1990 -0.57 -0.82 0.78 3.43 3.04 1.61 0.59 -0.77
## 1991 -1.17 -1.07 -0.70 -0.33 0.53 1.59 2.61 2.98 1.18 -0.87
## 1992 -0.74 -1.02 -1.60 -0.64 0.91 1.37 1.53 2.30 1.02 -0.95
## Nov Dec
## 1990 -1.18 -1.42
## 1991 -1.90 -1.74
## 1992 -2.23 -1.06

diff(window(gw, 1990, c(1992,12)), lag=12)

## Jan Feb Mar Apr May Jun Jul Aug Sep Oct
## 1991 1.49 0.96 1.36 1.45 1.11 -0.39 0.68 0.98 1.27 0.88
## 1992 0.98 0.61 0.08 0.30 0.46 0.08 -0.62 -0.60 -0.78 -0.68
## Nov Dec
## 1991 0.55 0.56
## 1992 -1.11 0.00

Q8 : What happens to the length of resulting series with different lags?

Jump to A8 •

Q9 : Do you expect the one-month differences to be the same for each

7
month within a year? Are they? Jump to A9 •

Q10 : Do you expect the one-month differences to be the same for the
same month interval in different years? Are they? Jump to A10 •

Specifying the differences argument to diff computes higher-order

differences, that is, differences of differences (order 2), etc.

Task 10 : Compute the first, second and third order differences of the
series from 1990 – 1993. •
diff(window(gw, 1990, c(1993,12)), lag=12, differences=1)

## Jan Feb Mar Apr May Jun Jul Aug Sep Oct
## 1991 1.49 0.96 1.36 1.45 1.11 -0.39 0.68 0.98 1.27 0.88
## 1992 0.98 0.61 0.08 0.30 0.46 0.08 -0.62 -0.60 -0.78 -0.68
## 1993 -0.29 0.20 0.46 0.47 0.60 1.21 1.62 1.24 1.50 1.62
## Nov Dec
## 1991 0.55 0.56
## 1992 -1.11 0.00
## 1993 2.57 1.45

diff(window(gw, 1990, c(1993,12)), lag=12, differences=2)

## Jan Feb Mar Apr May Jun Jul Aug Sep Oct
## 1992 -0.51 -0.35 -1.28 -1.15 -0.65 0.47 -1.30 -1.58 -2.05 -1.56
## 1993 -1.27 -0.41 0.38 0.17 0.14 1.13 2.24 1.84 2.28 2.30
## Nov Dec
## 1992 -1.66 -0.56
## 1993 3.68 1.45

diff(window(gw, 1990, c(1993,12)), lag=12, differences=3)

## Jan Feb Mar Apr May Jun Jul Aug Sep Oct
## 1993 -0.76 -0.06 1.66 1.32 0.79 0.66 3.54 3.42 4.33 3.86
## Nov Dec
## 1993 5.34 2.01

Q11 : What is the interpretation of these differences? Jump to A11 •

Task 11 : Plot the first differences for the whole time series. •
plot(diff(gw), ylab="One-month differences in groundwater depth (m)",
main="Anatolia well 1")

8
Anatolia well 1

One−month differences in groundwater depth (m)

2
0
−2
−4
−6

1975 1980 1985 1990 1995 2000 2005

Time

This gives us a very different view of the sequence, compared to the time
series itself.

Q12 : What are the outstanding features of the first differences? Jump
to A12 •

Task 12 : Identify the months with the largest extractions and recharges.
•
The which function identifies elements in a vector which meet some cri-
terion. The which.min and which.max are shorthand for finding the
minimum and maximum.
We first find the most extreme extractions and recharge, and then all of
these where the level changed by more than 2 m in one month, in either
direction:
i <- which.min(diff(gw))
diff(gw)[i]

## [1] -7.36

time(gw)[i]

## [1] 1988.167

cycle(gw)[i]

## [1] 3

i <- which.max(diff(gw))
diff(gw)[i]

## [1] 2.74

9
time(gw)[i]

## [1] 2000.417

cycle(gw)[i]

## [1] 6

i <- which(abs(diff(gw)) > 2)

diff(gw)[i]

## [1] -7.36 2.34 -2.98 2.51 2.74 2.70 2.57 2.07

time(gw)[i]

## [1] 1988.167 1990.333 1996.000 1998.500 2000.417 2001.500 2002.333

## [8] 2003.333

cycle(gw)[i]

## [1] 3 5 1 7 6 7 5 5

Note the use of the time function on the series to get the dates corre-
sponding to the selected measurements; the resulting vector of dates is
subsetted with the [] indexing operator. Similarly, the cycle function
is used to display the position in the cycle, here the month.
The extreme recharge (about 7.5 m) in March 1988 draws our attention;
is this correct, given than no other month in the time series had more
than about 2.5 m recharge?
First, we take a closer look at the measurements for this and surrounding
years:
plot(window(gw, start=1986, end=1990), ylab="Groundwater depth (m)",
main="Anatolia well 1", type="h", col="blue")
lines(window(gw, start=1986, end=1990), lty=2)

10
Anatolia well 1

46
Groundwater depth (m)

44
42
40

1986 1987 1988 1989 1990

Time

Q13 : Is the pattern for Spring 1987 – Spring 1988 consistent with the
surrounding years? Jump to A13 •

Here are the actual measurements for the relevant time period:
window(gw, start=c(1987,3), end=c(1988,6))

## Jan Feb Mar Apr May Jun Jul Aug Sep Oct
## 1987 39.64 39.43 40.12 41.39 42.73 43.58 43.49 44.18
## 1988 46.06 46.42 46.78 39.42 39.96 40.58
## Nov Dec
## 1987 44.94 45.53
## 1988

Q14 : How could this anomaly be explained? Jump to A14 •

2.2 Example 2: Daily rainfall

The second example dataset is a series of daily rainfall records from a

station in the Lake Tana basin, Ethiopia, for 26 years (1981 – 2005).

Q15 : What could be some research questions for this time series?
Jump to A15 •

This is a typical “messy” Excel file; we must do some substantial manip-

ulations to get it into useful format for R. It is possible to reformat and
clean up the dataset in Excel, but much more difficult than the systematic
approach we can take in R.
Here is a screenshot of the original file:

11
This is a nice format to view the data but not to analyze as a time series.
First, to quote the R Data Import/Export manual [17, §8]:

“The most common R data import/export question seems to

be: ‘how do I read an Excel spreadsheet?’ . . . The first piece of
advice is to avoid doing so if possible!”

The recommended procedure is to export each sheet of the Excel file to

a separate comma-separated value (“CSV”) file, using Excel or another
program that can read Excel files and write CSV files.
We have done this6 ; the CSV file is Tana_Daily.csv.

Note: However, recently several packages have been written which work
well to exchange Excel files and R data structures, for example the readxl
package, which has an excel_sheets function to list the sheets in an
Excel workbook, and a read_excel function to read an Excel sheet as a
data frame.

Task 13 : View the contents of the CSV file. •

Again we use the file.show function:
file.show("./ds_tsa/Tana_Daily.csv")

Here are the first and last lines of the file:

BahirDar,,,,,,,,,,,,,
6
using the Numbers application on Mac OS X 10.6

12
YEAR,DATE,JAN,FEB,MAR,APRIL,MAY,JUNE,JULY,AUG,SEP,OCT,NOV,DEC
1981,1,0,0,0,0,0,0.8,26.3,14.9,13.4,0,1.4,0
,2,0,0,0,0,0,0,12.9,31.3,0.3,0.9,0,0
...
,28,0.0,0.0,0.0,0.0,28.0,33.2,28.1,0.9,36.0,0.5,0,
,29,0.0,,0.0,0.0,0.5,24.0,18.5,2.8,6.8,32.7,0,
,30,0.0,,0.0,0.0,0.0,3.6,32.1,11.5,1.0,3,0,
,31,0.0,,0.0,,15.0,,85.7,0.6,,0,,

Task 14 : Read the CSV file into an R object and examine its structure.
•
We use the very flexible read.csv function, which is a version of the
more general read.table method. These have quite some useful op-
tional arguments (see ?read.table for details); here we use:

• skip=1 to skip over the first line, which is just the station name;
• header=T to specify that the first line read (after skipping) contains
the variable names, here the months;
• colClasses to specify the data type of each field (column); this
is because we want to treat all the rainfall amounts as character
strings to fix the “trace amount” entries specified with the string
TR;
• na.strings="N.A" to specify that any string that is identically N.A
is a missing value; note blanks are also considered missing.
• blank.lines.skip=T to skip blank lines.

Note that optional arguments sep and dec can be used if the separa-
tor between fields is not the default “,” or the decimal point is not the
default “.”.
tana <- read.csv("./ds_tsa/Tana_Daily.csv", skip=1, header=T,
colClasses=c(rep("integer",2), rep("character",12)),
blank.lines.skip=T,na.strings=c("N.A","NA"," "))
str(tana)

## 'data.frame': 831 obs. of 14 variables:

## $ YEAR : int 1981 NA NA NA NA NA NA NA NA NA ...
## $ DATE : int 1 2 3 4 5 6 7 8 9 10 ...
## $ JAN : chr "0" "0" "0" "0" ...
## $ FEB : chr "0" "0" "0" "0" ...
## $ MAR : chr "0" "0" "0" "0" ...
## $ APRIL: chr "0" "0" "0" "0" ...
## $ MAY : chr "0" "0" "0" "0" ...
## $ JUNE : chr "0.8" "0" "0" "0" ...
## $ JULY : chr "26.3" "12.9" "8.9" "29.6" ...
## $ AUG : chr "14.9" "31.3" "0.4" "27.6" ...
## $ SEP : chr "13.4" "0.3" "1.5" "0.4" ...
## $ OCT : chr "0" "0.9" "17.6" "0" ...
## $ NOV : chr "1.4" "0" "0" "0" ...
## $ DEC : chr "0" "0" "0" "0" ...

tana[1:35,]

## YEAR DATE JAN FEB MAR APRIL MAY JUNE JULY AUG SEP OCT NOV DEC
## 1 1981 1 0 0 0 0 0 0.8 26.3 14.9 13.4 0 1.4 0

13
## 2 NA 2 0 0 0 0 0 0 12.9 31.3 0.3 0.9 0 0
## 3 NA 3 0 0 0 0 0 0 8.9 0.4 1.5 17.6 0 0
## 4 NA 4 0 0 0 0 0 0 29.6 27.6 0.4 0 0 0
## 5 NA 5 0 0 0 0 0 10.8 16.2 7.8 9.5 0.3 0 0
## 6 NA 6 0 0 0 0 0 5.2 5.3 16.2 5.5 8.4 0.9 0
## 7 NA 7 0 0 0 0 0 0 7.3 2.9 0.4 3.7 0 0
## 8 NA 8 0 0 0 0 3.7 0 108.7 20.1 1.5 0 0 0
## 9 NA 9 0 0 0 0 1.2 0.2 17.6 8.1 4.9 26.8 0 0
## 10 NA 10 0 0 0 0 0 0 6 0 0 0 0 0
## 11 NA 11 0 0 0 0 0 0 7 1 2.7 0 0 0
## 12 NA 12 0 0 0 0 0 0.2 0 58.9 3.8 0 0 0
## 13 NA 13 0 0 0 0 0 0 0 0.7 8.8 0 0 0
## 14 NA 14 0 0 0 0 0 10.3 2.4 1.5 0 0 0 0
## 15 NA 15 0 0 0 0 7.1 0.2 0.8 30.3 0 0 0 0
## 16 NA 16 0 0 0 0 0 0 28.9 1.1 6.3 0 0 0
## 17 NA 17 0 0 0 0 0 2.2 30 6.5 1.6 0 0 0
## 18 NA 18 0 0 0 0 2.7 0 11.4 23.6 8.8 0 0 0
## 19 NA 19 0 0 0 0.3 1.3 0 21.4 27.7 11.5 0 0 0
## 20 NA 20 0 0 0 0 0 6.9 25.2 0 5.8 0 0 0
## 21 NA 21 0 0 0 0 4.4 3.5 7.5 4.1 3.5 0 0 0
## 22 NA 22 0 0 0 14.7 8.6 19.9 20.7 25 32.3 0 0 0
## 23 NA 23 0 0 0 0.4 0 0.9 21.5 11.3 6.7 0 1.7 0
## 24 NA 24 0 0 0 52.8 0 4.4 48.9 1.2 0 0 3.8 0
## 25 NA 25 0 0 0 0 0 0 21.8 23.5 0.7 0 0.2 0
## 26 NA 26 0 0 0 0.3 16.3 0 32.6 25.8 0.4 0 0 0
## 27 NA 27 0 0 0 0 0 0.5 26.6 0.4 0 0 0 0
## 28 NA 28 0 0 0 0 0 0 0 1.4 0 0 0 0
## 29 NA 29 0 0 0 0 0 11.2 8 2 0 0 0
## 30 NA 30 0 0 0 0 0 64.8 0 0 0 0 0
## 31 NA 31 0 0 0 14.9 1.4 0 0
## 32 NA NA
## 33 1982 1 0 0 0 0 0 0 0.9 6.5 4.9 2.2 0 0
## 34 NA 2 0 0 0 0 0 0 3 11.3 0.2 0.3 0 0
## 35 NA 3 0 0 30 0 0 0.3 11.8 24.6 5.7 <NA> 0 0

We can see that each year has 31 lines followed by one lines with only two
NA missing values. Only the first line of each year has the year number
in the first field.
The read.csv function creates a so-called dataframe, which is a matrix
with named fields (columns).

Q16 : What is in each field of the dataframe? Jump to A16 •

There are many missing values, which can be identified with is.na func-
tion; the sum function then shows how many in total. We also compute
the number of blank records; the na.rm argument is needed to remove
missing values before summing:
sum(is.na(tana[,3:14]))

## [1] 170

sum(tana[,3:14]=="",na.rm=TRUE)

## [1] 457

Note that the null values are not missing, they are for days that do not
exist (e.g. 30-February).
We can see all the values with the unique function, and sort these for
easy viewing with sort. To get all the months as one vector we stack

14
columns 3 through 14 with the stack function:
head(sort(unique(stack(tana[,3:14])$values)))

## [1] "" "0" "0.0" "0.01" "0.1" "0.2"

tail(sort(unique(stack(tana[,3:14])$values)))

## [1] "9.8" "9.9" "90.5" "95.5" "tr" "TR"

Q17 : What are the meanings of the "" (empty string), 0, 0.0, and "TR"
(also written "tr") values? Jump to A17 •

Let’s see how many of each of the problematic values there are, and how
many zeroes:
sum(tana[,3:14]=="TR", na.rm=TRUE)

## [1] 69

sum(tana[,3:14]=="tr", na.rm=TRUE)

## [1] 2

sum(tana[,3:14]=="0.01", na.rm=TRUE)

## [1] 14

sum(tana[,3:14]=="0", na.rm=TRUE)

## [1] 4920

The trace values are conventionally set to half the measurement preci-
sion, or one order of magnitude smaller, or (since they have very little
effect on rainfall totals) to zero.

Q18 : What is the measurement precision? Jump to A18 •

Task 15 : Set the trace values and any measurements below 0.1 to
zero. •
For this we use the very useful recode function in the car “Companion
to Applied Regression” package from John Fox [9]. The require function
loads the library if it is not already loaded.
require(car)

## Loading required package: car

## Loading required package: carData

for (i in 3:14) {
tana[,i] <- recode(tana[,i], "c('TR','tr','0.01')='0'")
}

head(sort(unique(stack(tana[,3:14])$values)),12)

## [1] "" "0" "0.0" "0.1" "0.2" "0.3" "0.4" "0.5" "0.6" "0.7" "0.8"
## [12] "0.9"

15
tail(sort(unique(stack(tana[,3:14])$values)),12)

## [1] "9.0" "9.1" "9.2" "9.3" "9.4" "9.5" "9.6" "9.7" "9.8"
## [10] "9.9" "90.5" "95.5"

The problematic values have been replaced by zeroes, as we can verify

by repeated the summary of “problematic” values:
sum(tana[,3:14]=="TR", na.rm=TRUE)

## [1] 0

sum(tana[,3:14]=="tr", na.rm=TRUE)

## [1] 0

sum(tana[,3:14]=="0.01", na.rm=TRUE)

## [1] 0

sum(tana[,3:14]=="0", na.rm=TRUE)

## [1] 5005

Task 16 : Organize the daily values as one long vector of values, as

required for time series analysis. •
This is complicated by the varying month length, so it is not possible
simply to stack the 12 vectors. Also, the sequence must be by year;
but each month’s vector contains all the years. Finally, February had 29
days in 1984, 1988, . . . 2004, so these years had 366, not 365 days. To
detect seasonality we need equal-length years. Fortunately in this case,
February is a dry month, and there was no rain on this date in any of the
leap years:
tana[tana$DATE==29,"FEB"]

## [1] "" NA "" NA "" NA "0" NA "" NA ""

## [12] NA "" NA "0" NA "" NA "" NA "" NA
## [23] "0.0" NA "" NA NA NA NA NA "0" NA NA
## [34] NA NA NA NA NA "0" NA "" NA "" NA
## [45] "" NA "0.0" NA "" NA ""

So a simple if somewhat inelegant solution is to ignore records for 29-

February7
We use the c “catentate” function to stack vectors, specifying their length
by our knowledge of the length of each month. Note the zero-length
“months” which will match with the first two columns of the dataframe
(fields YEAR and DATE).
tana.ppt <- NULL;
month.days <- c(0,0,31, 28, 31, 30, 31, 30, 31, 31, 30, 31, 30, 31)
for (yr.first.row in seq(from=1, by=32, length=(2006 - 1981 + 1))) {
for (month.col in 3:14) {
tana.ppt <-
c(tana.ppt, tana[yr.first.row:(yr.first.row + month.days[month.col]-1),
month.col])
}

7
Apologies to anyone born on this date!

16
};
str(tana.ppt)

## chr [1:9490] "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" ...

rm(month.days, yr.first.row, month.col)

Check that this is an integral number of years:

length(tana.ppt)/365

## [1] 26

Task 17 : Convert this to a time series with the appropriate metadata.

•
Again, the ts function is used to convert the series; the frequency ar-
gument specifies a cycle of 365 days and the start argument specifies
the beginning of the series (first day of 1981):
tana.ppt <- ts(tana.ppt, start=1981, frequency=365)
str(tana.ppt)

## Time-Series [1:9490] from 1981 to 2007: 0 0 0 0 ...

We enhance the plot by highlighting the missing values, showing them

as red vertical bars near the top of the plot:

plot(tana.ppt, main="Lake Tana rainfall", ylab="mm")

abline(h=100, col="gray")
points(xy.coords(x=time(tana.ppt), y=100, recycle=T),
pch=ifelse(is.na(tana.ppt),"l",""), col="red")
grid()

Lake Tana rainfall

100

l ll l l llllllll l l
mm

60
20
0

1980 1985 1990 1995 2000 2005

Time

There are six years with a few missing observations, and a long series of
missing observations in 1991.
To zoom in on the within-year structure, we display one-year windows
for the years with missing values, with these highlighted, and the most
recent year. The points function is used to place points on top of a bar
graph created with the plot function (with the optional type="h" argu-
ment). To compare several years side-by-side, we compute the maximum

17
daily rainfall with the max function, and use it to set a common limit with
the optional ylim argument to plot.

Note: A small complication is that ylim requires numeric arguments, but

max returns a character value, even on a numeric time series. This must
be converted to a number with as.numeric before use in ylim. This is
also the case for the sum function used in the graph subtitle.

Also, the optional extend to the window function, allows the time series
to be extended by the start and end arguments.
yrs <- c(1982, 1983, 1988, 1989,1991,1998,1999, 2006); ymax <- 0
for (i in yrs) {
ymax <- as.numeric(max(ymax, window(tana.ppt,
start=i, end=i+1, extend=TRUE),
na.rm=T))
}
(ymax <- ceiling(ymax))

## [1] 91

18
par(mfrow=c(4,2))
for (i in yrs) {
plot(window(tana.ppt, start=i, end=i+1, extend=TRUE),
type="h", ylab="mm", ylim=c(0,ymax));
title(main=paste("Lake Tana rainfall", i),
sub=paste("Annual total:",
sum(as.numeric(window(tana.ppt, start=i, end=i+1)),
na.rm=T)))
abline(h=ymax, col="gray")
points(xy.coords(x=time(window(tana.ppt, start=i, end=i+1, extend=TRUE)),
y=ymax, recycle=T),
pch=ifelse(is.na(window(tana.ppt, start=i, end=i+1, extend=TRUE)),"l",""),
col="red")
grid()
}

## Warning in window.default(x, ...): ’end’ value not changed

par(mfrow=c(1,1))

Lake Tana rainfall 1982 Lake Tana rainfall 1983

l l l
80

80
60

60
mm

mm
40

40
20

20
0

1982.0 1982.2 1982.4 1982.6 1982.8 1983.0 1983.0 1983.2 1983.4 1983.6 1983.8 1984.0

Time Time
Annual total: 894.6 Annual total: 1257.3

Lake Tana rainfall 1988 Lake Tana rainfall 1989

ll ll
80

80
60

60
mm

mm
40

40
20

20
0

1988.0 1988.2 1988.4 1988.6 1988.8 1989.0 1989.0 1989.2 1989.4 1989.6 1989.8 1990.0

Time Time
Annual total: 1314.1 Annual total: 1595.3

Lake Tana rainfall 1991 Lake Tana rainfall 1998

llllllllllllllllllllllllllllllllllllllllllllllllllllllllll l
80

80
60

60
mm

mm
40

40
20

20
0

1991.0 1991.2 1991.4 1991.6 1991.8 1992.0 1998.0 1998.2 1998.4 1998.6 1998.8 1999.0

Time Time
Annual total: 1429.3 Annual total: 1422.6

Lake Tana rainfall 1999 Lake Tana rainfall 2006

l l
80

80
60

60
mm

mm
40

19
20

20
0

1999.0 1999.2 1999.4 1999.6 1999.8 2000.0 2006.0 2006.2 2006.4 2006.6 2006.8 2007.0

Time Time
Annual total: 1474.4 Annual total: 1683.2
Q19 : Does there seem to be a seasonal difference in rainfall? Is it
consistent year-to-year? Jump to A19 •

This series has missing values; for some analyses complete series are
needed. The na.contiguous function finds the longest contiguous se-
quence of values:
str(tana.ppt)

## Time-Series [1:9490] from 1981 to 2007: 0 0 0 0 ...

sum(is.na(tana.ppt))

## [1] 127

tana.ppt.c <- na.contiguous(tana.ppt)

str(tana.ppt.c)

## Time-Series [1:2912] from 1999 to 2007: 0 7.9 0 0 ...

## - attr(*, "na.action")= 'omit' int [1:6578] 1 2 3 4 5 6 7 8 9 10 ...

frequency(tana.ppt.c)

## [1] 365

head(time(tana.ppt.c))

## [1] 1999.022 1999.025 1999.027 1999.030 1999.033 1999.036

head(cycle(tana.ppt.c))

## [1] 9 10 11 12 13 14

tail(time(tana.ppt.c))

## [1] 2006.984 2006.986 2006.989 2006.992 2006.995 2006.997

tail(cycle(tana.ppt.c))

## [1] 360 361 362 363 364 365

sum(is.na(tana.ppt.c))

## [1] 0

plot(tana.ppt.c, main="Lake Tana rainfall", ylab="mm", sub="continuous record")

Lake Tana rainfall

120
100
80
mm

60
40
20
0

2000 2002 2004 2006

Time
continuous record

Q20 : What is the extent of the contiguous time series? Jump to A20 •

Gap filling is discussed in §7.

20
2.3 Answers

A1 : Among the questions might be:

• Is the the groundwater level increasing or decreasing over time?

• Is any trend consistent over the measurement period?
• We expect an annual cycle corresponding to the rainy and dry seasons;
is this in fact observed? What is the lag of this cycle compared to the
rainfall cycle?
• Is the amplitude of the cycle constant over the measurement period or
does it change year-to-year?
• Are the trends and cycles the same for both wells?
• A practical issue: if measurements are missing from one of the time
series, can it be “reliably” estimated from (1) other observations in the
same series; (2) observations in the other series; (3) some combination
of these?

Return to Q1 •

A2 : No, it is just a list of numbers. We have to know from the metadata what
it represents. Return to Q2 •

A3 : The measurements are a 360-element vector. Return to Q3 •

A4 : print shows the actual value of each measurements; here the depth to
groundwater. cycle shows the position of each measurement in its cycle; here
this is the month of the year. time gives the fractional year. Return to Q4 •

A5 : frequency is the number of measurements within each cycle; here

there are 12 months in one year. deltat is the interval between successive
measurements in terms of a single cycle, so here deltat is fractional years:
1/12 = 0.83̄. Return to Q5 •

A6 :

1. Generally increasing trend over time since about 1983 and lasting till
2002; that is, depth is increasing so the groundwater is further from the
surface;
2. But, significant recharge 1975 – 1978;
3. Clear yearly cycle, but this is not seen in 1975–1978;
4. Severe draw-down in 1988, with rapid recharge.

21
Return to Q6 •

A7 : It is annual; the groundwater is closest to the surface in April and then

decreases rapidly until August; recharge begins in September. Return to Q7 •

A8 : The series gets shorter; the differences given are for the end date of
each lag, so that, for example, the one-year lag can only begin in January 1991
(difference with January 1990). Return to Q8 •

A9 : Differences between months should reflect the annual cycle: negative in

the fall and winter (recharge) and positive in the spring summer (extraction).
This in fact is observed. Return to Q9 •

A10 : If there is no variability in the recharge or extraction the monthly

differences (for example, March to April) should be the same in each year. This
is not observed; for example the recharge in 1991 vs. 1990 (January through
May) was much higher than the difference from 1992 vs. 1991. Return to Q10
•

A11 : The first differences are the year-to-year differences in the same month.
For example, from January 1990 to January 1991 the groundwater depth in-
creased by
, whereas the difference in the next year (January 1991 to January 1992) was
The second differences are the change in difference from one year to the next;
for example the difference from January 1991 to January 1992, compared to
the difference in the previous year (January 1990 to January 1991) is -0.51
. In this case the second year’s differences were less than the first, i.e., the
groundwater depth didn’t increase as much in the second year (January to
January), compared to the first.
The third differences are the change in two-year differences. Return to Q11 •

A12 :

1. The annual cycle is clear: month-to-month differences are positive (in-

creasing groundwater depth, i.e., extraction) in the spring and summer
(extraction) and negative (decreasing groundwater depth, i.e., recharge)
in the fall and winter;
2. The amplitude of the annual cycle increased until about 1999 and seems
to be stable since then;
3. There is one extreme extraction event, four times as much groundwater
lowering than any other.

Return to Q12 •

A13 : No. Not only is the magnitude of extraction and recharge more, the

22
recharge does not begin until March 1988, whereas in the other years it begins
in August. Note the small recharge in September 1988, which seems to be the
beginning of the recharge (fall and winter rains); but then this is interrupted
by six months of extraction during the (wet) winter. Return to Q13 •

A14 : To explain this there would have to have been continued extraction in
the winter of 1987–1988, perhaps because of failure of winter rains; we do not
have the rainfall data to see if this is possible. But also March 1988 would have
to had extreme rainfall.
Another possibility is that the records for winter 1987–1988 were incorrectly
entered into the data file, or perhaps measured in a different way, with this
being corrected in March 1988. However, they are consistent month-to-month
in this period, so it is unlikely to be a data entry error. Return to Q14 •

A15 :

• Is there an annual cycle in rainfall amount?

• If so, how many “rainy seasons” are there?
• How variable is the rainfall year-to-year?
• Is there a trend over time in the rainfall amount, either overall or in a
specific season?
• How consistent is rainfall day-to-day within the dry and rainy seasons?
In other words, how long is the auto-correlation period?
• What are probable values for missing measurements, and what is the
uncertainty of these predictions?

Return to Q15 •

A16 : YEAR is the year of measurement; however it is only entered for the first
day of each year (upper-left of the sheet).
DATE is the day of the month (all months), from 1 .. 31
JAN . . . DEC are the rainfall amounts for the given day of the named month.
Return to Q16 •

A17 : "" (empty string) means there is no data at all, i.e., no day in the month
(here, 29 – 31 February); 0 means no rainfall, as does 0.0, and "TR" means
trace rainfall. Return to Q17 •

A18 : Only one decimal place is given; also the minimum measurement for
February was 0.1, so the precision is 0.1. January does have a 0.01 value,
which seems to be an inconsistent attempt to record the trace amount. Return
to Q18 •

A19 : There is a definite seasonality: rains from about May to about August

23
and the other months dry. Rains can begin early (1993) or there can be some
sporadic rains before the true start of the rainy season (1992, less in 1990).
Return to Q19 •

A20 : From the 9th day of 1999 through the end of 2006, i.e., almost eight
years. Return to Q20 •

3 Analysis of a single time series

3.1 Summaries

Summary descriptive statistics and graphics show the overall behaviour

of a time series.

3.1.1 Numerical summaries

Task 18 : Summarize the groundwater levels of the first well, for the
whole series. •
The summary function gives the overall distribution:
summary(gw)

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

## 29.90 34.90 41.63 41.58 46.80 57.68

More useful is a summary grouped by some attribute of the time series,

typically cycle or position in the cycle.

Task 19 : Summarize the groundwater levels of the first well, for each
year separately. •
The time-series data structure (one long vector with attributes) is not
suitable for grouping by year or position in cycle. We create a data frame,
one column being the time series and the other two factors giving the
year and cycle. Recall the time function returns the time of observation
(here, as fractional years); these are converted to year number with the
floor function. Similarly, the cycle function returns the position in
the cycle, from 1 ...frequency(series). Both of these are converted
from time-series to numbers with the as.numeric function. We also
keep the fractional time axis, as field time.
gw.f <- data.frame(gw, year=as.numeric(floor(time(gw))),
cycle=as.numeric(cycle(gw)), time=time(gw))
str(gw.f)

## 'data.frame': 360 obs. of 4 variables:

## $ gw : Time-Series from 1975 to 2005: 34.4 34.5 34.7 34.8 34.9 ...
## $ year : num 1975 1975 1975 1975 1975 ...
## $ cycle: num 1 2 3 4 5 6 7 8 9 10 ...
## $ time : Time-Series from 1975 to 2005: 1975 1975 1975 1975 1975 ...

24
Now the year can be used as a grouping factor; the summary function
(specified with the FUN argument) is applied to each year with the by
function, with the IND “index” argument being the grouping factor:
head(by(gw.f$gw, IND=gw.f$year, FUN=summary))

## $`1975`
## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 34.36 34.77 35.22 35.18 35.62 35.86
##
## $`1976`
## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 33.73 34.34 34.76 34.72 35.20 35.51
##
## $`1977`
## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 30.61 31.47 31.61 31.81 32.16 33.40
##
## $`1978`
## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 29.90 30.07 30.34 30.41 30.75 30.97
##
## $`1979`
## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 30.42 30.53 31.15 31.50 32.45 32.96
##
## $`1980`
## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 31.60 31.91 32.28 32.37 32.74 33.33

Note that the function applied could be max (to get the deepest level),
min (the shallowest), median, quantile etc., in fact anything that sum-
marizes a numeric vector.
A single year can be extracted with the [[]] list extraction operator:
by(gw.f$gw, IND=gw.f$year, FUN=summary)[["1978"]]

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

## 29.90 30.07 30.34 30.41 30.75 30.97

by(gw.f$gw, IND=gw.f$year, FUN=max)[["1978"]]

## [1] 30.97

by(gw.f$gw, IND=gw.f$year, FUN=min)[["1978"]]

## [1] 29.9

by(gw.f$gw, IND=gw.f$year, FUN=quantile, probs=.9)[["1978"]]

## [1] 30.839

3.1.2 Graphical summaries

Boxplots, often grouped by cycle number or position in the cycle, reveal

the average behaviour of time series.

Task 20 : Display boxplots of the Anatolia well levels, grouped by year.

•
This is produced by the boxplot function, with the formula operator
~ showing the dependence of the left-hand side of the formula (here,

25
groundwater level) on the right-hand side (here, year):

boxplot(gw.f$gw ~ gw.f$year, main="Anatolia well 1",

ylab="groundwater level (m)")
grid()

Anatolia well 1
55
50
groundwater level (m)

45
40
35
30

1975 1977 1979 1981 1983 1985 1987 1989 1991 1993 1995 1997 1999 2001 2003

This gives a clear impression of the per-year variability.

Q21 : Is there a trend in the per-year amplitude of the annual cycle of

groundwater levels? Jump to A21 •

Task 21 : Display boxplots of the Anatolia well levels, grouped by

position in the cycle (month), after correcting for the overall trend. •
We add a field to the data frame that is the difference of each observation
from its annual mean, which is computed with the aggregate function
(see below, §3.2.1 for details of this function):
(ann.mean <- aggregate(gw, nfrequency=1, FUN=mean))

## Time Series:
## Start = 1975
## End = 2004
## Frequency = 1
## [1] 35.17750 34.71833 31.80750 30.41083 31.50333 32.36917 31.28667
## [8] 31.89667 34.50333 36.51417 38.27750 40.09167 42.08583 42.10417
## [15] 40.78417 41.66000 42.56833 42.46167 43.51583 45.49667 47.74917
## [22] 46.78500 44.99417 45.89000 47.85417 49.62000 52.94750 54.59083
## [29] 53.53667 54.21333

time(ann.mean)

## Time Series:
## Start = 1975
## End = 2004

26
## Frequency = 1
## [1] 1975 1976 1977 1978 1979 1980 1981 1982 1983 1984 1985 1986 1987
## [14] 1988 1989 1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000
## [27] 2001 2002 2003 2004

We subtract the correct annual mean from each observation, using the
match function to find the position in the vector of annual means that
corresponds to the year of the observation:
gw.f$in.yr <- as.numeric(gw - ann.mean[match(gw.f$year, time(ann.mean))])
str(gw.f)

## 'data.frame': 360 obs. of 5 variables:

Now we can display the grouped boxplot:

boxplot(gw.f$in.yr ~ gw.f$cycle, xlab="Month",
ylab="Deviation from annual mean (m)",
main="Anatolia groundwater well 1")

Anatolia groundwater well 1

●
4

●
●
●

●
Deviation from annual mean (m)

2
0

●
●
−2

●
−4

1 2 3 4 5 6 7 8 9 10 11 12

Month

Q22 : Is there an annual cycle? Are all the months equally variable? Are
there exceptions to the pattern? Jump to A22 •

3.2 Smoothing

Often we are interested in the behaviour of a time series with short-term

variations removed; this is called smoothing or low-pass filtering. A ma-
jor use of filtering is to more easily detect an overall trend, or deviations
from the overall trend that are of longer duration than one time-series
interval.

27
3.2.1 Aggregation

Sometimes we want to view the series at coarser intervals than pre-

sented. The aggregate function changes the frequency of the series.
This has arguments:
1. nfrequency (by default 1), the new number of observations per
unit of time; this must be a divisor of the original frequency. For
example, a quarterly summary of an annual time series would spec-
ify nfrequency=4.
2. FUN (by default sum), the function to apply when aggregating.

Task 22 : Convert the monthly time series of well levels from 1980
through 1985 into a quarterly series of mean well levels for the quarter.
•
The aggregation function here must could be mean; the default sum has
no physical meaning. Other reasonable choices, depending on objective,
would be max, min, or median.
gw.q <- aggregate(window(gw, 1980, 1986), nfrequency=4, FUN=mean)
str(gw.q)

## Time-Series [1:24] from 1980 to 1986: 32.2 31.7 33 32.6 31.7 ...

par(mfrow=c(1,2))
plot(gw.q, ylab="Depth to water table (m)",
main="Anatolia Well 1, quarterly", type="b")
plot(window(gw, 1980, 1986), ylab="Depth to water table (m)",
main="Anatolia Well 1, monthly", type="b")
par(mfrow=c(1,1))

Anatolia Well 1, quarterly Anatolia Well 1, monthly

● ●●
40

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●
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38

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●
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Depth to water table (m)

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36

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36

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1980 1981 1982 1983 1984 1985 1980 1981 1982 1983 1984 1985 1986

Time Time

Q23 : What are the differences between the monthly and quarterly se-
ries? How much resolution is lost? Jump to A23
•

28
3.2.2 Smoothing by filtering

A simple way to smooth the series is to apply a linear filter, using the
filter function. By default this uses a moving average of values on
both sides (before and after) each measurement. The method requires a
filter, which is a vector of coefficients to provide the weights, in reverse
time order.
The moving average for a given measurement is a weighted sum of 2p+1
measurements (the preceding p, the 1 original measurement, and the
following p measurements); 2p + 1 is called the order of the filter. Note
that filtering shortens the time series, because it can not be computed at
the p first and last measurements:

p
X
st = wj yt+j ; t = p + 1 . . . n − p (1)
j=−p

The weights wj must sum to 1; generally w−j = w+j (symmetry) but this
is not required.

Task 23 : Filter the series with a symmetric seven-month filter that

gives full weight to the measurement month, three-quarters weight to ad-
jacent months, half weight to months two removed, and quarter weight
to months three removed. •
k <- c(.25,.5,.75,1,.75,.5,.25)
(k <- k/sum(k))

## [1] 0.0625 0.1250 0.1875 0.2500 0.1875 0.1250 0.0625

fgw <- filter(gw, sides=2, k)

plot.ts(gw, main="Anatolia Well 1, 7-month filter",
ylab="groundwater depth (m)")
lines(fgw, col="red")

29
Anatolia Well 1, 7−month filter

55
50
groundwater depth (m)

45
40
35
30

1975 1980 1985 1990 1995 2000 2005

Time

Q24 : What is the effect of this filter? Jump to A24 •

Task 24 : Repeat the seven-month filter with equal weights for each
month; also compute an annual filter (12 months equally weighted); plot
the three filtered series together for the period 1990–1995. •
fgw.2 <- filter(gw, sides=2, rep(1,7)/7)
fgw.3 <- filter(gw, sides=2, rep(1,12)/12)
plot.ts(gw, xlim=c(1990,1995), ylim=c(37,48),
ylab="groundwater depth (m)")
title(main="Anatolia Well 1, three filters")
lines(fgw, col="blue", lty=2)
lines(fgw.2, col="red")
lines(fgw.3, col="magenta")
text(1995,40,"1/4,1/2,1 filter", col="blue", pos=2)
text(1995,39,"1,1,1 filter", col="red",pos=2)
text(1995,38,"annual filter", col="magenta",pos=2)

30
Anatolia Well 1, three filters

48
46
groundwater depth (m)

44
42
40

1/4,1/2,1 filter

1,1,1 filter
38

annual filter

1990 1991 1992 1993 1994 1995

Time

Q25 : What is the effect of giving equal weights to the measurements in

the filter? Jump to A25 •

Q26 : What is the effect of the annual filter? Jump to A26 •

Task 25 : Plot the annual filter for the complete series. •

plot.ts(gw, main="Anatolia Well 1, annual filter",
ylab="groundwater depth (m)")
lines(fgw.3, col="magenta", lwd=1.5)

31
Anatolia Well 1, annual filter

55
50
groundwater depth (m)

45
40
35
30

1975 1980 1985 1990 1995 2000 2005

Time

3.2.3 Smoothing by local polynomial regression

Another way to visualize the trend is to use the lowess “Local Polyno-
mial Regression Fitting” method [6], which fits the data points locally,
using nearby (in time) points. These are weighted by their distance (in
time) from the point to be smoothed; the degree of smoothing is con-
trolled by the size of the neighbourhood. This results in a smooth curve.

Task 26 : Display the time series and its smoothed series for the default
smoothing parameter (2/3), and three other values of the parameter, one
smoother, one finer, and one very fine (little smoothing). •
plot.ts(gw, main="Anatolia well 1 with smoothers",
ylab="groundwater depth (m)")
lines(lowess(gw), col="blue")
lines(lowess(gw, f=1), col="green")
lines(lowess(gw, f=1/3), col="red")
lines(lowess(gw, f=1/10), col="purple")
text(1990, 36, "Smoothing parameter: 2/3 (default)", col="blue", pos=4)
text(1990, 34, "Smoothing parameter: 1", col="green", pos=4)
text(1990, 32, "Smoothing parameter: 1/3", col="red", pos=4)
text(1990, 30, "Smoothing parameter: 1/10", col="purple", pos=4)

32
Anatolia well 1 with smoothers

55
50
groundwater depth (m)

45
40

Smoothing parameter: 2/3 (default)

Smoothing parameter: 1
Smoothing parameter: 1/3
30

Smoothing parameter: 1/10

1975 1980 1985 1990 1995 2000 2005

Time

Q27 : What is the effect of the smoothing parameter? Which seems to

give the most useful summary of this series? Jump to A27 •

3.3 Decomposition

Many time series can be decomposed into three parts:

1. A trend;
2. A cycle after accounting for the trend;
3. A residual, also known as noise, after accounting for any trend and
cycle.
These correspond to three processes:
1. A long-term process that operates over the time spanned by the
series;
2. A cyclic process that operates within each cycle;
3. A local process which causes variability between cycles.
Each of these processes is of interest and should be explained by the
analyst.

Task 27 : Decompose the groundwater level time series. •

33
The workhorse function for decomposition is stl “Seasonal Decomposi-
tion of Time Series by Loess”, i.e., using a similar smooth trend removal
as the lowess function used above in §3.2.3. This has one required argu-
ment, s.window, which is the (odd) number of lags for the loess window
for seasonal extraction; for series that are already defined to be cyclic
(as here), this can be specified as s.window="periodic", in which case
the cycle is known from the attributes of the time series, extracted here
with the frequency function:
frequency(gw)

## [1] 12

Then, the mean of the cycle at each position is taken:

tapply(gw, cycle(gw), mean)

## 1 2 3 4 5 6 7
## 41.01700 40.59800 40.25900 39.82733 40.38933 41.22433 42.07233
## 8 9 10 11 12
## 43.03767 43.30633 42.93767 42.33233 41.96433

This is subtracted from each value, leaving just the non-seasonal compo-
nent. Here we show two years’ adjustments numerically, and the whole
series’ adjustment graphically:
head(gw, 2*frequency(gw))

## [1] 34.36 34.45 34.70 34.80 34.88 35.16 35.60 35.86 35.86 35.70 35.48
## [12] 35.28 35.22 35.18 34.98 35.20 35.51 35.32 34.45 34.54 34.39 34.18
## [23] 33.92 33.73

head(gw-rep(tapply(gw, cycle(gw), mean),

length(gw)/frequency(gw)), 2*frequency(gw))

## 1 2 3 4 5 6 7
## -6.657000 -6.148000 -5.559000 -5.027333 -5.509333 -6.064333 -6.472333
## 8 9 10 11 12 1 2
## -7.177667 -7.446333 -7.237667 -6.852333 -6.684333 -5.797000 -5.418000
## 3 4 5 6 7 8 9
## -5.279000 -4.627333 -4.879333 -5.904333 -7.622333 -8.497667 -8.916333
## 10 11 12
## -8.757667 -8.412333 -8.234333

par(mfrow=c(2,1))
plot(gw, ylab="depth to groundwater", main="Original series")
plot(gw-rep(tapply(gw, cycle(gw), mean), length(gw)/frequency(gw)),
ylab="difference from cycle mean", main="Seasonally-corrected series")
abline(h=0, lty=2)
par(mfrow=c(2,1))

34
Original series

55
depth to groundwater

50
45
40
35
30

1975 1980 1985 1990 1995 2000 2005

Time

Seasonally−corrected series
15
10
difference from cycle mean

5
0
−5
−10

1975 1980 1985 1990 1995 2000 2005

Time

Q28 : What has changed in the numeric and graphical view of the time
series, after adjustment for cycle means? Jump to A28 •

This series, without the seasonal component, is then smoothed as fol-

lows.
The stl function has another required argument, but with a default.
This is t.window, which is the span (in lags,not absolute time) of the
loess window for trend extraction; this must also be odd. For the peri-
odic series (s.window="periodic"), the default is 1.5 times the cycle,
rounded to the next odd integer, so here 12 ∗ 1.5 + 1 = 19, as is proven
by the following example:
gw.stl <- stl(gw, s.window="periodic")
str(gw.stl)

## List of 8
## $ time.series: Time-Series [1:360, 1:3] from 1975 to 2005: -0.271 -0.75 -1.149 -1.635 -1.
## ..- attr(*, "dimnames")=List of 2
## .. ..$ : NULL
## .. ..$ : chr [1:3] "seasonal" "trend" "remainder"
## $ weights : num [1:360] 1 1 1 1 1 1 1 1 1 1 ...
## $ call : language stl(x = gw, s.window = "periodic")
## $ win : Named num [1:3] 3601 19 13
## ..- attr(*, "names")= chr [1:3] "s" "t" "l"

35
## $ deg : Named int [1:3] 0 1 1
## ..- attr(*, "names")= chr [1:3] "s" "t" "l"
## $ jump : Named num [1:3] 361 2 2
## ..- attr(*, "names")= chr [1:3] "s" "t" "l"
## $ inner : int 2
## $ outer : int 0
## - attr(*, "class")= chr "stl"

tmp <- stl(gw, s.window="periodic", t.window=19)

unique(tmp$time.series[,"trend"]-gw.stl$time.series[,"trend"])

## [1] 0

rm(tmp)

Q29 : What is the structure of the decomposed series object? Jump to

A29 •

Task 28 : Display the decomposed series as a graph •

The plot function specialises to plot.stl, which shows the original
series and its decomposition on a single graph.
plot(gw.stl)
50
data
40
30

1.5
seasonal

0.5
−0.5
−1.5
30 35 40 45 50 55
trend

0 1 2 3 4
remainder

−2

1975 1980 1985 1990 1995 2000 2005

time

36
The components of the decomposed series can be extracted; for example
to see just the trend:
plot(gw.stl$time.series[,"trend"],
main="Anatolia well 1, trend",
ylab="Groundwater level (m)")

Anatolia well 1, trend

55
Groundwater level (m)

50
45
40
35
30

1975 1980 1985 1990 1995 2000 2005

Time

Another way to see the decomposition is with the ts.plot function; this
shows several time series (here, the components) on the same scale of
a single graph, thus visualizing the relative contribution of each compo-
nent:
ts.plot(gw.stl$time.series, col=c("black","blue","red"),
main="Anatolia well 1, decomposition",
ylab="Groundwater level (m)")
tmp <- attributes(gw.stl$time.series)$dimnames[[2]]
for (i in 1:3) {
text(1995, 24-(i*4), tmp[i], col=c("black","blue","red")[i], pos=4)
}
grid()

Anatolia well 1, decomposition

10 20 30 40 50
Groundwater level (m)

seasonal
trend
remainder
0

1975 1980 1985 1990 1995 2000 2005

Time

Q30 : What are the magnitudes of the three components? Which is

contributing most to the observed changes over the time series? Jump
to A30 •

The decomposition with s.window="periodic" determines the seasonal

component with the average of each point in the cycle (e.g., average all
Januarys). This can not account for changes in cycle amplitude with time,
as is observed here. For this, s.window must be set to an odd number
near to the cycle or some multiple of it (to average a few years).

37
Task 29 : Decompose the groundwater time series, with a two-year
window for the seasonal component. •
gw.stl <- stl(gw, s.window=2*frequency(gw)+1)
plot(gw.stl)

50
data
40
30

2
seasonal

1
0
−1
−2
30 35 40 45 50 55
trend

0 1 2 3 4
remainder

1975 1980 1985 1990 1995 2000 2005 −2

time

Q31 : How does this decomposition differ from the pure periodic de-
composition? Jump to A31
•

The smoothness of the lowess fit is controlled with the t.window argu-
ment; by default this is:
nextodd(ceiling((1.5*period) / (1-(1.5/s.window))))
so that for a 25-month seasonal window on a 12-month cycle of this
example the trend window is the next higher odd number of d(1.5 ∗
12)/(1 − (1.5/25))e = 20, i.e., 21.

Note: This is for the case when the period is explicitly given. If the
window is specified as s.window="periodic" the smoothness parameter
is one more than 1.5 times the cycle length, see 3.3.

38
For a smoother trend this should be increased, for a finer trend de-
creased. The smoothness of the trend depends on the analyst’s knowl-
edge of the process. The previous decomposition has a very rough trend,
let’s see how it looks with a smoother trend.

Task 30 : Recompute and plot the decomposition of the time series

with a smoother trend than the default. •
gw.stl <- stl(gw, s.window=25, t.window=85)
plot(gw.stl)
50
data
40
30

2
seasonal

1
0
−1
−2
35 40 45 50 55
trend

6
remainder

4
2
0
−2

1975 1980 1985 1990 1995 2000 2005

time

Q32 : What is the difference between this smooth and the default de-
compositions? Which best represents the underlying process? Jump to
A32 •

3.4 Serial autocorrelation

In almost all time series, successive measurements are not independent;

rather, they are correlated. Since there is only one variable, this is called

39
autocorrelation and is an example of the second-order summary8
The first way to visualize this is to produce scatterplots of measure-
ments compared to others with various lags, i.e., time periods before
the given measurement. The lag.plot function produces this.

Task 31 : Display the auto-correlation scatter plots of groundwater

levels for twelve lags (i.e., up to one year of differences). •

lag.plot(gw, lags=12, main="Anatolia well 1", cex=0.3, pch=20, lty=1)

Anatolia well 1
30 40 50 60 30 40 50 60

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40

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lag 1 lag 2 lag 3

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40

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lag 10 lag 11 lag 12

30 40 50 60

Note that positive values of the lags argument refer to lags before an
8
The first-order summary is the expected value, either constant mean or trend.

40
observation. This is used also in the lag function, which produces a
lagged series with the same indices as the original series, i.e., the series
is not shifted.
window(gw, 2000, 2001)

## Jan Feb Mar Apr May Jun Jul Aug Sep Oct
## 2000 48.07 47.75 47.26 46.84 47.73 48.24 50.98 51.71 52.38 52.39
## 2001 50.11
## Nov Dec
## 2000 51.42 50.67
## 2001

lag(window(gw, 2000, 2001), 1)

## Jan Feb Mar Apr May Jun Jul Aug Sep Oct
## 1999
## 2000 47.75 47.26 46.84 47.73 48.24 50.98 51.71 52.38 52.39 51.42
## Nov Dec
## 1999 48.07
## 2000 50.67 50.11

lag(window(gw, 2000, 2001), 2)

## Jan Feb Mar Apr May Jun Jul Aug Sep Oct
## 1999
## 2000 47.26 46.84 47.73 48.24 50.98 51.71 52.38 52.39 51.42 50.67
## Nov Dec
## 1999 48.07 47.75
## 2000 50.11

lag(window(gw, 2000, 2001), -1)

## Jan Feb Mar Apr May Jun Jul Aug Sep Oct
## 2000 48.07 47.75 47.26 46.84 47.73 48.24 50.98 51.71 52.38
## 2001 50.67 50.11
## Nov Dec
## 2000 52.39 51.42
## 2001

lag(window(gw, 2000, 2001), -2)

## Jan Feb Mar Apr May Jun Jul Aug Sep Oct
## 2000 48.07 47.75 47.26 46.84 47.73 48.24 50.98 51.71
## 2001 51.42 50.67 50.11
## Nov Dec
## 2000 52.38 52.39
## 2001

Q33 : Describe the evolution of auto-correlation as the lags increase.

Jump to A33 •

By default if the time series is longer than 150 (as here), individual mea-
surements are not labelled nor joined by lines. For shorter series they
are.

Task 32 : Display the auto-correlation scatter plots of groundwater

levels for twelve lags (i.e., up to one year of differences) for 1990 through
1992. •
lag.plot(window(gw, start=1990, end=1993), lags=12, main="Anatolia well 1")

41
Anatolia well 1
38 40 42 44 46 38 40 42 44 46

45
21 20 21 20 21 20

32 32 32

window(gw, start = 1990, end = 1993)

22 33 33 22 33
22
8 8 8

44
19 19 19
9 9 9
34 34 34
10 31 10 31 10
23 7 23 7 23 7 31

43
11 11 11
25 36 24 6 25 24 6 24
25 6
30 18 30 18 30 18

42
35 35
12 12 12
29 29 29
26
13 26
13 13 26
17 17 17

41
14 28 14 28 14 28
15 27 15 27 27
15
16 16 16

5 5 5
40

2 1 2 1 1 2

3 3 3
39

4 4 4

lag 1 lag 2 lag 3

45
20
21 21 20 21 20

32 32
window(gw, start = 1990, end = 1993)

window(gw, start = 1990, end = 1993)

22 33 22 22
8 8 8

44
19 19 19
9 9 9

10 31 10 31 10 31
23 7 23 7 7 23

43
11 11 11
24 25 6 24 25 6 6 24 25
30 18 30 18 30
18

42
12 12 12
29 29 29
13 26 13 26 13 26
17 17 17

41
14 27 28 14 28 27 28 27 14
15 15 15
16 16 16

5 5 5

40
1 2 1 2 1 2

3 3 3

39
4 4 4

lag 4 lag 5 lag 6

20
21 20 21 20 21
window(gw, start = 1990, end = 1993)

window(gw, start = 1990, end = 1993)

22 22 22
8 8 8
44

19 19 19
9 9 9

10 10 10
7 23 7 23 7 23
43

11 11 11
6 24 25 6 25 24 6 25 24
30 18 18 18
42

12 12 12
29 29
26 13 26 13 26 13
17 17 17
41

28 27 14 27 28 14 28 27 14
15 15 15
16 16 16

5 5 5
40

2 1 2 1 2 1

3 3 3
39

4 4 4

lag 7 lag 8 lag 9

45
20 21 20 21 21 20
window(gw, start = 1990, end = 1993)

window(gw, start = 1990, end = 1993)

22 22 22
8 8 8

44
19 19 19
9 9 9

10 10 10
7 23 7 23 23 7

43
11 11 11
6 25 24 6 24 25 6 24
25
18 18 18

42
12 12 12

26 13 26 13 13
17 17 17

41
14
27 15 14 14
15 15
16 16 16

5 5 5

40
2 1 2 1 2 1

3 3 3

39
4 4 4

lag 10 lag 11 lag 12

38 40 42 44 46

Q34 : What additional information is provided by the labelled points

and joining lines? Jump to A34 •

Autocorrelation ranges from −1 (perfect negative correlation) through

0 (no correlation) through +1 (perfect positive correlation). It is com-
puted by acf “Autocorrelation” function. By default acf produces a
graph showing the correlation at each lag; to see the actual values the
result must be printed. The default number of lags to compute for a
single series is d10 · log 10ne, where n is the lenth of the series; for the
groundwater example this is 26.
print(acf(gw, plot=F))

##
## Autocorrelations of series 'gw', by lag
##
## 0.0000 0.0833 0.1667 0.2500 0.3333 0.4167 0.5000 0.5833 0.6667 0.7500
## 1.000 0.988 0.970 0.950 0.930 0.914 0.903 0.898 0.898 0.901
## 0.8333 0.9167 1.0000 1.0833 1.1667 1.2500 1.3333 1.4167 1.5000 1.5833
## 0.906 0.907 0.903 0.891 0.874 0.854 0.834 0.818 0.807 0.800
## 1.6667 1.7500 1.8333 1.9167 2.0000 2.0833
## 0.799 0.800 0.803 0.803 0.797 0.784

acf(gw, main="Autocorrelation, groundwater levels, Anatolia well 1")

42
Autocorrelation, groundwater levels, Anatolia well 1

1.0
0.8
0.6
ACF

0.4
0.2
0.0

0.0 0.5 1.0 1.5 2.0

Lag

Q35 : Are successive observations correlated? Positively or negatively?

How strong is the correlation? How does this change as the lag between
observations increases? Jump to A35 •

Clearly the autocorrelation holds for longer lags.

Task 33 : Display the autocorrelation of groundwater levels for five

years. •
acf(gw, lag.max=60, main="Autocorrelation, groundwater levels, Anatolia well 1")

43
Autocorrelation, groundwater levels, Anatolia well 1

1.0
0.8
0.6
ACF

0.4
0.2
0.0

0 1 2 3 4 5

Lag

Some of the autocorrelation can be explained by the trend and seasonal

components.

Task 34 : Display the autocorrelation of the remainder groundwater

levels, after trend and seasonal components have been removed, using
the smooth trend removal and a smoothing window of two years. •
Again we use stl to decompose the series. The remainder series, i.e.,
after computing the trend and cycle, is extracted from the result as field
time.series (using the $ field extraction operator), column "remainder",
and saved as a separate object for convenience:
gw.stl <- stl(gw, s.window=2*frequency(gw), t.window=84)
gw.r <- gw.stl$time.series[,"remainder"]
plot(gw.r, ylab="Remainder (m)")
title(main="Anatolia well 1 level, remainder from trend & cycle")
abline(h=0, lty=2, col="red")

Anatolia well 1 level, remainder from trend & cycle

6
4
Remainder (m)

2
0
−2

1975 1980 1985 1990 1995 2000 2005

Time

44
print(acf(gw.r, plot=F))

##
## Autocorrelations of series 'gw.r', by lag
##
## 0.0000 0.0833 0.1667 0.2500 0.3333 0.4167 0.5000 0.5833 0.6667 0.7500
## 1.000 0.887 0.769 0.659 0.559 0.468 0.385 0.324 0.270 0.231
## 0.8333 0.9167 1.0000 1.0833 1.1667 1.2500 1.3333 1.4167 1.5000 1.5833
## 0.193 0.147 0.098 0.056 0.001 -0.058 -0.111 -0.169 -0.222 -0.271
## 1.6667 1.7500 1.8333 1.9167 2.0000 2.0833
## -0.314 -0.345 -0.357 -0.370 -0.398 -0.397

acf(gw.r, main="Autocorrelation of remainders, Anatolia well 1")

Autocorrelation of remainders, Anatolia well 1

1.0
0.8
0.6
0.4
ACF

0.2
0.0
−0.2
−0.4

0.0 0.5 1.0 1.5 2.0

Lag

The blue dashed lines show correlations that are not provably different
from zero.

Q36 : Describe the autocorrelation of the remainders, and interpret in

terms of the processes causing the groundwater level to vary. Jump to
A36 •

3.5 Partial autocorrelation

A more subtle concept is partial autocorrelation of a time series. This

gives the correlation between measurements and their lagged measure-
ments that is not explained by the correlations with a shorter lag. For
example, if all autocorrelation can be explained at lag 1, then there is no
partial autocorrelation at lags 2, 3, . . . , so that the apparent autocorrela-
tion at these lags which we see in the acf function can be explained by
repeated lag-1 correlations.
For lag k, the partial autocorrelation is the autocorrelation between zt
and zt+k with the linear dependence of zt on zt+1 . . . zt+k−1 removed.

45
The partial and ordinary autocorrelations for lag 1 are the same.
Partial autocorrelations are computed as follows:

Pk φk = ρk (2)
ρ1 ρ2 ρk−1

1

···
 ρ 1 ρ1 ··· ρk−2 
 1
Pk =  (3)

 . . . ··· .


ρk−1 ρk−2 ρk−3 ··· 1
ρj = φk,1 ρj−1 + · · · + φk,k ρj−k , j = 1, 2, . . . k (4)
where φk,j is coefficient j of an autoregressive process of order k.

Note: The partial autocorrelation function is used to estimate the order

of ARIMA models (§4.4).

Task 35 : Compute and display the partial autocorrelation of the

groundwater levels. •
These are produced by the pacf “partial autocorrelation” function.
print(pacf(gw,plot=F))

##
## Partial autocorrelations of series 'gw', by lag
##
## 0.0833 0.1667 0.2500 0.3333 0.4167 0.5000 0.5833 0.6667 0.7500 0.8333
## 0.988 -0.242 -0.047 0.033 0.151 0.127 0.159 0.123 0.128 0.014
## 0.9167 1.0000 1.0833 1.1667 1.2500 1.3333 1.4167 1.5000 1.5833 1.6667
## -0.070 -0.124 -0.179 -0.086 -0.053 0.019 0.061 0.029 0.021 0.064
## 1.7500 1.8333 1.9167 2.0000 2.0833
## 0.010 0.038 -0.049 -0.081 -0.085

pacf(gw, main="Partial autocorrelation, Anatolia well 1")

Partial autocorrelation, Anatolia well 1

1.0
0.8
0.6
Partial ACF

0.4
0.2
0.0
−0.2

0.5 1.0 1.5 2.0

Lag

46
As with the graph produced by acf, the blue dashed lines show correla-
tions that are not provably different from zero.

Q37 : What are the partial autocorrelations that are different from zero?
Jump to A37 •

Task 36 : Display the autocorrelation of the remainder groundwater

levels, after trend and seasonal components have been removed, using
the smooth trend removal and a smoothing window of two years. •
The required remainders were computed in the previous setion.
print(pacf(gw.r,plot=F))

##
## Partial autocorrelations of series 'gw.r', by lag
##
## 0.0833 0.1667 0.2500 0.3333 0.4167 0.5000 0.5833 0.6667 0.7500 0.8333
## 0.887 -0.082 -0.028 -0.022 -0.025 -0.021 0.042 -0.015 0.031 -0.032
## 0.9167 1.0000 1.0833 1.1667 1.2500 1.3333 1.4167 1.5000 1.5833 1.6667
## -0.064 -0.043 -0.004 -0.103 -0.062 -0.031 -0.091 -0.046 -0.058 -0.057
## 1.7500 1.8333 1.9167 2.0000 2.0833
## -0.016 0.014 -0.067 -0.121 0.084

pacf(gw.r, main="Parial autocorrelation of remainders")

Parial autocorrelation of remainders

0.8
0.6
Partial ACF

0.4
0.2
0.0

0.5 1.0 1.5 2.0

Lag

Q38 : What are the partial autocorrelations that are different from zero?
How does this differ from the partial autocorrelations of the original
series? What is the interpretation? Jump to A38 •

47
3.6 Spectral analysis

Another second-order summary is provided by spectral analysis. This is

based on the theory, due to Fourier, that any second-order stationary se-
ries (i.e., with trend removed and auto-covariance not dependent on po-
sition in the series) can be decomposed into sums of sines and cosines
with increasing frequencies, each of varying amplitude or “power”. In
some cases we can guess these already (e.g., annual cycles for the ground-
water wells), but for some series we do not know a priori. The peri-
odogram also reveals the relative density (roughly, importance of the
component) at each frequency..
The frequency ω is defined as the number of divisions of one cycle. So
for a one-year cycle (as in the groundwater levels), ω = 12 is a monthly
frequency. By the Nyquist-Shannon sampling theorem, a function is com-
pletely determined by sampling at a rate of 1/2ω, so that if we have a
time series with n samples per cycle we can estimate spectral densities
for n/2 frequencies.
The theoretical decomposition of the covariance sequence γt into spec-
tral densities f is:

1 +1/2 2π iωt
Z
γt = e f (2π ωf )dωf
2π −1/2
where ωf is the frequency expressed as cycles per unit of time.
This can be inverted to give the density at each frequency:
" ∞
X
#
f (ω) = γ0 1 + 2 ρt cos(ωt)
i

where γ0 is the overall covariance.

The spectral density is estimated by the periodogram, which relates the
density to frequency. The periodogram at a given frequency ω is defined
as the squared correlation between the time series X and the sine/cosine
waves at that frequency:

2
1
X
−iωt

I(ω) = e X t

n t

The spectrum function computes and graphs the power spectrum. By

default it removes any linear trend, it tapers the series at its ends, and it
presents the spectrum on a logarithmic scale.
The spectrum is scaled by 1/ω, i.e., the inverse of the frequency, so
that the spectral density is computed over the range −ω/2 . . . + ω/2;
since the function is symmetric, it is displayed for 0 . . . + ω/2. In the
groundwater example, the frequency is 12 and so the decomposition is
from 0 . . . 6 periods per cycle. One period per cycle is annual, 6 periods
is bi-monthly.

48
The raw spectrum is too noisy to interpret, so it is usually smoothed with
so-called Daniell windows, which give half-weight to end values. The
window width is specified with the spans optional argument; optional
values are trial-and-error, until the main features of the periodogram are
revealed.

Task 37 : Compute and display a smoothed periodogram of the ground-

water levels, on the default logarithmic scale. •
s <- spectrum(gw, spans=c(5,7)); grid()
str(s)

## List of 16
## $ freq : num [1:180] 0.0333 0.0667 0.1 0.1333 0.1667 ...
## $ spec : num [1:180] 7.5 7.28 6.92 6.43 5.62 ...
## $ coh : NULL
## $ phase : NULL
## $ kernel :List of 2
## ..$ coef: num [1:6] 0.1667 0.1562 0.125 0.0833 0.0417 ...
## ..$ m : int 5
## ..- attr(*, "name")= chr "mDaniell(2,3)"
## ..- attr(*, "class")= chr "tskernel"
## $ df : num 14.3
## $ bandwidth: num 0.0726
## $ n.used : int 360
## $ orig.n : int 360
## $ series : chr "x"
## $ snames : NULL
## $ method : chr "Smoothed Periodogram"
## $ taper : num 0.1
## $ pad : num 0
## $ detrend : logi TRUE
## $ demean : logi FALSE
## - attr(*, "class")= chr "spec"

head(s$spec, n=12)

## [1] 7.4972852 7.2767232 6.9218806 6.4268515 5.6236966 4.4911276

## [7] 3.3260429 2.4309815 1.8019706 1.3133122 0.9278068 0.6206158

49
Series: x
Smoothed Periodogram

5e+00
5e−01
spectrum

5e−02
5e−03

0 1 2 3 4 5 6

frequency
bandwidth = 0.0726

Note that the spectrum is displayed on logarithmic scale in the plot. The
blue vertical line (upper right corner) gives the 95% confidence interval
that the reported density is different from zero.
The x-axis of the spectrum shows the period, i.e., the inverse of the de-
clared frequency. For example “1” is a full period (one cycle), “2” is half a
cycle, “3” is one-third of a cycle, etc.; these are the harmonics. So in this
example with ω = 12, the spectral density at x = 1 is for one cycle (12
months, one year) and the density at x = 2 is for a half-cycle (6 months,
half-year).
The resolution of the decomposition is determined by the length of the
time series (here, 360 observations); the resulting spectral decomposi-
tion is half this length (here, 360/2 = 180), and this is estimated by the
number of total cycles in the series (here, 360/12 = 30 annual cycles),
so the finest period is ω/2, here 12/2 = 6, each period divided into total
cycles:
frequency(gw)

## [1] 12

length(gw)/frequency(gw)

## [1] 30

head(s$freq,n=length(gw)/frequency(gw))

## [1] 0.03333333 0.06666667 0.10000000 0.13333333 0.16666667 0.20000000

## [7] 0.23333333 0.26666667 0.30000000 0.33333333 0.36666667 0.40000000
## [13] 0.43333333 0.46666667 0.50000000 0.53333333 0.56666667 0.60000000
## [19] 0.63333333 0.66666667 0.70000000 0.73333333 0.76666667 0.80000000
## [25] 0.83333333 0.86666667 0.90000000 0.93333333 0.96666667 1.00000000

50
Q39 : At what frequencies are the largest periodic components of the
Fourier decomposition? What is the interpretation? Jump to A39 •

We find the largest components by sorting the spectrum, using the sort
function with the optional index.return argument to save the positions
of each sorted element in the original vector, and grouping nearby peaks.
ss <- sort(s$spec, decreasing=T, index.return=T)
str(ss)

## List of 2
## $ x : num [1:180] 7.5 7.28 6.92 6.43 5.62 ...
## $ ix: int [1:180] 1 2 3 4 5 6 7 30 29 31 ...

hi <- ss$x>.15
which(hi)

## [1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22
## [23] 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39

ss$x[hi]

## [1] 7.4972852 7.2767232 6.9218806 6.4268515 5.6236966 4.4911276

## [7] 3.3260429 2.8008863 2.6526631 2.6311885 2.4309815 2.1987844
## [13] 2.1528798 1.8019706 1.5936610 1.5100103 1.3133122 0.9948927
## [19] 0.9278068 0.8599072 0.6206158 0.5479999 0.3993403 0.3815691
## [25] 0.3620958 0.3602574 0.3351769 0.3055965 0.2987287 0.2668042
## [31] 0.2600752 0.2258021 0.2248440 0.2041092 0.2024376 0.1789095
## [37] 0.1699968 0.1681654 0.1557876

ss$ix[hi]

## [1] 1 2 3 4 5 6 7 30 29 31 8 28 32 9 27 33 10 26 11 34 12 25
## [23] 13 24 35 23 22 14 21 15 20 19 16 18 17 60 61 59 36

sort(s$freq[ss$ix[hi]])

## [1] 0.03333333 0.06666667 0.10000000 0.13333333 0.16666667 0.20000000

The list of indices is in units of inverse frequency; we can see three peaks:
near zero (corresponding to no cycles, i.e., the mean), near one (annual),
and centred on two (6-month); this harmonic is not provably different
from zero.
The log scale display for the spectral density is the default in order
to more easily show the lower-power components. The raw density is
shown by specifying the optional log="no" argument; specifying log="dB"
argument shows the spectrum as decibels9 as is conventional in signal
processing.

Task 38 : Compute and display the periodogram of the groundwater

levels, on three scales: linear, log, and decibel. •
9
10 · log 10(I(ω))

51
par(mfrow=c(1,3))
spectrum(gw, spans=c(5,7), log="no", main="Anatolia groundwater level",
sub="annual cycle, smoothed")
grid()
spectrum(gw, spans=c(5,7), log="yes", main="Anatolia groundwater level",
sub="annual cycle, smoothed")
grid()
spectrum(gw, spans=c(5,7), log="dB", main="Anatolia groundwater level",
sub="annual cycle, smoothed")
grid()
par(mfrow=c(1,1))

Anatolia groundwater level Anatolia groundwater level Anatolia groundwater level

10
5e+00

5
6

0
5e−01

spectrum (dB)
spectrum

spectrum

−5
4

−10
5e−02

−15
2

−20
5e−03
0

0 1 2 3 4 5 6 0 1 2 3 4 5 6 0 1 2 3 4 5 6

frequency frequency frequency

annual cycle, smoothed annual cycle, smoothed annual cycle, smoothed

The annual cycle is well-known; indeed we have already (§3.3) decom-

posed the time series into trend, cycle and remainder. By removing the
dominant cycle we may get a sharper view of other frequencies.

Task 39 : Compute and display the periodogram of the groundwater

levels, after removing trend and annual cycles. •
sp.gw <- spectrum(gw.r, span=c(5,7), log="dB", main="Periodogram, residuals",
sub="annual cycle, smoothed")
grid()

52
Periodogram, residuals

0
−5
spectrum (dB)

−10
−15
−20
−25

0 1 2 3 4 5 6

frequency
annual cycle, smoothed

Notice that there is no peak corresponding to one year; this has been
removed with the annual cycle. There are also no peaks at the harmonics
(1/2, 1/3 etc. years).
Zooming in on the first two frequencies, i.e., one and one-half year, with
two different views:
par(mfrow=c(1,2))
spectrum(gw.r, span=c(5,7), log="no", main="Periodogram, residuals",
sub="annual cycle, smoothed", xlim=c(0,2), type="h")
grid()
s <- spectrum(gw.r, span=c(5,7), log="dB", main="Periodogram, residuals",
sub="annual cycle, smoothed", xlim=c(0,2))
grid()
sp.gw$freq[which.max(s$spec)]

## [1] 0.2333333

frequency(gw)/(s$freq[which.max(s$spec)])

## [1] 51.42857

which.max(s$spec[16:30])

## [1] 8

sp.gw$freq[which.max(s$spec[16:30])+15]

## [1] 0.7666667

frequency(gw)/(s$freq[which.max(s$spec[16:30])+15])

## [1] 15.65217

par(mfrow=c(1,1))

53
Periodogram, residuals Periodogram, residuals

0
1.5

−5
spectrum (dB)
spectrum

1.0

−10
−15
0.5

−20
0.0

−25
0.0 0.5 1.0 1.5 2.0 0.0 0.5 1.0 1.5 2.0

frequency frequency
annual cycle, smoothed annual cycle, smoothed

Q40 : What are the periods of the highest spectral densities? How can
these be explained physically? Jump to A40 •

3.7 Answers

A21 : Until 1981 the amplitude is small, less than 2 m. It then increases but
there are year-to-year differences. In 2002 the amplitude was highest. Return
to Q21 •

A22 : There is a definite annual cycle: September has the deepest levels (at
the end of the extractive period) and April the shallowest (at the end of the
winter rains). Winter months are a bit more variable than summer. Obvious
outliers from the overall pattern are the deep levels in one December – March
period. Return to Q22 •

A23 : The monthly series has thrice the points and thus more detail; however
the pattern remains clear and the high/low values for each cycle are not much
different, so the lower temporal resolution does not much affect interpretation.
Return to Q23 •

A24 : The peaks and valleys are less extreme, and some month-to-month
irregularities are removed. Return to Q24 •

A25 : The peaks and valleys are further smoothed, month-to-month irregular-
ities are removed. Return to Q25
•

A26 : The annual cycle is removed, this shows the year-to-year variation.

54
Return to Q26 •

A27 : The default parameter (2/3) shows the overall trend (increasing ground-
water) depth) slightly adjusted for local phenonomena; increasing the param-
eter to 1 removes almost all variation and results in almost a straight line;
decreasing to 1/3 adjusts more closely to trends that go over a few years, for
example the initial overall decrease in depth for the first three years, and the
unusual extraction in 1988. The paramater value 1/10 adjusts very closely to
each year and obscures the overall trend. The parameter value of 1/3 seems
most useful here. Return to Q27 •

A28 : Numerically, the mean is zero and the numbers represent deviations
from the cycle at each position in it. Thus at the earlier years the groundwater
is shallower (negative values), later it is deeper (positive values). For most of
the series the seasonal fluctuations have been mostly removed, but prior to
1980 they are amplified. This is because in that period there was not much
seasonal fluctuation, so averaging the cycle over all years amplifies these early
small fluctuations. Return to Q28 •

A29 : The decomposed series has class stl and consists of three named time
series: “seasonal”, “trend”, and “remainder”, organized as a matrix of class mts
(“multiple time series”) with three columns (one for each series). Return to
Q29 •

A30 : The average seasonal component has amplitude ≈ ±1.5m depth; the
trend ranges over 25m depth and generally increases, after an initial decrease;
the remainder ranges from ≈ −2 . . . 4.5m, but all except 1988 are within a
more restricted range, ≈ ±1.5m. The remainders show strong auto-correlation
within each cycle. Thus the trend is by far the largest componet; the seasonal
and remainer are similar orders of magnitude. Return to Q30 •

A31 : The seasonal component can change with time; here the amplitude
increases until about 2000 and then stabilizes. The cycles themselves may
have different shapes: note the “shoulder” in the decreasing level in 1983-
1990, which is absent from later yeard. The amplitude of the remainder has
been reduced, because the cycles are more closely fit. Return to Q31 •

A32 : The smoother decomposition has a smoother trend (of course); the
seasonal component is the same, so the remainders are larger and their serial
auto-correlation extends over a longer span. The smooth trend seems to repre-
sent a long-term change in groundwater, probably due to increasing extraction
for agriculture. The rough trend has noise that does not seem to be due to a
long-term process. Return to Q32 •

A33 : The auto-correlations gets weaker for the first six or seven months, but

55
then strengthens; this reflects the annual cycles. Return to Q33 •

A34 : The detailed scatterplot shows which measurements are more or less
correlated to the lagged measurement; also the lines show an evolution of this
over time: i.e., whether the correlation is systematically greater or less. Return
to Q34 •

A35 : Groundwater levels are highly positively correlated, decreasing from

0.9878 at lag 1 to 0.7965 at two years (24 months). The correlation increases
locally at cycle lengths (one and two years, i.e., 12 and 24 months).
Physically, this reflects the fact that groundwater level can not fluctuate rapidly
month-to-month; the change in level must be smooth. Return to Q35 •

A36 : The remainders are positively autocorrelated within one year (up to 11
months); they are then not different from zero (no correlation) until the 16th
month, after which the autocorrelation is increasingly negative.
The removal of the trend has taken away most of the autocorrelation due to
the continuous nature of groundwater level change. Removal of the cycle has
taken away any autocorrelation due to seasonality (i.e., extraction and recharge
at the same seasons each year), which is reflected in the lack of correlation in
the year to year remainders (lag 12).
The remainder represents the local effects after accounting for trend and cycle.
There is positive autocorrelation within one year, because in a wet (or dry) year
the level can not fluctuate rapidly and so tends to stay relatively high (or low).
The negative autocorrelation between subsequent years means that relatively
wet (dry) years tend to be followed by relatively dry (wet) remainders, i.e., after
accounting for trend and cycle. Return to Q36 •

A37 : Lag 2 has a substantial negative partial autocorrelation: -0.2415. Then

months 5 – 9 have slightly positive partial autocorrelations; the negative partial
autocorrelation appears again at 12 and 13 months. Return to Q37 •

A38 : The only partial autocorrelation provably different from zero is the first
lag (one month). Once this is accounted for, the other lags have no autocorre-
lation. The remainders have only a one-month autocorrelation, and thus could
be modelling by a first-order autoregressive process (§4.4.1). Return to Q38 •

A39 : At frequency 1 (one year) there is a large component (-9 dB); i.e., a
strong annual cycle. There is also a much weaker component (-16.51 dB) at the
six-month frequency. Return to Q39 •

A40 : The highest spectral density is at 7/30 = 0.23̄ cycles per year, i.e.,
51.4 months per cycle, or about 4 years 3 months. A much smaller peak is
at 23/30 = 0.76̄ cycles per year, i.e., 15.7 months, or about 1 year 3 months.
These seem to be artefacts of the particular data series. Return to Q40 •

56
4 Modelling a time series

A model of a time series is a mathematical formulation that summarizes

the series. This formulation has a model form and several parameters.
A simple example is modelling monthly temperature as a sine wave; this
would have a mean, amplitude, and phase (the period would be defined
as one year). The twelve monthly temperatures could then be recovered
from these three parameters.
There are several aims of modelling a time series:
1. Understand the underlying process(es) that produced it;
2. Use the model to predict into the future (forecasting), at missing
data points, or into the past;
3. Use the model to simulate similar time series (§8).
We begin with an examination of some model forms. These arise from
different processes in time. A requirement of successful time series
modelling is to fit the model form to the actual process. We may have
some idea of the process from physical or social principles. Or, we can
see which model form best fits the series, and hope that this continues
into the future for forecasting.

4.1 Modelling by decomposition

We have already seen (§3.3) that a time series can be decomposed into
a trend, cycle, and residual using the stl function. The residual is by
definition noise in this decomposition, the other two components are a
model, representing the long-term and cyclic behaviour of the series.
The problem with this approach is that the trend removal is empirical:
its smoothness must be adjusted by the analyst. Recall the two decom-
positions of the groundwater data, with different smoothness:
plot(stl(gw, s.window="periodic")$time.series,
main="Well 1, periodic decomposition")

57
Well 1, periodic decomposition

1.5
seasonal
0.5
−0.5
55 −1.5
50
trend
45
40
35
4 30
3
remainder
2
1
0
−2

1975 1980 1985 1990 1995 2000 2005

Time

plot(stl(gw, s.window=25, t.window=85)$time.series,

main="Anatolia well 1, s=25, t=85 decomposition")

58
Anatolia well 1, s=25, t=85 decomposition

2
1
seasonal
0
−1
55 −2
50
trend
45
40
35
6
remainder
4
2
0
−2

1975 1980 1985 1990 1995 2000 2005

Time

The first decomposition makes no assumptions other than the annual

cycle; the second specifies a (1) s.window, the span (number of lags)
of the loess window for seasonal extraction; (2) t.window, the span for
trend extraction. There is no theoretical way to determine these.
The decomposition gives insight into the processes underlying the time
series.

Q41 : What could be the processes that control groundwater level in

this well, as revealed by the decomposition? Jump to A41 •

However, there is no way to extrapolate (predict), because there is no

model of the underlying process for the trend, nor of the amplitude of
the period, only an empirical fit. We now examine some models that do
allow prediction.

4.2 Modelling by OLS linear regression

The standard techniques of linear modelling can be applied to the time

series, considering each observation as a function of time and position
in the cycle. This may include interactions between cycle and position.
However, cyclic components are better-handled by decomposition (§4.1);
regression is more typically used to model a trend over time. Linear
models can also be used for interpolation (gap filling) and extrapolation

59
(prediction).

Task 40 : Build a linear model of the trend in groundwater level, and

evaluate its success and suitability. •
The lm function computes linear models, using predictors and responses
from a dataframe; thus the dataframe gw.f must be used instead of the
raw time series.
m.gw <- lm(gw ~ time, data=gw.f)
summary(m.gw)

##
## Call:
## lm(formula = gw ~ time, data = gw.f)
##
## Residuals:
## Min 1Q Median 3Q Max
## -4.9134 -1.8445 -0.3193 1.4857 6.6562
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) -1.576e+03 3.053e+01 -51.64 <2e-16 ***
## time 8.130e-01 1.534e-02 53.00 <2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 2.521 on 358 degrees of freedom
## Multiple R-squared: 0.887,Adjusted R-squared: 0.8867
## F-statistic: 2809 on 1 and 358 DF, p-value: < 2.2e-16

Task 41 : Plot the time series, with the fits from the linear model
superimposed. •
plot(gw.f$time, gw.f$gw, type="l", col="darkgreen",
ylab="Groundwater level (m)", xlab="Year")
title("Anatolia well 1, linear trend")
lines(x=as.numeric(gw.f$time), y=fitted(m.gw), col="red")

60
Anatolia well 1, linear trend

55
50
Groundwater level (m)

45
40
35
30

1975 1980 1985 1990 1995 2000 2005

Year

Q42 : How much of the variation in groundwater level is explained by

this model? How well does it appear to explain the trend? What is the
average annual increase in depth? Jump to A42 •

Note that the adjusted R 2 and slope can be extracted from the model
object:
summary(m.gw)$adj.r.squared

## [1] 0.8866509

coefficients(m.gw)["time"]

## time
## 0.8130209

Task 42 : Display a diagnostic plot of residuals vs. fitted values. •

plot(m.gw, which=1)

61
Residuals vs Fitted

8
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2
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●
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−6

30 35 40 45 50

Fitted values
lm(gw ~ time)

The diagnostic plot shows that this model violates one assumption of
linear modelling: there be pattern to the residuals with respect to fitted
values; most of the problem is at low fitted values, i.e., the beginning
of the time series. There is also a large discrepency near 40 m, which
corresponds to the anomalous year 1988.

4.3 Modelling by GLS linear regression

If residuals are correlated in time (as in this case), the OLS regression
is not optimal. Instead, the trend should be fit by Generalized Least
Squares (GLS).
In OLS the residuals ε are assumed to be independently and identically
distributed with the same variance σ 2 :

y = Xβ + ε, ε ∼ N (0, σ 2 I) (5)

Whereas, in GLS residuals are considered to be a random variable η that

has a covariance structure:

y = Xβ + η, η ∼ N (0, V) (6)

where V is a positive-definite variance-covariance matrix of the model

residuals. In a time series, the covariances in this matrix (off-diagonals)
are naturally based on the time distance between observations, using
some model of temporal correlation, e.g. AR(1) (§4.4.1, below).
The solution is:

β̂GLS = (XT V−1 X)−1 XT V−1 y (7)

62
where V the variance-covariance matrix of the residuals V = σ 2 C, where
σ 2 is the variance of the residuals and C is the correlation matrix.
The computations are performed with the gls function of the nlme ‘Non-
linear mixed effects models’ package [2].

Task 43 : Set up and solve a GLS model, using the covariance structure
estimated from the variogram of the OLS residuals. •
The linear model formulation is the same as for lm. However:
• It has an additional argument correlation, which specifies the
correlation structure.
• This is built with various correlation models; we use corAR1 for
AR(1) temporal correlation. This requires two arguments:
– value the value of the lag 1 autocorrelation, which must be
between -1 and 1;
– form a one-sided formula specifying the time covariate, if any.
In this case there is no covariate, so only an intercept is speci-
fied as ~1.
The value can be changed during optimization and will be reported
in the results.
We obtain the initial value from the acf function; the second value is the
one-lag autocorrelation.

Note: For a list of the predefined model forms see ?corClasses. Users
can also define their own corStruct classes.
library(nlme)
(cor.value <- acf(gw, plot=FALSE)$acf[2])

## [1] 0.9878291

summary(m.gw.gls <- gls(model=gw ~ time, data=gw.f,

correlation=corAR1(value=cor.value, form = ~1)))

## Generalized least squares fit by REML

## Model: gw ~ time
## Data: gw.f
## AIC BIC logLik
## 908.7075 924.2297 -450.3538
##
## Correlation Structure: AR(1)
## Formula: ~1
## Parameter estimate(s):
## Phi
## 0.9571062
##
## Coefficients:
## Value Std.Error t-value p-value
## (Intercept) -1500.4356 200.05311 -7.500186 0
## time 0.7751 0.10053 7.709787 0
##
## Correlation:
## (Intr)
## time -1

63
##
## Standardized residuals:
## Min Q1 Med Q3 Max
## -1.9019852 -0.7551349 -0.2290400 0.4591564 2.1482906
##
## Residual standard error: 2.911948
## Degrees of freedom: 360 total; 358 residual

coef(m.gw)

## (Intercept) time
## -1576.2972795 0.8130209

coef(m.gw.gls)

## (Intercept) time
## -1500.4355894 0.7750657

Q43 : What is the estimate of the AR(1) temporal correlation returned

by gls? How does this compare with the initial value estimated with
pacf? Jump to A43 •

Task 44 : Plot this GLS trend on the time series, with the OLS trend for
comparison. •
plot(gw.f$time, gw.f$gw, type="l", col="darkgreen",
ylab="Groundwater level (m)", xlab="Year")
title("Anatolia well 1, linear trend")
abline(m.gw.gls, col="darkgreen")
lines(x=as.numeric(gw.f$time), y=fitted(m.gw), col="red")
legend("topleft", c("GLS","OLS"), lty=1, col=c("darkgreen","red"))

Anatolia well 1, linear trend

GLS
OLS
55
50
Groundwater level (m)

45
40
35
30

1975 1980 1985 1990 1995 2000 2005

Year

Q44 : How has the slope of the trend changed from the OLS to GLS

64
model? Jump to A44 •

Higher-order trend The trend seems to have two inflection points (around
1980 and 1985), so perhaps fitting a cubic trend might give a better
model. The anova function compares two models.
m.gw.3 <- lm(gw ~ I(time^3) + time, data=gw.f)
summary.lm(m.gw.3)

##
## Call:
## lm(formula = gw ~ I(time^3) + time, data = gw.f)
##
## Residuals:
## Min 1Q Median 3Q Max
## -4.7362 -1.9403 -0.1648 1.6461 7.4775
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 2.864e+04 4.985e+03 5.746 1.96e-08 ***
## I(time^3) 1.917e-06 3.163e-07 6.062 3.42e-09 ***
## time -2.197e+01 3.758e+00 -5.845 1.14e-08 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 2.403 on 357 degrees of freedom
## Multiple R-squared: 0.8975,Adjusted R-squared: 0.8969
## F-statistic: 1563 on 2 and 357 DF, p-value: < 2.2e-16

anova(m.gw.3, m.gw)

## Analysis of Variance Table

##
## Model 1: gw ~ I(time^3) + time
## Model 2: gw ~ time
## Res.Df RSS Df Sum of Sq F Pr(>F)
## 1 357 2062.1
## 2 358 2274.4 -1 -212.25 36.746 3.424e-09 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

plot(gw.f$time, gw.f$gw, type="l", col="darkgreen",

ylab="Groundwater level (m)", xlab="Year")
title("Anatolia well 1, cubic trend")
lines(x=as.numeric(gw.f$time), y=fitted(m.gw.3), col="red")

65
Anatolia well 1, cubic trend

55
50
Groundwater level (m)

45
40
35
30

1975 1980 1985 1990 1995 2000 2005

Year

Q45 : Is the cubic trend model better than the linear trend? Jump to
A45 •

Splitting the series Clearly the series to about 1978 is different from
that after; perhaps the extraction did not begin until then?

Task 45 : Model the trend since 1978 with both an OLS and a GLS
model. •
The subset function is used to limit the time series in the dataframe. We
have to re-compute the starting values for the autocorrelation parameter
of the GLS model from just this part of the series.
gw.f.78 <- subset(gw.f, gw.f$year > 1977)
summary(m.gw.78 <- lm(gw ~ time, data=gw.f.78))

##
## Call:
## lm(formula = gw ~ time, data = gw.f.78)
##
## Residuals:
## Min 1Q Median 3Q Max
## -5.0422 -1.4399 -0.0702 1.3550 7.3310
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) -1763.3608 30.4744 -57.86 <2e-16 ***
## time 0.9068 0.0153 59.26 <2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 2.147 on 322 degrees of freedom
## Multiple R-squared: 0.916,Adjusted R-squared: 0.9157
## F-statistic: 3511 on 1 and 322 DF, p-value: < 2.2e-16

66
(cor.value <- acf(gw.f.78, plot=FALSE)$acf[2])

## [1] 0.9841868

summary(m.gw.78.gls <- gls(model=gw ~ time, data=gw.f.78,

correlation=corAR1(value=cor.value, form = ~1)))

## Generalized least squares fit by REML

## Model: gw ~ time
## Data: gw.f.78
## AIC BIC logLik
## 843.0141 858.1123 -417.507
##
## Correlation Structure: AR(1)
## Formula: ~1
## Parameter estimate(s):
## Phi
## 0.9224721
##
## Coefficients:
## Value Std.Error t-value p-value
## (Intercept) -1764.3798 143.9822 -12.25416 0
## time 0.9073 0.0723 12.54906 0
##
## Correlation:
## (Intr)
## time -1
##
## Standardized residuals:
## Min Q1 Med Q3 Max
## -2.23240755 -0.64109407 -0.03336087 0.59381099 3.23268822
##
## Residual standard error: 2.265006
## Degrees of freedom: 324 total; 322 residual

plot(gw.f.78$time, gw.f.78$gw, type="l", col="darkgreen",

ylab="Groundwater level (m)", xlab="Year")
title("Anatolia well 1, linear trend since 1978")
lines(x=as.numeric(gw.f.78$time),
y=fitted(m.gw.78.gls), col="red")
abline(m.gw.78, col="red")
abline(m.gw.78.gls, col="darkgreen")
legend("topleft", c("GLS","OLS"), lty=1, col=c("darkgreen","red"))

Anatolia well 1, linear trend since 1978

GLS
55

OLS
Groundwater level (m)

50
45
40
35
30

1980 1985 1990 1995 2000 2005

Year

For this portion of the time series the GLS and OLS models are almost
identical:
coef(m.gw.78)

## (Intercept) time

67
## -1763.3607555 0.9067699

coef(m.gw.78.gls)

## (Intercept) time
## -1764.379848 0.907287

Task 46 : Compare the GLS model since 1978 with the GLS model for
the whole series. •
coefficients(m.gw.gls)["time"]

## time
## 0.7750657

coefficients(m.gw.78.gls)["time"]

## time
## 0.907287

Q46 : Is the average annual change different for the model fit on the
entire series versus the model fit on the post-1977 section? Which would
you use in extrapolating into the future? Jump to A46 •

Task 47 : Predict the groundwater level in January 2010. •

The generic predict method specialized to the predict.lm function
when applied to a linear model object. The confidence interval of the
fit is returned if the interval argument is provided; the "prediction"
option returns the upper and lower bounds of the prediction at the spec-
ified confidence level:
predict(m.gw.78, data.frame(time=2010), interval="prediction", level=0.9)

## fit lwr upr

## 1 59.24676 55.66909 62.82443

Task 48 : Predict the groundwater level from 2005 to 2055; graph this
with its 95% confidence interval of prediction. •
Again we use the predict.lm method, this time with a sequence of times
at which to predict.
gw.2050 <- predict.lm(m.gw.78, data.frame(time=2005:2050),
interval="prediction", level=0.95)
str(gw.2050)

## num [1:46, 1:3] 54.7 55.6 56.5 57.4 58.3 ...

## - attr(*, "dimnames")=List of 2
## ..$ : chr [1:46] "1" "2" "3" "4" ...
## ..$ : chr [1:3] "fit" "lwr" "upr"

plot(gw.f$time, gw.f$gw, type="l", col="darkgreen",

ylab="Groundwater level (m)", xlab="Year",
xlim=c(1978,2050),
ylim=c(floor(min(gw.f$gw)),ceiling(max(gw.2050[,"upr"])) ))
title("Anatolia well 1, linear trend since 1978")

68
grid()
abline(v=2005, lty=2)
lines(x=as.numeric(gw.f$time[gw.f$year > 1977]),
y=fitted(m.gw.78), col="blue")
lines(2005:2050, gw.2050[,"fit"])
lines(2005:2050, gw.2050[,"upr"], col="red", lty=2)
lines(2005:2050, gw.2050[,"lwr"], col="red", lty=2)
text(1990,60,"fit", col="blue")
text(2030,60,"extrapolation")

Anatolia well 1, linear trend since 1978

100
90
80
Groundwater level (m)

70
60

fit extrapolation
50
40
30

1980 1990 2000 2010 2020 2030 2040 2050

Year

Q47 : Do you expect the groundwater level to be below 80 m by 2040?

What factors determine how long the modelled trend may continue in
the future? Jump to A47 •

4.3.1 Modelling a decomposed series

If we are interested in modelling an overall trend, the seasonal com-

ponent of a series is not interesting. Recall that this component can
be identified by decomposition (§3.3); if this is removed the smoothed
trend and residual components can be used as the basis of trend mod-
elling. The residual noise quantifies the uncertainty of the parametric
fit.

Task 49 : Fit a linear trend to the non-seasonal component of the

groundwater level. •
We first add a field to the time series dataframe and then use it for
modelling. Again, the trend since 1978 is modelled.
gw.stl <- stl(gw, s.window=2*frequency(gw)+1)
gw.f$nonseas <- gw.stl$time.series[,"trend"] + gw.stl$time.series[,"remainder"]
str(gw.f)

69
## 'data.frame': 360 obs. of 6 variables:
## $ gw : Time-Series from 1975 to 2005: 34.4 34.5 34.7 34.8 34.9 ...
## $ year : num 1975 1975 1975 1975 1975 ...
## $ cycle : num 1 2 3 4 5 6 7 8 9 10 ...
## $ time : Time-Series from 1975 to 2005: 1975 1975 1975 1975 1975 ...
## $ in.yr : num -0.818 -0.727 -0.477 -0.378 -0.297 ...
## $ nonseas: Time-Series from 1975 to 2005: 34.5 34.8 35.3 35.8 35.6 ...

m.gw.nonseas <- lm(nonseas ~ time, data=subset(gw.f, gw.f$year > 1977))

summary(m.gw.nonseas)

##
## Call:
## lm(formula = nonseas ~ time, data = subset(gw.f, gw.f$year >
## 1977))
##
## Residuals:
## Min 1Q Median 3Q Max
## -3.9693 -0.9538 -0.1106 0.8762 8.2621
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) -1.757e+03 2.558e+01 -68.70 <2e-16 ***
## time 9.036e-01 1.284e-02 70.36 <2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 1.802 on 322 degrees of freedom
## Multiple R-squared: 0.9389,Adjusted R-squared: 0.9387
## F-statistic: 4950 on 1 and 322 DF, p-value: < 2.2e-16

plot(gw.f$time, gw.f$gw, type="l", col="darkgreen",

ylab="Groundwater level (m)", xlab="Year")
title("Anatolia well 1, linear trend since 1978, non-seasonal component")
lines(x=as.numeric(gw.f$time), y=gw.f$nonseas, col="blue")
lines(x=as.numeric(gw.f$time[gw.f$year > 1977]),
y=fitted(m.gw.nonseas), col="red")
text(1995, 38, col="darkgreen", pos=4, "time series")
text(1995, 36, col="blue", pos=4, "non-seasonal component")
text(1995, 34, col="red", pos=4, "linear trend")

Anatolia well 1, linear trend since 1978, non−seasonal component

55
50
Groundwater level (m)

45
40

time series

non−seasonal component
35

linear trend
30

1975 1980 1985 1990 1995 2000 2005

Year

70
Task 50 : Compare this linear model (with the seasonal component
removed) to the linear model of the series since 1978 computed in the
previous subsection. Consider (1) the amount of variability explained;
(2) the slope of the trend. •
(tmp <- summary(m.gw.nonseas)$adj.r.squared -
summary(m.gw.78)$adj.r.squared)

## [1] 0.02299186

tmp/summary(m.gw.78)$adj.r.squared

## [1] 0.02510743

coefficients(m.gw.nonseas)["time"]

## time
## 0.9035588

coefficients(m.gw.78)["time"]

## time
## 0.9067699

Q48 : By how much does the proportion of variability explained by the

model change when the seasonal component is removed before mod-
elling the trend? Jump to A48
•

Q49 : By how much does the slope of the trend change when the sea-
sonal component is removed before modelling the trend? Jump to A49
•

4.3.2 Non-parametric tests for trend

A non-parametric test is one that does not assume any underlying distri-
bution. In the trend analysis of the previous section (§4.3.1) we assumed
that the residuals (after accounting for seasonality and trend) was inde-
pendently and identically normally-distributed (IIND); this is a require-
ment for using ordinary least squares (OLS) to fit a linear model.

Task 51 : Check that the residuals of the trend analysis are IID. •
There are various formal tests, but we will visualize the regression di-
agnostics with the plot function applied to linear model results, using
the which argument to select graphs 1 (residuals vs. fitted values) and 2
(normal quantile-quantile plot of residuals).
par(mfrow=c(1,2))
plot(m.gw.nonseas, which=1:2)
par(mfrow=c(1,1))

71
Residuals vs Fitted Normal Q−Q

159 ● 159 ●

8
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Fitted values Theoretical Quantiles

Q50 : Do the residuals appear to be IIND? Jump to A50 •

Since the residuals do not meet the criteria for OLS, the confidence inter-
vals computed for the slope may not be accurate; further the apparent
trend may not be real. In this case the trend is quite strong so this is
not an issue. Still, we discuss how to detect trend in a series where OLS
models are not justified.
One approach is to use a robust regression [3] to estimate the trend its
confidence limits.
Another approach is to use a non-parametric test. Hirsch et al. [11]
present the Mann-Kendall test for trend, which has been included in the
Kendall package written by Ian McLeod (co-author of [10]).

Task 52 : Check for a trend in the groundwater levels time series since
1978. •
The MannKendall function of the Kendall package computes this test
for a time series. The SeasonalMannKendall function does the same
under the alternative hypothesisis that for one or more months the sub-
sample is not distributed identically. In the present case the series is
clearly seasonal, so we can either compute the seasonal test for the se-
ries or the non-seasonal test for the decomposed series (i.e., we remove
the seasonality).These should give similar results.
require(Kendall)

## Loading required package: Kendall

gw.1978 <- window(gw, start=c(1978,1), end=c(2005,12), extend=TRUE)

SeasonalMannKendall(gw.1978)

## tau = 0.892, 2-sided pvalue =< 2.22e-16

gw.nonseas.1978 <- ts(subset(gw.f, gw.f$year > 1977)$nonseas)

MannKendall(gw.nonseas.1978)

## tau = 0.862, 2-sided pvalue =< 2.22e-16

72
The τ-value is a test statistic that is then compared to a theoretical value,
resulting in the probability that a τ-value this large could have occurred
by chance in a series with no true trend.

Q51 : What is the probability that there is no trend in this series? Jump
to A51 •

Hirsch et al. [11] also propose a non-parametric estimator of slope: com-

pute all differences between the same month in all pairs of years:
xij − xik
dijk = , i = 1 . . . 12, 1 ≤ k < j ≤ n
j−k

where n is the number of years. Then, estimate the slope B by their

median. Note that if the number of positive and negative differences
are equal, the slope is estimated as zero (no trend). The differences
(xij − xik ) are for the twelve months indexed by i and the years indexed
by k < j and then normalized by the number of years between each pair
of values. So each dijk is a slope between two years for a given month.

Task 53 : Write a function to compute this non-parametric slope, also

displaying a histogram of the individual slope estimates. •
MKslope <- function(ts) {
f <- frequency(ts)
n <- length(ts)/f
d <- NULL
for (j in n:2)
for (k in (j-1):1)
for (i in 1:f)
d <- c(d, (ts[i + (j-1)*f] - ts[i + (k-1)*f])/(j-k));
hist(d, main="individual slope estimates", xlab="slope")
print(summary(d))
return(median(na.omit(d)))
}

Note the use of na.omit to account for the possibility of missing values
in the time series, and hence missing differences; this will be used in the
following example (§4.3.3).

Task 54 : Estimate the non-parametric slope with this function and

compare it to the parametric (OLS) estimate. •
The appropriate slope for comparison is the linear model of the decom-
posed series (with seasonality removed):
print(MKslope(gw.1978))

## Min. 1st Qu. Median Mean 3rd Qu. Max. NA's

## -6.9700 0.6877 0.9050 0.9132 1.1134 7.1400 324
## [1] 0.905

coefficients(m.gw.nonseas)["time"]

## time
## 0.9035588

73
individual slope estimates

2500
2000
1500
Frequency

1000
500
0

−5 0 5

slope

These are very close in this case.

4.3.3 A more difficult example

The trend is not always so obvious, and the deviations from IIND resid-
uals much stronger, in some time series. For example, the Kendall
package includes the sample dataset GuelphP, a monthly time series of
phosphorous (P) concentrations in mg l-1, Speed River, Guelph, Ontario,
January 1972 through January 1977.

Task 55 : Load this dataset and plot as a time series. •

data(GuelphP)
plot(GuelphP, type="b", ylab="P concentration, mg l-1",
main="Speed River water quality")

74
Speed River water quality

1.0
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1972 1973 1974 1975 1976 1977 1978

Time

Q52 : Describe this time series qualitatively (in words). Does there seem
to be a linear trend? Jump to A52 •

Task 56 : Test for a trend and, if present, estimate its slope. •

SeasonalMannKendall(GuelphP)

## tau = -0.562, 2-sided pvalue =1.758e-07

print(guelphP.b <- MKslope(GuelphP))

## Min. 1st Qu. Median Mean 3rd Qu. Max. NA's

## -1.042000 -0.135125 -0.056333 -0.090538 -0.002667 0.275000 20
## [1] -0.05633333

75
individual slope estimates

100
80
Frequency

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slope

Q53 : Is there a trend? If so, what is its slope? Is this slope meaningful?
Jump to A53 •

4.4 Autoregressive integrated moving-average (ARIMA) models

Box et al. [5] developed an approach to time series analysis known as

ARIMA (“autoregressive (AR) integrated (I) moving averages (MA)”), which
is especially useful for forecasting. We first examine the “AR” and “MA”
aspects, and then add the “I”.

4.4.1 Autoregressive (AR) models

The simplest model form is the autoregressive (AR) model. Here the
values in the series are correlated to some number of immediately pre-
ceding values. The strength of the correlation, relative to the white noise,
gives the continuity of the series.
The AR process is defined such that each Yt in the sequence is computed
from some set of previous values Ys , s < t, plus white noise Zt . This
white noise is independently and identicall distributed (IID) at each time
step.
This model implies an underlying process with no trend, where the the
value at one time point is partly retained at the next in an AR(1) process;
this can be considered inertia in the process. The autocorrelation is not
perfect, this allows white noise, i.e., completely random processes, to
alter the next value(s).
To simplify computations, the series is centred by subtracting the over-

76
all mean µ and considering the differences:
p
X
(Yt − µ) = αl (Yt−l − µ) + Zt (8)
l=1

where the Zt form a white noise (purely random) sequence {Zt }.

The order p of the process controls the number of previous values of
Yt considered; the magnitude of αl is the degree of autocorrelation with
the lth previous value. The new (Yt − µ) are computed from previous
values of (Yt−l − µ) up to the order, plus some new IID white noise {Zt }.

AR(1) models This model only considers the immediately preceding

value, along with white noise:

(Yt − µ) = α1 (Yt−1 − µ) + Zt (9)

This has the same form as a linear regression, and the single parameter
α1 can be computed in the same way.
This series is sometimes called a red noise process, because the white
noise represented by the sequence {Zt } has the high-frequency varia-
tions (“blue”, by analogy with the light spectrum) smoothed out by the
autocorrelation. The low-frequency (“red”) random variations are pre-
served.
In §3.5 we saw that the remainders for the groundwater levels of well 1
had no partial autocorrelations, after the first order was accounted for.
This indicates an AR(1) model.
Note that the mean of the remainders should be zero, if we’ve accounted
for the trend and cycles; in this case it is very close:
mean(gw.r)

## [1] -0.06420781

Task 57 : Estimate the autocorrelation parameter for the remainders

for the groundwater levels of well 1. •
First, examine the autocorrelation as a scatterplot; this was already done
in §3.4, using the lag.plot function:
lag.plot(gw.r, lags=1, main="Anatolia well 1 remainders, lag 1 scatterplot")

77
Anatolia well 1 remainders, lag 1 scatterplot

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lag 1

Clearly a linear relation between the series of remainders and its first
lagged series is justified. We compute this relation first with the stan-
dard lm method; note we must relate an observation to the preceding
observation (time flows in one direction!). We must first produce a time-
series offset by one month. We saw in §3.4 that the lag function lags
the time series but does not shift it; here we need a shift in order to
relate the previous month’s level to the current month’s level. The shift
is effected by subscripting, using the [] operator.
We first construct the two series, subtracting in each case the mean:
gw.r.0 <- gw.r[2:(length(gw.r)-1)] - mean(gw.r)
gw.r.1 <- lag(gw.r,1)[1:(length(gw.r)-2)] - mean(gw.r)

plot(gw.r.0 ~ gw.r.1, xlab="Lag 1",ylab="Original")

title(main="Anatolia well 1, remainders, series vs. lag-1 series")
m.lag1 <- lm(gw.r.0 ~ gw.r.1)
summary(m.lag1)

##
## Call:
## lm(formula = gw.r.0 ~ gw.r.1)
##
## Residuals:
## Min 1Q Median 3Q Max
## -5.9367 -0.2370 -0.0304 0.2109 1.5253
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 0.001855 0.029559 0.063 0.95
## gw.r.1 0.887310 0.024360 36.424 <2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 0.5593 on 356 degrees of freedom
## Multiple R-squared: 0.7884,Adjusted R-squared: 0.7878
## F-statistic: 1327 on 1 and 356 DF, p-value: < 2.2e-16

abline(m.lag1)

78
(alpha.1 <- cor(gw.r.0,gw.r.1))

## [1] 0.8879416

Anatolia well 1, remainders, series vs. lag−1 series

6
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Lag 1

Q54 : How much of the variation in the remainder of groundwater

level (after accounting for trend and seasonality) is accounted for by
knowledge of the remainder at the previous lag? Jump to A54 •

Note that the comparable figure for the uncorrected series is much higher,
because of the inherent continuity within the annual cycle:
cor(gw[2:(length(gw)-1)] - mean(gw),
lag(gw,1)[1:(length(gw)-2)] - mean(gw))

## [1] 0.9934396

The correlation coefficient should be the first autocorrelation calculated

with the acf “autocorrelation” function, as shown in §3.4.
acf(gw.r, lag.max=1, plot=F)$acf[2,,]

## [1] 0.8868833

Note: The slight difference between this estimate 0.8869 and the esti-
mate directly from linear correlation 0.8879 may be due to how the two
computations deal with the ends of the series.

Finally, the innovation variance is the variance of the white noise of Eq.
9. This is computed as [20, §8.3.1]:

σZ2 = (1 − α2 )σY2 (10)

where σY2 is the variance of the time series. That is, the noise is reduced
from the observed noise in the series by the autocorrelation – that much

79
of the noise is accounted for by the model. This illustrates the “red shift”
mentioned above. For sampled time series of length n, the series vari-
ance σY2 is estimated from the sample variance sY2 , the true correlation α
is estimated as α̂ and the noise must be corrected for bias:

n−1
sZ2 = (1 − α̂2 )sY2 (11)
n−2

In the current case:

var(gw.r)

## [1] 1.469715

(var.ar.1 <- (length(gw.r)-1)/(length(gw.r)-2) * (1 - alpha.1^2) * var(gw.r))

## [1] 0.3118009

We will return to this example and simulate an AR(1) series with this
these fitted parameters in §8.

AR(2), AR(3) . . . models In an AR(1) model the entire prior behaviour

of a series is given by the previous value and the one autocorrelation
coefficient; this is known as the first-order Markov process. For the
example series of remainders of groundwater level, we saw from the
partial autocorrelations that this is a reasonable assumption. However,
it is possible that the current state is also influenced by earlier states,
other than the immediately preceding one; this is the case for the original
series of groundwater levels:
par(mfrow=c(1,2))
pacf(gw)
pacf(gw.r)
par(mfrow=c(1,1))
pacf(gw, lag.max=5, plot=F)$acf

## , , 1
##
## [,1]
## [1,] 0.98782910
## [2,] -0.24150277
## [3,] -0.04679133
## [4,] 0.03321400
## [5,] 0.15111996

pacf(gw.r, lag.max=5, plot=F)$acf

## , , 1
##
## [,1]
## [1,] 0.88688330
## [2,] -0.08180894
## [3,] -0.02809817
## [4,] -0.02235775
## [5,] -0.02513076

80
Series gw Series gw.r

1.0

0.8
0.8

0.6
0.6
Partial ACF

Partial ACF
0.4

0.4
0.2

0.2
0.0

0.0
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0.5 1.0 1.5 2.0 0.5 1.0 1.5 2.0

Lag Lag

Once the preceding lag is taken into account (high positive correlation,
high continuity) we see that the second lag is negatively correlated (lack
of continuity). Even for the remainders, this is the case but not quite at
the level of significance.

Q55 : What is the physical interpretation of this result? Jump to A55 •

For higher-order AR models, the parameters are fit simultaneously; the

most common method is with the Yule-Walker equations, which relate
the parameters to the sample autocorrelations. For the AR(2) model
these are:

r1 = αˆ1 + αˆ2 r1
r2 = αˆ1 r2 + αˆ2

which can be solved as simultaneous equations. These generalize to any

higher order.
The red-noise variance is then estimated as:

n−1
(1 − r12 )sY2
sZ2 (2) = (1 − α̂22 ) (12)
n−2
where r1 is the sample correlation at lag 1. Thus the original white noise
is reduced yet further, as the degree of the AR model increases.
The ar function not only solves these equations, but also solves them
for all orders from AR(1), AR(2) . . . until the higher-order fit is not better,
as judged by the AIC.

Task 58 : Fit AR(n) models to the remainder series. •

Here we show the optional method argument; the default "yule-walker"
is used. The red noise variance is printed with the solution; it is also
stored with the model object.

81
(ar.gw.r <- ar(gw.r, method="yule-walker"))

##
## Call:
## ar(x = gw.r, method = "yule-walker")
##
## Coefficients:
## 1 2
## 0.9594 -0.0818
##
## Order selected 2 sigma^2 estimated as 0.3133

ar.gw.r$var.pred

## [1] 0.3133392

ar.gw.r$ar

## [1] 0.95943829 -0.08180894

For comparison, we re-fit the AR(1) series also, using the order.max
argument to force ar to only fit this order.
(ar.gw.r.1 <- ar(gw.r, order.max=1))

##
## Call:
## ar(x = gw.r, order.max = 1)
##
## Coefficients:
## 1
## 0.8869
##
## Order selected 1 sigma^2 estimated as 0.3146

ar.gw.r.1$ar

## [1] 0.8868833

Q56 : What order of AR model is selected by the ar function? How

well is the remainder series modelled by an AR(2) process? How much
improvement is this over the AR(1) process? Jump to A56 •

Note: An AR(1) model is always stationary, but higher-order models

may not be. The parameters must jointly satisfy some constraints. See
texts (e.g., Wilks [20, §8.3.2]) for details. The ar function reports non-
stationarity in the fit.

We will return to this example and simulate an AR(2) series with these
fitted parameters in §8.

4.4.2 Moving average (MA) models

The MA process is simply a linear filter of some previous white noise,

plus the white noise for the current time:
q
X
Yt = βj Zt−j + Zt (13)
j=1

82
The βj weight the relative contributions of the previous values. The time
series results from random noise, which (if any βj 6= 0) can “drift” into
an apparent trend, which in fact is the result of the stochastic process,
not a true trend. Thus, MA models are often used to model apparent
trends.

4.4.3 ARMA models

Autoregressive moving-average (ARMA) models combine the AR and

MA explained above, so that the observed time series is the result of
these two types of random processes.
The theory behind ARMA models is that a time series, written as a se-
quence of values over time {Yt }, can be considered as the contribution
of four components:
1. An overall mean level µ; this can be subtracted from the series,
leaving a series centred on zero;
2. An autoregressive (AR) component, where values in the series are
correlated to some number of immediately preceding values;
3. A moving average (MA), where values in the series are some linear
combination of earlier values of white noise, but with no correlation
between successive values of this noise;
4. white noise, a random component with zero mean and some con-
stant variance, conventionally represented as {Zt }.

4.4.4 ARIMA models

The “I” in ARIMA stands for “integrated”. These are ARMA models with
an additional element: the degree of differencing applied to the series
before ARMA analysis. ARMIMA models are conventionally specified
with three components (p, d, q), which are:
1. p: the AR order;
2. d: the degree of differencing; and
3. q: the MA order.
Differencing is applied so that the series is second-order stationary, i.e.,
the expected value and covariance do not depend on the position in the
series.
ARIMA models are fit with the arima function. This requires at least
two arguments: the series and the order. To illustrate, we re-fit the
AR(2) model of the well level residuals (§4.4.1) with arima. The order is
(2, 0, 0):
(arima.gw.r <- arima(gw.r, order=c(2,0,0)))

##
## Call:
## arima(x = gw.r, order = c(2, 0, 0))

83
##
## Coefficients:
## ar1 ar2 intercept
## 0.9624 -0.0851 -0.0925
## s.e. 0.0524 0.0525 0.2341
##
## sigma^2 estimated as 0.3078: log likelihood = -299.48, aic = 606.95

Q57 : Does the ARIMA(2,0,0) fit give the same coefficients as the AR(2)
fit? Jump to A57 •

The coefficients for model fit by ar are in field ar; for a model fit by
arima in field coef:
ar.gw.r$ar

## [1] 0.95943829 -0.08180894

arima.gw.r$coef

## ar1 ar2 intercept

## 0.96236062 -0.08513407 -0.09246881

We will examine model fitting in detail just below.

4.4.5 Periodic autoregressive (PAR) models

To fit an AR model, we had to establish stationarity. Clearly a cyclic

series is not first-order stationary, yet it seems somehow unnatural to
remove the cycle, model the series, and add the cycle back in. With
periodic autoregressive (PAR) models, both are modelled together.
The PAR process is defined like the AR process, with with a fluctuating
average µτ instead of an overall average µ. The values Y are indexed
by the cycle number η and the position in the cycle τ, i.e., Yη,τ . The
autoregressive parameter is also indexed by the position in the cycle, as
well as the order l, i.e., αl,τ . Finally, the white noise depends on the
position in the cycle as well: Zη,τ . Putting these together, Equation 9 is
replaced with:

p
X
(Yη,τ − µτ ) = αl,τ (Yη,τ−l − µτ ) + Zη,τ (14)
l=1

Note: Note that a PAR model can not have any trend, just the cyclic com-
ponent. If there is an overall trend it must be removed before modelling.

These models are widely-used for modelling monthly rainfall series or

streamflows. They are appropriate when the periodic component is much
larger than the white noise.
These are fit with the arima function, by specifying the optional seasonal
argument, which, like the ARIMA order, is a list of the three components
(p, d, q).

84
Task 59 : Fit a PAR model to the de-trended time series of groundwater
levels of Anatolia well 1 since 1978. •
Recall that the behaviour before 1978 was qualitatively different than
that since; we suspect that extraction began in 1978. In §4.2 a linear
trend was established for that period:
gw.f.78 <- subset(gw.f, gw.f$year > 1977)
coef(m.gw.78 <- lm(gw ~ time, data=gw.f.78))

## (Intercept) time
## -1763.3607555 0.9067699

We subtract the fits from this model from each observation (using the
fitted extractor function on the linear model), to get the de-trended
series. We also need to extract the time-series window, using window.
gw.1978 <- window(gw, c(1978,1), c(2004,12))
str(gw.1978)

## Time-Series [1:324] from 1978 to 2005: 30.4 30.3 30.1 29.9 29.9 ...

str(fitted(m.gw.78))

## Named num [1:324] 30.2 30.3 30.4 30.5 30.5 ...

## - attr(*, "names")= chr [1:324] "37" "38" "39" "40" ...

str(gw.1978.0 <- gw.1978 - fitted(m.gw.78))

## Time-Series [1:324] from 1978 to 2005: 0.1199 -0.0457 -0.2813 -0.5568 -0.5924 ...
## - attr(*, "names")= chr [1:324] "37" "38" "39" "40" ...

plot(gw.1978.0, ylab="Deviations from linear trend, m",

main="Anatolia well 1", pch=20)
grid()
abline(h=0, lty=2)

Anatolia well 1
6
Deviations from linear trend, m

4
2
0
−2
−4

1980 1985 1990 1995 2000 2005

Time

We now fit a PAR model, with AR(2) for the non-seasonal part (as revealed

85
by our previous analysis) and different AR orders for the seasonal part.
A seasonal order of (0, 0, 0) corresponds to the same cycle each year.
Higher-order AR represent autocorrelation of cycles year-to-year; e.g.,
a high-amplitude cycle tends to be preceded and followed by a similar
amplitude

Note: The frequency can be specified as part of the seasonal argu-

ment, but defaults to the known frequency of the series, as given by the
frequency function.
(par.gw.1978 <- arima(gw.1978.0, order=c(2,0,0), seasonal=c(0,0,0)))

##
## Call:
## arima(x = gw.1978.0, order = c(2, 0, 0), seasonal = c(0, 0, 0))
##
## Coefficients:
## ar1 ar2 intercept
## 1.3306 -0.4585 -0.0046
## s.e. 0.0492 0.0492 0.3326
##
## sigma^2 estimated as 0.5983: log likelihood = -377.66, aic = 763.32

(par.gw.1978 <- arima(gw.1978.0, order=c(2,0,0), seasonal=c(1,0,0)))

##
## Call:
## arima(x = gw.1978.0, order = c(2, 0, 0), seasonal = c(1, 0, 0))
##
## Coefficients:
## ar1 ar2 sar1 intercept
## 1.1142 -0.2404 0.4272 -0.0026
## s.e. 0.0639 0.0640 0.0593 0.5293
##
## sigma^2 estimated as 0.5159: log likelihood = -354.63, aic = 719.27

(par.gw.1978 <- arima(gw.1978.0, order=c(2,0,0), seasonal=c(2,0,0)))

##
## Call:
## arima(x = gw.1978.0, order = c(2, 0, 0), seasonal = c(2, 0, 0))
##
## Coefficients:
## ar1 ar2 sar1 sar2 intercept
## 1.0657 -0.1691 0.3604 0.2144 -0.0118
## s.e. 0.0618 0.0635 0.0562 0.0571 0.8162
##
## sigma^2 estimated as 0.4923: log likelihood = -347.92, aic = 707.84

The fit of the models, accounting for number of parameters, is given by

the AIC; lower is better.

Q58 : How much does modelling the seasonal component improve the
fit? Which degree of autoregression among seasons is indicated? Jump
to A58 •

4.5 Modelling with ARIMA models

ARIMA models were developed primarily for forecasting, so modelling

an observed time series with ARIMA models is intended to fit a good

86
empirical model that can be used for this purpose. Interpretation in
terms of underlying processes is not straightforward.
Modelling with an ARIMA model has three stages:

1. Model identification;
2. Parameter estimation;
3. Diagnostic checking of model suitability.

These stages are iterated until the model is deemed “suitable”; then the
model is ready to use for process interpretation or forecasting.

4.5.1 Checking for stationarity

The first step in model identification is to determine if any differencing

is needed. There are two indications that a series is not stationary:

• A time series that appears to have different overall levels or degrees

of autocorrelation in different sections of the series;
• A correlogram (ACF) that does not decay to zero.

Task 60 : Plot the groundwater time series and evaluate its stationarity;
also zoom in on a three-year window to see the fine structure. •
par(mfrow=c(1,2))
plot(gw, main="Anatolia well 1",
ylab="Groundwater level (m)")
plot(window(gw, 1990, 1994), main="Anatolia well 1",
ylab="Groundwater level (m)")
par(mfrow=c(1,2))

Anatolia well 1 Anatolia well 1

46
55

45
44
50
Groundwater level (m)

Groundwater level (m)

43
45

42
40

41
35

40
30

1975 1980 1985 1990 1995 2000 2005 1990 1991 1992 1993 1994

Time Time

Q59 : Does there appear to be a trend and/or cycle (i.e., non-constant

expected value?) Does the variance appear to be constant? Jump to
A59 •

A trend can be removed with one difference.

87
Task 61 : Plot the first difference of the groundwater time series and
evaluate its stationarity; also zoom in on a three-year window to see the
fine structure. •
par(mfrow=c(1,2))
plot(diff(gw), main="Anatolia well 1",
ylab="Groundwater level (m), delta-1")
plot(diff(window(gw, 1990, 1994)), main="Anatolia well 1",
ylab="Groundwater level (m), delta-1")
par(mfrow=c(1,2))

Anatolia well 1 Anatolia well 1

2
Groundwater level (m), delta−1

Groundwater level (m), delta−1

1
−2

0
−4
−6

−1

1975 1980 1985 1990 1995 2000 2005 1990 1991 1992 1993 1994

Time Time

Q60 : Does there appear to be a trend and/or cycle (i.e., non-constant

expected value?) Does the variance appear to be constant? Jump to
A60 •

We difference the series once more:

Task 62 : Plot the second difference of the groundwater time series and
evaluate its stationarity. •
par(mfrow=c(1,2))
plot(diff(diff(gw)), main="Anatolia well 1",
ylab="Groundwater level (m), delta-2")
plot(diff(diff(window(gw, 1990, 1994))), main="Anatolia well 1",
ylab="Groundwater level (m), delta-2")
par(mfrow=c(1,2))

88
Anatolia well 1 Anatolia well 1

2.0
1.5
5
Groundwater level (m), delta−2

Groundwater level (m), delta−2

1.0
0.5
0

0.0
−0.5
−1.0
−5

−1.5
1975 1980 1985 1990 1995 2000 2005 1991 1992 1993 1994

Time Time

Task 63 : Repeat, with the third differences. •

par(mfrow=c(1,2))
plot(diff(diff(diff(gw))), main="Anatolia well 1",
ylab="Groundwater level (m), delta-3")
plot(diff(diff(diff(window(gw, 1990, 1994)))),
main="Anatolia well 1",
ylab="Groundwater level (m), delta-3")
par(mfrow=c(1,2))

Anatolia well 1 Anatolia well 1

2
Groundwater level (m), delta−3

Groundwater level (m), delta−3

1
5

0
−1
0

−2
−5

−3

1975 1980 1985 1990 1995 2000 2005 1991 1992 1993 1994

Time Time

There seems to be little change between the second and third differences.
Another way to look at the stationary is with the autocorrelation function
plotted by acf.

Task 64 : Plot the autocorrelation functions for the original time series
and the first three differences. •
par(mfrow=c(2,2))
acf(gw)
acf(diff(gw))
acf(diff(diff(gw)))
acf(diff(diff(diff(gw))))
par(mfrow=c(1,1))

89
Series gw Series diff(gw)

1.0

1.0
0.8
0.8

0.6
0.6

0.4
ACF

ACF
0.4

0.2
0.2

0.0
−0.2
0.0

−0.4
0.0 0.5 1.0 1.5 2.0 0.0 0.5 1.0 1.5 2.0

Lag Lag

Series diff(diff(gw)) Series diff(diff(diff(gw)))

1.0

1.0
0.8
0.6

0.5
0.4
ACF

ACF
0.2

0.0
0.0
−0.2

−0.5

0.0 0.5 1.0 1.5 2.0 0.0 0.5 1.0 1.5 2.0

Lag Lag

Q61 : Describe the behaviour of the ACF with increasing differencing.

Jump to A61 •

In conclusion, two differencing operations seem to result in a more or

less second-order stationary time series.

4.5.2 Determining the AR degress

The next step in model identification is to examine the autocorrelations

and partial autocorrelations using acf and pacf, respectively.
If the process is AR(p), the partial autocorrelation is zero at lag ≥ p + 1.
So, the sample partial autocorrelation plot is examined to identify the
order: find the lag where the partial autocorrelations for all higher lags
are not significantly different from zero.
We can see this nicely for the groundwater data since 1978.
pacf(gw.1978)

90
Series gw.1978

1.0
0.8
0.6
Partial ACF

0.4
0.2
0.0
−0.2 0.5 1.0 1.5 2.0

Lag

Here the significant partial correlations are at 1, 2, 5 . . . 9, 12 and 13

months (“lag” on this plot refers to the 12-month cycle). So we could try
to fit an AR(13) model.
However, since we’ve already determined that two differences are needed
for stationarity, we evaluate the PACF of the differenced series:
par(mfrow=c(1,2))
pacf(diff(gw.1978))
pacf(diff(diff(gw.1978)))
par(mfrow=c(1,1))

Series diff(gw.1978) Series diff(diff(gw.1978))

0.4

0.1
0.3

0.0
0.2
Partial ACF

Partial ACF

−0.1
0.1
0.0

−0.2
−0.1

−0.3
−0.2

0.5 1.0 1.5 2.0 0.5 1.0 1.5 2.0

Lag Lag

These also show partial autocorrelation to 13 months, although the ab-

solute correlation coefficients decrease with increasing differencing.
acf(diff(diff(gw.1978)))

91
Series diff(diff(gw.1978))

1.0
0.8
0.6
0.4
ACF

0.2
0.0
−0.2 0.0 0.5 1.0 1.5 2.0

Lag

The second step is to estimate the model parameters, using the arima
function. This must be supplied with three parameters, which specify the
model type; these are conventionally known as p (the AR order), d (the
degree of differencing), and q (the MA order), as explained above. ARIMA
models may also declare a periodic (also called seasonal) component,
with the same parameters.

Task 65 : Calibrate an ARIMA model for the groundwater level. •

(m.ar <- arima(gw.1978, order=c(13,2,0)))

##
## Call:
## arima(x = gw.1978, order = c(13, 2, 0))
##
## Coefficients:
## ar1 ar2 ar3 ar4 ar5 ar6 ar7
## -0.8569 -0.8617 -0.8759 -0.9057 -0.8682 -0.8971 -0.8651
## s.e. 0.0556 0.0719 0.0801 0.0834 0.0839 0.0820 0.0828
## ar8 ar9 ar10 ar11 ar12 ar13
## -0.9231 -0.8893 -0.7707 -0.5805 -0.2637 -0.0708
## s.e. 0.0816 0.0835 0.0830 0.0798 0.0715 0.0553
##
## sigma^2 estimated as 0.4767: log likelihood = -340.38, aic = 708.76

The third step is model checking; the tsdiag function produces three
diagnostic plots for ARIMA models:
1. standardized residuals (should show no pattern with time);
2. autocorrelation function (ACF) of residuals (should have no signifi-
cant autocorrelation);
3. the Ljung-Box statistic for the null hypothesis of independence in
the time series of residuals.
We can see the effect of a poor model fit by under-fitting the groundwater
levels with an AR model:
m.ar <- arima(gw.1978, c(3,2,0))
tsdiag(m.ar)

92
Standardized Residuals

6
4
2
0
−2
−4
−6
−8
1980 1985 1990 1995 2000 2005

Time

ACF of Residuals
1.0
0.8
0.6
ACF

0.4
0.2
0.0
−0.2

0.0 0.5 1.0 1.5 2.0

Lag

p values for Ljung−Box statistic

1.0

●
0.8

●
0.6

●
p value

0.4
0.2
0.0

● ● ● ● ● ● ●

2 4 6 8 10

lag

Notice the significant autocorrelation of the residuals at 4, 6, 12 and 13

months, and the low p-values of the Ljung-Box statistic after lag 4; this
means that we can not reject the null hypothesis of serial dependence at
these lags. At a more appropriate order the diagnostics are satisfactory:
m.ar <- arima(gw.1978, c(13,2,0))
tsdiag(m.ar)

93
Standardized Residuals

2
0
−2
−4
−6
−8
−10
1980 1985 1990 1995 2000 2005

Time

ACF of Residuals
1.0
0.8
0.6
ACF

0.4
0.2
0.0

0.0 0.5 1.0 1.5 2.0

Lag

p values for Ljung−Box statistic

1.0

● ● ● ● ● ● ● ● ●
●
0.8
0.6
p value

0.4
0.2
0.0

2 4 6 8 10

lag

These diagnostics look very good.

4.6 Predicting with ARIMA models

Finally, ARIMA models can be used to predict.

Task 66 : Predict groundwater levels from 2005 through 2012, using

the AR(13) model just fit. •
For ARIMA models, the generic predict method specializes to the
predict.Arima function; this returns both the predictions and their
standard errors. The argument n.ahead gives the number of prediction
points, here months:
p.ar <-predict(m.ar, n.ahead=12*(2013-2005))
str(p.ar)

## List of 2
## $ pred: Time-Series [1:96] from 2005 to 2013: 54 53.3 52.9 53.1 53.8 ...
## $ se : Time-Series [1:96] from 2005 to 2013: 0.69 1.05 1.32 1.54 1.72 ...

plot(p.ar$pred, ylim=c(35, 75), ylab="Predicted groundwater level, m",

main="Anatolia well 1")

94
lines(p.ar$pred+p.ar$se, col="red", lty=2)
lines(p.ar$pred-p.ar$se, col="red", lty=2)
grid()

Anatolia well 1

70
Predicted groundwater level, m

60
50
40

2006 2008 2010 2012

Time

Q62 : What happens to the prediction as the time forward from the
known series increases? What happens to the confidence intervals? As
a groundwater manager, how far ahead would you be willing to use this
predicted series? Jump to A62 •

4.7 Answers

A41 : (1) There is a long-term trend, to a slightly shallower level until 1980
and then steadily to a deeper level. The slope of the trend (groundwater level
vs. time interval) varies a bit over the 1980- 2005, which may reflect rainfall
differences. The trend is most likely due to increased extraction for irrigation,
since the quantity of far exceeds annual rainfall; which we see in . . . (2) There is
a seasonal cycle in groundwater level, due to recharge in the winter (rains) and
extraction in the summer; however the magnitude of the fluctuation appears
to increase from about 1983–1995 and has since stabilized. The increasing
fluctuation may be caused by more extraction but is also balanced by more
rainfall. (3) The remainder is of similar magnitude to the annual cycle (±2m)
and is strongly auto-correlated; the explanation for this is unclear. The very
large remainder in 1988 was discussed in §2.1. Return to Q41 •

A42 : The proportion of variation explained is given by the adjusted R 2 , here

0.89. The overall trend is fairly well-explained by the line. The average annual

95
increase is given by the slope coefficient, 0.813 Return to Q42 •

A43 : The estimate of the AR(1) temporal correlation returned by gls is

0.9571, quite close to our original estimate 0.9878. Return to Q43 •

A44 : The slope is somewhat shallower: GLS 0.7751 vs. OLS 0.813. Return to
Q44 •

A45 : Yes, the proportion of variation explained has increased to 0.9; the
ANOVA shows a highly significant improvement in fit. The cubic adjusts some-
what to the initial part of the series. Return to Q45
•

A46 : The average annual increase has changed considerably, increasing from
0.775 for the whole series to 0.907 for the shorter series. The steeper slope
ignores the earliest part of the series, when the process was different, and so
seems to better reflect current conditions and is preferable for predicting in
the short term. Return to Q46 •

A47 : The trend can not continue forever – for example, at a certain point the
groundwater level will be too deep to pump economically and will stabilize at
that level. Also, future rainfall patterns and future demand for irrigation water
may change. Return to Q47 •

A48 : The variance explained increases 2.51% compared to the fit to the
original time series, because there is less overall variability. Return to Q48 •

A49 : The slope of the trend is almost identical; the fit without the seasonal
component predicts 3.21 mm less drawdown per year. Return to Q49 •

A50 : There are definite discrepencies. First, there is clear periodicity in

the residuals vs. fitted values: high (positive) residuals around fitted values of
32, 48, 46, and 52 m and low (negative) at 34, 44, 48 m. Second, the highest
residuals are far too positive (i.e., very strong underprediction); this is the year
1988 anomaly. Return to Q50 •

A51 : Effectively zero. There is certaintly a trend. Return to Q51 •

A52 : The series from 1972 – 1974 has large fluctuations and high concentra-
tions; after 1974 these are both much lower, except for some spikes in 1975.
There seems to be a seasonal component. Some observations are missing.
There is no linear trend, instead there seems to be a discontinuity in 1974,

96
from high to low concentrations. Return to Q52 •

A53 : The probability that the observed trend, estimated as -0.056 (mg l-1)
yr-1, is due to sampling variation is very small, about 1 in 107 . Return to Q53
•

A54 : Proportionally, 0.788 of the variance is explained. This is a high degree

of continuity, even after accounting for trend and cycle. Return to Q54 •

A55 : After correcting for immediate continuity (since this is ground water,
to be expected) the lag-2 level or remainder introduces a negative correction.
That is, going two steps forward with a single AR(1) model would over-state
the continuity, compared to an AR(2) model. Return to Q55 •

A56 : An AR(2) series is selected; thus the lag-2 component can be modelled.
The residual variance decreases slightly, from 0.3146 to 0.3133. Most of the
variance reduction was from the original series to the AR(1) series; the AR(2)
series is only a small improvement. Return to Q56 •

A57 : No, there are slight differences. The AR(2) fit gives the two coefficients
as 0.9594 and -0.0818; for the ARIMA(2,0,0) fit these are computed as 0.9624
and -0.0851 Return to Q57 •

A58 : The standard error of the best seasonal ARIMA fit is 0.4923, compare
to 0.3133 for the non-seasonal model; this is somewhat higher, i.e., the fit is
worse. But, the seasonal model also includes the seasonal component, which
was removed from the time series fit with the non-seasonal model. Return to
Q58 •

A59 : There seems to be a clear trend to deeper levels since 1982; further the
expected values seem to follow an annual cycle. Both are indications that this
is not a first-order stationary series. The variance increases over time. So, this
is not second-order stationary. Return to Q59 •

A60 : There is no apparent trend, but there still seems to be an annual cycle.
So, this is not first-order stationary. The variance increases over time. So, this
is not second-order stationary. Return to Q60 •

A61 : The ACF of the original series does not decay to zero; this indicates a
trend. Once this is removed by the first difference, the ACF shows clear cyclic
behaviour. This is largely removed by the second difference and completely by
the third. Return to Q61 •

A62 : The prediction becomes more uniform the further out we predict, i.e.,

97
the cyclic behaviour is damped and approaches the overall linear trend. The
upper and lower confidence limits become wider and also are damped; but
they rapidly become much larger than the annual cycle. The prediction does
not seem very useful to the manager; it seem more logical to use the average
behaviour of the cycles in the known series and add it to the trend. Return to
Q62 •

5 Intervention analysis

Time series may arise completely or mostly from natural processes (e.g.,
rainfall, temperature) but may also be influenced by human activities.
These interventions may be one-time (e.g., damming a river) or pulsed
(e.g., streamflow with controlled releases from dams). Hipel and McLeod
[10, Ch. 19] is an excellent explanation of intervention analysis, which
has two main uses:
1. Determining the effect of a known intervention (e.g., has a new
sewage treatment plant improved water quality?);
2. Identifying probable unknown interventions (e.g., is there a new
source of pollutants?).
Each of these may affect the series in several ways, known as transfer
functions:

• An immediate, single effect (e.g., one day’s streamflow is affected);

• An immediate, permanent effect (e.g., a pollutant is at a different
level and maintains that level);
• An asymptotic effect, reaching a new equilibrium over time;
• An immediate effect, then relaxing to the original condition;
• Any of these may be delayed;
• Any of these may be multiple.

5.1 A known intervention

We return to the example of the phosphorous (P) concentrations briefly

presented in §4.3.3. This is included in the Kendall package as a sam-
ple dataset GuelphP, a monthly time series of phosphorous (P) concen-
trations in mg l-1, Speed River, Guelph, Ontario, January 1972 through
January 1977. It is known [10, p. 655] that in February 1974 a new P
treatment was introduced in the sewage treatment plant.

Task 67 : Load this dataset and plot as a time series, showing the
known intervention. •
require(Kendall)
data(GuelphP)
str(GuelphP)

98
## Time-Series [1:72] from 1972 to 1978: 0.47 0.51 0.35 0.19 0.33 NA 0.365 0.65 0.825 1 ...
## - attr(*, "title")= chr "Phosphorous Data,Speed River,Guelph,1972.1-1977.1"

plot(GuelphP, type="b", ylab="P concentration, mg l-1",

main="Speed River water quality")
abline(v=1974+2/12, col="red", lwd=2)
text(x=1974+2/12, y=1,"known intervention", col="red", pos=4)

Speed River water quality

1.0
● known intervention
●
P concentration, mg l−1
●

0.8
●
0.6

● ●
● ●
0.4

● ●
● ● ●
●
● ●
●
●
0.2

●
● ● ●
● ●
● ● ● ● ●●
● ●● ● ●● ●● ●● ●
● ● ● ● ●● ●
● ●●
● ●●● ● ● ●● ●● ●●
●
● ●
0.0

1972 1973 1974 1975 1976 1977 1978

Time

Note the use of the abline function to add a line to the graph, specifying
the v argument to specify a vertical line at the indicated date.

Q63 : Describe the effect of the new P treatment. Jump to A63 •

How can we reliably quantify this difference? One obvious way is to split
the series and compare the means, medians, or variances.

Task 68 : Split the series at February 1974 and compare the means,
medians, or variances. •
Since these statistics do not involve time series, and there are missing
values, we convert to ordinary vectors with as.vector and remove the
NA’s with na.omit:
(guelph.1 <- na.omit(as.vector(window(GuelphP, start=NULL,
end=1974+1/12))))

## [1] 0.470 0.510 0.350 0.190 0.330 0.365 0.650 0.825 1.000 0.385 0.900
## [12] 0.295 0.140 0.220 0.200 0.140 0.400 0.495 1.100 0.590 0.270 0.300
## [23] 0.065
## attr(,"na.action")
## [1] 6 19 25
## attr(,"class")
## [1] "omit"

(guelph.2 <- na.omit(as.vector(window(GuelphP, start=1974+2/12,

end=NULL))))

## [1] 0.240 0.058 0.079 0.065 0.120 0.091 0.058 0.120 0.120 0.110 0.460
## [12] 0.150 0.086 0.028 0.110 0.360 0.180 0.065 0.130 0.120 0.190 0.150
## [23] 0.107 0.047 0.055 0.080 0.071 0.121 0.108 0.169 0.066 0.079 0.104
## [34] 0.157 0.140 0.070 0.056 0.042 0.116 0.106 0.094 0.097 0.050 0.079
## [45] 0.114
## attr(,"na.action")
## [1] 15

99
## attr(,"class")
## [1] "omit"

mean(guelph.1); mean(guelph.2)

## [1] 0.4430435
## [1] 0.1159556

median(guelph.1); median(guelph.2)

## [1] 0.365
## [1] 0.106

sd(guelph.1); sd(guelph.2)

## [1] 0.2839124
## [1] 0.07789123

Q64 : Describe the difference in the two sub-series. Jump to A64 •

We would like to state that these are significant differences (not due
to chance) but we can’t use a t-test, because the observations are not
independent – they are clearly serially and seasonally correlated. So we
need to build a time-series model that includes the intervention.

5.2 Answers

A63 : The mean P concentration decreases dramatically, and the month-to-

month variability is much less. Return to Q63
•

A64 : The later series has a much lower mean, median, and especially standard
deviation (variability). Return to Q64 •

6 Comparing two time series

Task 69 : Read the second well’s time series in R, convert to a time-

series object, and plot it. •
gw.2 <- ts(scan("./ds_tsa/anatolia_alibe.txt"), start=1975, frequency=12)
plot(gw.2, ylab="Groundwater level (m)", main="Anatolia well 2")

100
Anatolia well 2

20
Groundwater level (m)

15
10
5

1975 1980 1985 1990 1995 2000 2005

Time

Task 70 : Create a “multiple time series” object covering the common

time period of the two wells. •
The plot.ts function can plot several series together, if they are in a
common object. Two (or more) time series can be bound together with
the ts.intersect and ts.union functions; these produce an object of
class mts “multiple time series”, with one column vector for each original
series.
These differ in that ts.union pads non-overlapping portions of one or
more series with NA’s, whereas ts.intersect limits the multivariate
series to their common times. In the present case both have the same
period so there is no difference.
gw2 <- ts.intersect(gw,gw.2)
class(gw2)

## [1] "mts" "ts" "matrix"

str(gw2)

## Time-Series [1:360, 1:2] from 1975 to 2005: 34.4 34.5 34.7 34.8 34.9 ...
## - attr(*, "dimnames")=List of 2
## ..$ : NULL
## ..$ : chr [1:2] "gw" "gw.2"

Task 71 : Plot the two wells’ time series on the same graph. •
plot(gw2, plot.type="single", main="Anatolia wells 1 and 2",
ylab="Groundwater depth (m)")
lines(lowess(gw, f=1/3), col="red")
lines(lowess(gw.2, f=1/3), col="red")

101
Anatolia wells 1 and 2

50
Groundwater depth (m)

40
30
20
10

1975 1980 1985 1990 1995 2000 2005

Time

gw gw.2
Jan 1975 34.36 13.87
Feb 1975 34.45 13.79
...
Nov 2004 55.55 15.67
Dec 2004 54.83 15.93
summary(gw2)

## gw gw.2
## Min. :29.90 Min. : 5.34
## 1st Qu.:34.90 1st Qu.:11.55
## Median :41.63 Median :13.74
## Mean :41.58 Mean :13.85
## 3rd Qu.:46.80 3rd Qu.:16.19
## Max. :57.68 Max. :22.47

Another way to see the two series is each on their own panel. This has
the effect of stretching or compressing the response (here, groundwater
level) to the same scale:
plot(gw2, plot.type="multiple", main="Anatolia, two wells")

102
Anatolia, two wells

50
gw

40
30
20
15
gw.2

10
5

1975 1980 1985 1990 1995 2000 2005

Time

Q65 : Is there a systematic difference between the wells? Do they appear

to have the same temporal pattern? Jump to A65 •

The obvious question is how well are the two series correlated? Function
ccf computes the cross-correlation of two univariate series at a series
of lags. Note that the highest correlation between two series might not
be at lag 0 (same time), one series may lag ahead or behind the other (for
example, stream flow at different distances from the source).
By convention the first series named is moved ahead of the second when
computing; so the cross-correlation is between xt+k of the first series
and yt of the second. So a positive lag has the first series ahead of the
second, a negative lag the second is ahead of the first.

Task 72 : Compute and display the cross-correlation between the two

wells. •
The ccf function has an argument lag.max which by default is the in-
teger nearest 10 · log 10N/m, here 23, i.e. almost two years. This is
computed in both directions.
(cc <- ccf(gw,gw.2))

##
## Autocorrelations of series 'X', by lag
##
## -1.8333 -1.7500 -1.6667 -1.5833 -1.5000 -1.4167 -1.3333 -1.2500
## 0.681 0.693 0.703 0.709 0.710 0.712 0.716 0.724
## -1.1667 -1.0833 -1.0000 -0.9167 -0.8333 -0.7500 -0.6667 -0.5833
## 0.733 0.745 0.759 0.776 0.790 0.802 0.811 0.815
## -0.5000 -0.4167 -0.3333 -0.2500 -0.1667 -0.0833 0.0000 0.0833
## 0.819 0.824 0.827 0.831 0.841 0.853 0.864 0.874
## 0.1667 0.2500 0.3333 0.4167 0.5000 0.5833 0.6667 0.7500

103
## 0.879 0.885 0.890 0.888 0.881 0.873 0.863 0.855
## 0.8333 0.9167 1.0000 1.0833 1.1667 1.2500 1.3333 1.4167
## 0.852 0.856 0.860 0.863 0.863 0.860 0.853 0.839
## 1.5000 1.5833 1.6667 1.7500 1.8333
## 0.823 0.809 0.786 0.771 0.762

plot(cc, main="Cross-correlation, Anatolia well 1 vs. well 2")

gw & gw.2

0.8
0.6
ACF

0.4
0.2
0.0

−1 0 1

Lag

Cross−correlation, Anatolia well 1 vs. well 2

0.8
0.6
ACF

0.4
0.2
0.0

−1 0 1

Lag

Q66 : What is the correlation at zero lag, i.e. the same month and year?
What is the correlation at one month positive and negative lag? Jump
to A66 •

104
Q67 : Why is this graph not symmetric about zero-lag? Jump to A67 •

Task 73 : Find the highest correlation and its lag. •

The max function finds the maximum in a vector, and which.max identi-
fies its index. The structure (using str) shows that the acf field of the
object returned by ccf has the correlation, and the lag field has the lag,
here in years. To get the lag in months, multiply by the cycle length (i.e.
12).
str(cc)

## List of 6
## $ acf : num [1:45, 1, 1] 0.681 0.693 0.703 0.709 0.71 ...
## $ type : chr "correlation"
## $ n.used: int 360
## $ lag : num [1:45, 1, 1] -1.83 -1.75 -1.67 -1.58 -1.5 ...
## $ series: chr "X"
## $ snames: chr "gw & gw.2"
## - attr(*, "class")= chr "acf"

max(abs(cc$acf)) # check highest correlation

## [1] 0.8896892

(i <- which.max(abs(cc$acf)))

## [1] 27

cc$acf[i]

## [1] 0.8896892

cc$acf[i]^2

## [1] 0.7915468

cc$lag[i] # check maximum lag

## [1] 0.3333333

12*cc$lag[i] # maximum lag, in months

## [1] 4

Q68 : What is the highest correlation and its lag? Which series leads?
Jump to A68 •

Q69 : Looking at the graphs and the numeric results, how closely corre-
lated are the two series? Jump to A69
•

Task 74 : Compare the spectra of the two series. •

We can also compare the spectral decomposition of the two wells, using

105
the spectrum function, as in 3.6. Since there are two series, we can also
compute their coherency, i.e., how much they agree at each frequency;
this is essentially their correlation. Further, it is possible that the series
are similar but lagged. An example is monthly rainfall at two stations
where a monsoon or other seasonal frontal system reaches one station
later than the other. The coherency and phase plots are specified with
the plot.type optional argument to spectrum.

par(mfrow=c(1,3))
spectrum(gw2, spans=c(5,7), lty=1, col=c("black","red"), plot.type="marginal")
spectrum(gw2, spans=c(5,7), lty=1, col=c("black","red"), plot.type="coherency")
spectrum(gw2, spans=c(5,7), lty=1, col=c("black","red"), plot.type="phase")
par(mfrow=c(1,1))

Series: x
Series: x −− Squared Coherency Series: x −− Phase spectrum
Smoothed Periodogram
1.0
5e+00

3
2
0.8
5e−01

1
squared coherency

0.6
spectrum

phase

0
0.4

−1
5e−02

0.2

−2
−3
5e−03

0.0

0 1 2 3 4 5 6 0 1 2 3 4 5 6 0 1 2 3 4 5 6

frequency frequency frequency

bandwidth = 0.0726

In the first plot, we can see that the two periodigrams are quite similar,
although the second series has somewhat less power at one and two
years. There seems to be a slight lag of the second series behind the
first, this is most obvious at frequencies 0.5 (two years) and 2 (half-year).
In the second plot, we see the coherency between them at each period.
This confirms the impression from the first plot that the same climate
forcing applies to both. The lack of coherency near frequencies 0.5 and
2 is also shown here.
The third plot shows the a phase differences. There are clear phase
differences at frequencies 0.5, 1, and 2 (series 2 lags) and 1.2–1.8 (series
2 leads). The large swings in phase (±) at 3.4 and 5 cycles must be
artefacts of the low power at these frequencies.

6.1 Answers

A65 : The second well is much closer to the surface than the first. Both have
annual cycles but the trend towards deeper levels is much more pronounced

106
in the first well. The second well appears to have more rapid fluctuations. The
timing of rapid extractions and recharges is different for the two wells. Return
to Q65 •

A66 : At lag 0 the correlation is 0.864; with the first well ahead by one month
it is 0.874; for the first well behind by one month 0.853 Return to Q66 •

A67 : Shifting one series ahead of the other (i.e., lagging it positively) is not the
same as shifting it behind. Think for example of correlating January rainfall
of one station with March in another (first station lagged +2) or correlating it
with November (lag -2); there is no reason to think these will have the same
correlation. Return to Q67 •

A68 : The highest correlation is 0.89 at lag 4; the first well’s records are moved
forward to match the second well’s records. Return to Q68 •

A69 : Although the two wells are in the same region with similar climate and
land use, the highest correlation is not even 0.9; the coefficient of variation
(proportion of variation explained, R 2 ) is only 0.792. Return to Q69 •

7 Gap filling

Many uses of time series require complete series, without any gaps. In
practice many series contain such gaps because of mechanical failure or
observer error; an example is the daily rainfall records from Lake Tana
(§2.2).
Gap filling is reviewed by Salas [15, §19.4].
We first list several approaches to gap filling and their areas of applica-
tion. Several of these are then illustrated with examples.

Interpolation If the series is expected to be continuous (no abrupt changes,

e.g. groundwater depths) and if the gap is not long (e.g. a single missing
well depth), a simple interpolation from nearby values will usually give
satisfactory results.
The interpolation can be linear from the two nearest values, or as a
weighted average of nearby values; these are both linear filters.

Functional interpolation Again if the series is expected to be continu-

ous and if the gap is not long, another way to interpolate from nearby
values is to fit a function to the series, either global or (more commonly)
some local function such as a local polynomial or spline. This function
can then be evaluated at the missing value’s time. An example is a peri-
odic function fit to an annual cycle.

107
Estimatation from other cycles For a cyclic series (e.g. annual) a miss-
ing value may be estimated by some function (typically the mean) of
values at the same position in the cycle. If there is a trend the estimation
of and from deviation from trend.
For example, missing June rainfall for one year in a 30-year series could
be estimated as the mean of the other 29 June rainfalls. This assumes
the year is not overall wetter or drier, which may not be a reasonable
assumption.

Estimation from other series If the series with missing values is well-
correlated to one or more other series (e.g. one gauging station among a
network, or one weather station in a group), a (multivariate) regression
equation can be developed for the time series as a function of the other
series.

Estimation from the autocorrelation structure If the series is auto-

correlated, as revealed by the correlogram and autocorrelation analysis,
a gap can be estimated from the observations with which it should be
correlated. A typical example is a missing daily weather observation
(temperature, dewpoint, etc.). Rainfall can also be estimated, but its au-
tocorrelation structure is usually much weaker.

Estimation from a model If the time series is modelled either by struc-

tural decomposition or ARIMA, the model can be used to predict at a
gap, or even to extend the series.

7.1 Simulating short gaps in a time series

To illustrate gap filling, we simulate gaps by removing known records

from a series; we can then assess the success of the method by compar-
ing the reconstructed series to the known series.

Task 75 : Remove five months at random from the first Anatolia well.
•
Recall, this is in time series gw:
str(gw)

## Time-Series [1:360] from 1975 to 2005: 34.4 34.5 34.7 34.8 34.9 ...

First, set up the series with simulated gaps, initially the same as the
known series:
gwg <- gw

Second, pick five separate positions to delete, using the sample function.
So your results match these, we use set.seed to set the random number
generator to a known starting position.
set.seed(0044)
(ix <- sample(length(gw), size=5))

108
## [1] 268 102 182 206 12

sort(ix)

## [1] 12 102 182 206 268

Third, delete the values at these positions, replacing them with the miss-
ing value constant NA:
summary(gwg)

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

## 29.90 34.90 41.63 41.58 46.80 57.68

gwg[ix] <- NA
summary(gwg)

## Min. 1st Qu. Median Mean 3rd Qu. Max. NA's

## 29.90 34.89 41.70 41.62 46.92 57.68 5

Q70 : What is different in the summary of the simulated time series,

before and after deletion? Jump to A70 •

Task 76 : Plot the simulated series, showing the dates with missing
observations. •
plot(gwg, main="Groundwater depth, with gaps",
ylab="Groundwater depth (m)",
sub="Dates with missing values shown as red bars")
abline(h = min(gw), col = "gray")
abline(v=time(gw)[ix], , col = "red", lwd=1)
grid()

Groundwater depth, with gaps

55
Groundwater depth (m)

50
45
40
35
30

1975 1980 1985 1990 1995 2000 2005

Time
Dates with missing values shown as red bars

Task 77 : Try to decompose the time series with gaps into a trend,
seasonal component, and residuals. •
We use the best decomposition from §3.3, i.e. with a smoother trend and
two-year window on the seasonal amplitude. I know that this will pro-
duce an error; to avoid a fatal error I thus enclose the expression in a call

109
to the try function, and show the error message with the geterrmessage
function:
try(gwg.stl <- stl(gwg, s.window=25, t.window=85))

## Error in na.fail.default(as.ts(x)) : missing values in object

geterrmessage()

## [1] "Error in na.fail.default(as.ts(x)) : missing values in object\n"

The error message tells us that the stl function failed because there
are missing values . . . a fact we know! The usual R approach to missing
values is to specify a na.action, such as na.omit or na.exclude; in
this case neither help:
try(gwg.stl <- stl(gwg, s.window=25, t.window=85, na.action="na.exclude"),
silent=TRUE)
geterrmessage()

## [1] "Error in stl(gwg, s.window = 25, t.window = 85, na.action = \"na.exclude\") : \n ser

The missing observations have been taken out of the series, so it is no

longer periodic; stl correctly reports this. Clearly, the gaps have to be
filled before analyzing the series.

7.2 Gap filling by interpolation

In the previous example we are missing single observations. The first

attempt to fill the gaps is to interpolate from neighbouring values.

7.2.1 Linear interpolation

The simplest interpolation is as the average of neighbouring (non-missing)

values; the approx function implements this.

Task 78 : Predict the ground water depths at the dates with missing
values, using linear interpolation. •
Recall (§7.1) that we know the positions in the original time-series object
gw for which we deleted the values to make series gwg:
print(ix)

## [1] 268 102 182 206 12

gw[ix]

## [1] 42.86 33.86 39.89 41.46 35.28

gwg[ix]

## [1] NA NA NA NA NA

The dates of these are found with the time function on the original se-
ries, and the [] indexing operator, using the positions of the missing
observations as indices:
time(gw)[ix]

110
## [1] 1997.250 1983.417 1990.083 1992.083 1975.917

We now call the aspline function, specifying series to be interpolated as

the x and y values, and the missing times as the points to be interpolated
(argument xout).
gw.fill.linear <- approx(x=time(gwg), y=gwg, xout=time(gw)[ix])
str(gw.fill.linear)

## List of 2
## $ x: num [1:5] 1997 1983 1990 1992 1976
## $ y: num [1:5] 43.5 34.4 39.7 41.6 35.3

print(gw.fill.linear)

## $x
## [1] 1997.250 1983.417 1990.083 1992.083 1975.917
##
## $y
## [1] 43.525 34.385 39.665 41.620 35.350

Compare these to the known values:

time(gw)[ix]

## [1] 1997.250 1983.417 1990.083 1992.083 1975.917

gw.fill.linear$y

## [1] 43.525 34.385 39.665 41.620 35.350

gw[ix]

## [1] 42.86 33.86 39.89 41.46 35.28

summary((gw[ix] - gw.fill.linear$y))

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

## -0.665 -0.525 -0.160 -0.239 -0.070 0.225

The maximum difference is 0.66 m.

Task 79 : Plot the reconstructed points on the time series with missing
values, along with the original series. •
plot(gwg, main="Gap-filled time series",
sub="reconstructed values: red; true values: green",
ylab="Groundwater depth (m)")
points(gw.fill.linear$x, gw.fill.linear$y, col="red", cex=2)
points(gw.fill.linear$x, gw.fill.linear$y, col="red", pch=20)
points(time(gw)[ix], gw[ix], col="darkgreen", pch=20)

111
Gap−filled time series

55
Groundwater depth (m)

50
45
●
●
●
40 ●
●
●

●●
●

●
35

●
●
●
30

1975 1980 1985 1990 1995 2000 2005

Time
reconstructed values: red; true values: green

Q71 : How well did the linear interpolation fill the gaps? Jump to A71
•

7.2.2 Spline interpolation

The linear interpolation only takes into account neighbouring values;

a higher-order local curve fits to a neighbourhood. One example is a
spline, which is a smooth function that passes through known points
and preserves several derivatives, usually two. A nice implementation of
1D splines is the aspline function of the akima “ Linear or cubic spline
interpolation for irregular gridded data” package, based on methods de-
veloped by Akima [1].
The base R stats has a spline function that is similar but less sophis-
ticated; we will compare the Akima and default splines.
require(akima)

## Loading required package: akima

Task 80 : Predict the ground water depths at the dates with missing
values, using spline interpolation. •
We now call the aspline function, specifying series to be interpolated as
the x and y values, and the missing times as the points to be interpolated
(argument xout).
gw[ix]

## [1] 42.86 33.86 39.89 41.46 35.28

(gw.fill.aspline <- aspline(x=time(gwg), y=gwg, xout=time(gw)[ix]))$y

## [1] 43.22304 34.37567 39.66733 41.63453 35.32840

(gw.fill.spline <- spline(x=time(gwg), y=gwg, xout=time(gw)[ix]))$y

## [1] 43.17678 34.33328 39.76171 41.69033 35.29984

112
Compare these to each other and the linear interpolator:
summary(gw.fill.aspline$y - gw.fill.spline$y)

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

## -0.094384 -0.055798 0.028558 -0.006595 0.042386 0.046262

summary(gw.fill.aspline$y - gw.fill.linear$y)

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

## -0.301963 -0.021600 -0.009333 -0.063208 0.002326 0.014528

summary(gw.fill.spline$y - gw.fill.linear$y)

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

## -0.34822 -0.05172 -0.05016 -0.05661 0.07033 0.09671

Task 81 : Plot the reconstructed points on the time series with missing
values, computed by three methods (linear, default spline, Akima spline)
along with the original series: (1) for the whole series; (2) for a six-month
window centred on March 1997. •
plot(gwg, main="Gap-filled time series", type="l",
ylab="Groundwater depth (m)")
points(gw.fill.aspline$x, gw.fill.aspline$y, col="red", cex=2)
points(gw.fill.aspline$x, gw.fill.aspline$y, col="red", pch=20)
points(gw.fill.spline$x, gw.fill.spline$y, col="blue", cex=2)
points(gw.fill.spline$x, gw.fill.spline$y, col="blue", pch=20)
points(gw.fill.linear$x, gw.fill.linear$y, col="brown", cex=2)
points(gw.fill.linear$x, gw.fill.linear$y, col="brown", pch=20)
points(time(gw)[ix], gw[ix], col="darkgreen", cex=2)
points(time(gw)[ix], gw[ix], col="darkgreen", pch=20)
text(2000, 35.5, "linear", col="brown", pos=2)
text(2000, 34, "default spline", col="blue", pos=2)
text(2000, 32.5, "Akima spline", col="red", pos=2)
text(2000, 31, "true value", col="dark green", pos=2)

Gap−filled time series

55
50
Groundwater depth (m)

●
●
●
●
●
●

●
●
●
40

●●
●

● linear
35

●
●
●
● default spline
Akima spline
true value
30

1975 1980 1985 1990 1995 2000 2005

Time

plot(window(gwg, start=1997, end=1997.5), main="Gap-filled time series",

ylim=c(42,45), type="b", ylab="Groundwater depth (m)")
points(gw.fill.aspline$x, gw.fill.aspline$y, col="red", cex=2)
points(gw.fill.aspline$x, gw.fill.aspline$y, col="red", pch=20)
points(gw.fill.spline$x, gw.fill.spline$y, col="blue", cex=2)
points(gw.fill.spline$x, gw.fill.spline$y, col="blue", pch=20)

113
points(gw.fill.linear$x, gw.fill.linear$y, col="brown", cex=2)
points(gw.fill.linear$x, gw.fill.linear$y, col="brown", pch=20)
points(time(gw)[ix], gw[ix], col="darkgreen", cex=2)
points(time(gw)[ix], gw[ix], col="darkgreen", pch=20)
text(1997.5, 43, "linear", col="brown", pos=2)
text(1997.5, 42.7, "default spline", col="blue", pos=2)
text(1997.5, 42.5, "Akima spline", col="red", pos=2)
text(1997.5, 42.2, "true value", col="dark green", pos=2)

Gap−filled time series

45.0
●
Groundwater depth (m) ●

●
44.0 ●

●
● ●
●

●
●
43.0

●
linear
●
●
default spline
Akima spline
true value
42.0

1997.0 1997.1 1997.2 1997.3 1997.4 1997.5

Time

Q72 : How different are the three interpolators? Jump to A72 •

Task 82 : Make a full time series with the reconstructed values. •

First, copy the series with gaps, then fill in their values:
gwg.r <- gwg
sum(is.na(gwg.r))

## [1] 5

gwg.r[ix] <- gw.fill.aspline$y

str(gwg.r)

## Time-Series [1:360] from 1975 to 2005: 34.4 34.5 34.7 34.8 34.9 ...

sum(is.na(gwg.r))

## [1] 0

7.3 Simulating longer gaps in time series

The linear and spline interpolators had little problem with single gaps in
a smooth series. What happens with longer gaps?

7.3.1 Non-systematic gaps

These are like the short gaps; no systematic problem but the result of
carelessness or occasional problems with observations.

Task 83 : Remove one-fifth of the months at random from the first

114
Anatolia well. •
Again we use set.seed so your results will be the same. For convenience
in plotting, we also create a sorted version of the missing-observations
vector, using the sort function.
gwg <- gw
set.seed(0044)
(six <- sort(ix <- sample(length(gw), size=length(gw)/5)))

## [1] 1 4 8 12 19 21 23 27 33 37 41 42 51 52 56 63
## [17] 70 79 81 88 93 101 102 109 113 120 127 135 140 142 144 149
## [33] 151 152 154 158 159 161 165 168 173 177 182 183 190 206 208 211
## [49] 218 219 251 258 268 271 274 278 284 285 286 295 305 309 312 313
## [65] 321 322 324 331 334 335 338 359

time(gw)[six]

## [1] 1975.000 1975.250 1975.583 1975.917 1976.500 1976.667 1976.833

## [8] 1977.167 1977.667 1978.000 1978.333 1978.417 1979.167 1979.250
## [15] 1979.583 1980.167 1980.750 1981.500 1981.667 1982.250 1982.667
## [22] 1983.333 1983.417 1984.000 1984.333 1984.917 1985.500 1986.167
## [29] 1986.583 1986.750 1986.917 1987.333 1987.500 1987.583 1987.750
## [36] 1988.083 1988.167 1988.333 1988.667 1988.917 1989.333 1989.667
## [43] 1990.083 1990.167 1990.750 1992.083 1992.250 1992.500 1993.083
## [50] 1993.167 1995.833 1996.417 1997.250 1997.500 1997.750 1998.083
## [57] 1998.583 1998.667 1998.750 1999.500 2000.333 2000.667 2000.917
## [64] 2001.000 2001.667 2001.750 2001.917 2002.500 2002.750 2002.833
## [71] 2003.083 2004.833

gwg[ix] <- NA
summary(gwg)

## Min. 1st Qu. Median Mean 3rd Qu. Max. NA's

## 29.90 35.17 41.89 41.66 46.88 57.68 72

plot(gwg, ylab="Groundwater depth (m)", main="72 missing values")

abline(v=time(gw)[six], , col = "red", lwd=1)
grid()

72 missing values
55
Groundwater depth (m)

50
45
40
35
30

1975 1980 1985 1990 1995 2000 2005

Time

Task 84 : Fill these with linear interpolation and Akima splines; com-
pare the results. •
Again we use approx and aspline; for approx we must specify the rule
to be used at the end of the series (since in this case the first observation
was missing); the default rule=1 returns NA; to get a value we specify

115
rule=2:
gw.fill.linear <- approx(x=time(gwg), y=gwg, xout=time(gw)[six], rule=2)
gw.fill.aspline <- aspline(x=time(gwg), y=gwg, xout=time(gw)[six])
summary(gw.fill.linear$y - gw[six])

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

## -5.1467 -0.1750 -0.0050 -0.1980 0.1508 0.7950

summary(gw.fill.aspline$y - gw[six])

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

## -5.77350 -0.15037 -0.02987 -0.20920 0.06561 0.83871

summary(gw.fill.aspline$y - gw.fill.linear$y)

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

## -0.626830 -0.077590 -0.003457 -0.011213 0.031560 0.581801

plot(gwg, main="Gap-filled time series", type="l",

ylab="Groundwater depth (m)")
points(gw.fill.aspline$x, gw.fill.aspline$y, col="red", cex=2)
points(gw.fill.aspline$x, gw.fill.aspline$y, col="red", pch=20)
points(gw.fill.linear$x, gw.fill.linear$y, col="brown", cex=2)
points(gw.fill.linear$x, gw.fill.linear$y, col="brown", pch=20)
points(time(gw)[ix], gw[ix], col="darkgreen", cex=2)
points(time(gw)[ix], gw[ix], col="darkgreen", pch=20)
text(2000, 34, "linear", col="brown", pos=2)
text(2000, 32.5, "Akima spline", col="red", pos=2)
text(2000, 31, "true value", col="dark green", pos=2)

Gap−filled time series

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50

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Groundwater depth (m)

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40

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35

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linear
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true value
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30

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1975 1980 1985 1990 1995 2000 2005

Time

The period from mid-1987 to mid-1988 has, by chance, many missing

values, so we plot these in detail:
plot(window(gwg, start=1987, end=1989),
main="Gap-filled time series",
sub="True values in dark green", type="l",
ylab="Groundwater depth (m)", ylim=c(39,47))
points(x=time(gw), y=as.numeric(gw), col="darkgreen", lty=2, pch=20, type="b")
points(time(gw)[ix], gw[ix], col="darkgreen", cex=2)
points(gw.fill.aspline$x, gw.fill.aspline$y, col="red", cex=2, type="b", lty=1)
points(gw.fill.aspline$x, gw.fill.aspline$y, col="red", pch=20)
points(gw.fill.linear$x, gw.fill.linear$y, col="brown", cex=2, type="b", lty=1)
points(gw.fill.linear$x, gw.fill.linear$y, col="brown", pch=20)
text(1989, 46, "linear", col="brown", pos=2)
text(1989, 44.5, "Akima spline", col="red", pos=2)

116
text(1989, 43, "true value", col="dark green", pos=2)

Gap−filled time series

●
●

46
●
linear
●

●
Groundwater depth (m)

●
● Akima spline
●
●
●
44

●
●

●
●
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true value
● ●
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42

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1987.0 1987.5 1988.0 1988.5 1989.0

Time
True values in dark green

Q73 : How well did the interpolators fill the longer gaps? Jump to A73
•

7.3.2 Systematic gaps

These are when observations are not made for some block of time, per-
haps because of a broken instrument or budget problems. The most
interesting case is when an entire cycle is missing.

Task 85 : Simulate a missing year in the groundwater depth records. •

We know the years of the record, extracted from the full date with the
floor function:
unique(floor(time(gw)))

## [1] 1975 1976 1977 1978 1979 1980 1981 1982 1983 1984 1985 1986 1987
## [14] 1988 1989 1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000
## [27] 2001 2002 2003 2004

Select a “typical” year, 1997; remove it; to make the display easier to use
just consider the series since 1990, using the window function. We use
the which function to find the array indices for 1997.
gww <- window(gw, start=1990)
gwg <- gww
(six <- sort(which(floor(time(gwg))==1997)))

## [1] 85 86 87 88 89 90 91 92 93 94 95 96

gwg[six] <- NA
summary(gwg)

## Min. 1st Qu. Median Mean 3rd Qu. Max. NA's

## 39.07 43.92 47.21 47.78 51.71 57.68 12

117
plot(gwg, main="Missing year 1997", ylab="Groundwater depth (m)")

Missing year 1997

55
Groundwater depth (m)

50
45
40

1990 1995 2000 2005

Time

Task 86 : Interpolate the missing values with linear interpolation and

Akima splines. •
gw.fill.linear <- approx(x=time(gwg), y=gwg, xout=time(gww)[six], rule=2)
gw.fill.aspline <- aspline(x=time(gwg), y=gwg, xout=time(gww)[six])
summary(gw.fill.linear$y - gww[six])

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

## -2.0562 -0.9367 0.6662 0.3758 1.6392 2.7062

summary(gw.fill.aspline$y - gww[six])

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

## -1.5406 -0.4931 0.8019 0.5988 1.5852 2.7198

summary(gw.fill.aspline$y - gw.fill.linear$y)

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

## -0.11433 -0.00781 0.26119 0.22296 0.44363 0.51554

plot(window(gwg, start=1996, end=1999), main="Gap-filled time series",

type="l", ylab="Groundwater depth (m)", ylim=c(43,49))
points(gw.fill.aspline$x, gw.fill.aspline$y,
col="red", cex=2, lty=1, type="b")
points(gw.fill.aspline$x, gw.fill.aspline$y,
col="red", pch=20)
points(gw.fill.linear$x, gw.fill.linear$y,
col="brown", cex=2, lty=1, type="b")
points(gw.fill.linear$x, gw.fill.linear$y,
col="brown", pch=20)
points(time(gww)[six], gww[six],
col="darkgreen", cex=2, lty=1, type="b")
points(time(gww)[six], gww[six],
col="darkgreen", pch=20)
text(1999, 45, "linear", col="brown", pos=2)
text(1999, 44, "Akima spline", col="red", pos=2)
text(1999, 43, "true value", col="dark green", pos=2)

118
Gap−filled time series

49
48
Groundwater depth (m) ●
●

47
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45

● ●
● linear
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● ●

● ●
44

Akima spline
●
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●
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43

true value
●
●

1996.0 1996.5 1997.0 1997.5 1998.0 1998.5 1999.0

Time

Q74 : Are these satisfactory interpolators? Jump to A74 •

Another method is clearly called for.

7.4 Estimation from other series

For irregular series like rainfall or stream levels, where there are rapid
changes in short times, and often periods with zeroes (rainfall) or low
values (baseflow of streams), gap-filling with interpolation will not work.
One simple method is to estimate from correlated time series, that do
have some observations in common, and have observations at the same
times as the missing values.
This is complicated by the fact that correlations over the whole series
may not be consistent. For example, correlations of rainfall records in a
dry season may be very good (everything is low or zero most days) but
poor in a wet season (even if it rains on the same days, the amounts may
be considerably different).
To examine this method, we use two additional rainfall stations in the
Lake Tana basin, following the procedures from §2.2.

Task 87 : Read the CSV files for stations WeteAbay and Dangila into R
objects and examine their structures. •
tana.2<- read.csv("./ds_tsa/Tana_Daily_WeteAbay.csv", skip=1, header=T,
colClasses=c(rep("integer",2), rep("character",12)),
blank.lines.skip=T,na.strings=c("N.A","NA"," "))
str(tana.2)

## 'data.frame': 217 obs. of 14 variables:

## $ Year: int 2000 NA NA NA NA NA NA NA NA NA ...
## $ Date: int 1 2 3 4 5 6 7 8 9 10 ...
## $ Jan : chr "0" "0" "0" "0" ...
## $ Feb : chr "0" "0" "0" "0" ...

119
## $ Mar : chr "0" "0" "0" "0" ...
## $ Apr : chr "0" "0" "0" "12.9" ...
## $ May : chr "0" "0" "0" "12.6" ...
## $ Jun : chr "0" "12.6" "10.4" "10.3" ...
## $ Jul : chr "9" "0.3" "8.4" "46.6" ...
## $ Aug : chr "8.4" "4.4" "6.6" "6.4" ...
## $ Sep : chr "14" "0" "10.9" "1.4" ...
## $ Oct : chr "10.1" "27.8" "0" "20.2" ...
## $ Nov : chr "0" "0" "0" "0" ...
## $ Dec : chr "0" "0" "0" "0" ...

sum(is.na(tana.2[,3:14]))

## [1] 0

tana.3<- read.csv("./ds_tsa/Tana_Daily_Dangila.csv", skip=1, header=T,

colClasses=c(rep("integer",2), rep("character",12)),
blank.lines.skip=T,na.strings=c("N.A","NA"," "))
str(tana.3)

## 'data.frame': 620 obs. of 14 variables:

## $ Year: int 1987 NA NA NA NA NA NA NA NA NA ...
## $ Date: int 1 2 3 4 5 6 7 8 9 10 ...
## $ Jan : chr "0" "0" "0" "0" ...
## $ Feb : chr "0" "0" "0" "0" ...
## $ Mar : chr NA NA NA NA ...
## $ Apr : chr NA NA NA NA ...
## $ May : chr NA NA NA NA ...
## $ Jun : chr NA NA NA "0" ...
## $ Jul : chr "3.4" "7.8" "8.6" "13.3" ...
## $ Aug : chr "44.6" "22.3" "3.6" "22" ...
## $ Sep : chr "5.4" "1" "37.9" "2.2" ...
## $ Oct : chr "4.8" "2.2" "8.3" "4.5" ...
## $ Nov : chr "0" "0" "0" "0" ...
## $ Dec : chr "0" "0" "0" "0" ...

sum(is.na(tana.3[,3:14]))

## [1] 383

Task 88 : Set the trace values and any measurements below 0.1 to
zero. •
require(car)
for (i in 3:14) {
tana.2[,i] <- recode(tana.2[,i], "c('TR','tr','0.01')='0'")
}
for (i in 3:14) {
tana.3[,i] <- recode(tana.3[,i], "c('TR','tr','0.01')='0'")
}
sum(c(tana.2[,3:14],tana.3[,3:14])=="TR", na.rm=TRUE)

## [1] 0

sum(c(tana.2[,3:14],tana.3[,3:14])=="tr", na.rm=TRUE)

## [1] 0

sum(c(tana.2[,3:14],tana.3[,3:14])=="0.01", na.rm=TRUE)

## [1] 0

sum(c(tana.2[,3:14],tana.3[,3:14])=="0", na.rm=TRUE)

## [1] 0

120
Task 89 : Organize the daily values as one long vector of values, as
required for time series analysis. •
Which years do we have?
sort(unique(tana$YEAR))

## [1] 1981 1982 1983 1984 1985 1986 1987 1988 1989 1990 1991 1992 1993
## [14] 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006

sort(unique(tana.2$Year))

## [1] 2000 2001 2002 2003 2004 2005 2006

sort(unique(tana.3$Year))

## [1] 1987 1988 1989 1990 1991 1992 1993 1994 1995 1996 1997 1998 1999
## [14] 2000 2001 2002 2003 2004 2005 2006

tana.2[tana.2$DATE==29,"FEB"]

## NULL

tana.3[tana.3$DATE==29,"FEB"]

## NULL
month.days <- c(0,0,31, 28, 31, 30, 31, 30, 31, 31, 30, 31, 30, 31)
tana.2.ppt <- NULL;
for (yr.first.row in seq(from=1, by=32, length=(2006 - 2000 + 1))) {
for (month.col in 3:14) {
tana.2.ppt <-
c(tana.2.ppt,
tana.2[yr.first.row:(yr.first.row + month.days[month.col]-1),
month.col])
}
};
str(tana.2.ppt)

## chr [1:2555] "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" ...

length(tana.2.ppt)/365

## [1] 7

tana.3.ppt <- NULL;

for (yr.first.row in seq(from=1, by=32, length=(2006 - 1987 + 1))) {
for (month.col in 3:14) {
tana.3.ppt <-
c(tana.3.ppt,
tana.3[yr.first.row:(yr.first.row + month.days[month.col]-1),
month.col])
}
};
str(tana.3.ppt)

## chr [1:7300] "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" ...

length(tana.3.ppt)/365

## [1] 20

rm(month.days, yr.first.row, month.col)

Check that this is an integral number of years:

121
Task 90 : Convert this to a time series with the appropriate metadata.
•
Again, the ts function is used to convert the series; the frequency ar-
gument specifies a cycle of 365 days and the start argument specifies
the beginning of each series:
tana.2.ppt <- ts(tana.2.ppt, start=2000, frequency=365)
str(tana.2.ppt)

## Time-Series [1:2555] from 2000 to 2007: 0 0 0 0 ...

tana.3.ppt <- ts(tana.3.ppt, start=1987, frequency=365)

str(tana.3.ppt)

## Time-Series [1:7300] from 1987 to 2007: 0 0 0 0 ...

Task 91 : Plot the two time series, and the original station for compar-
ison •
plot(tana.ppt, main="Lake Tana rainfall, Station 1",
ylab="mm", sub="Missing dates with red bars")
abline(h=60, col="gray")
points(xy.coords(x=time(tana.ppt), y=60, recycle=T),
pch=ifelse(is.na(tana.ppt),"l",""), col="red")
grid()

Lake Tana rainfall, Station 1

100
mm

l ll l l llllllll l l
20
0

1980 1985 1990 1995 2000 2005

Time
Missing dates with red bars

plot(tana.2.ppt, main="Lake Tana rainfall, Station 2",

ylab="mm", sub="Missing dates with red bars")
abline(h=60, col="gray")
points(xy.coords(x=time(tana.2.ppt), y=60, recycle=T),
pch=ifelse(is.na(tana.2.ppt),"l",""), col="red")
grid()

Lake Tana rainfall, Station 2

ll l ll l ll l ll ll l ll l ll
40
mm

20
0

2000 2001 2002 2003 2004 2005 2006 2007

Time
Missing dates with red bars

plot(tana.3.ppt, main="Lake Tana rainfall, Station 3",

ylab="mm", sub="Missing dates with red bars")
abline(h=60, col="gray")
points(xy.coords(x=time(tana.3.ppt), y=60, recycle=T),
pch=ifelse(is.na(tana.3.ppt),"l",""), col="red")

122
grid()

Lake Tana rainfall, Station 3

80
60
llllllll l l ll ll l ll lllllllllllllllllllll l llllllllllllllllllllllll

40
20
0

1990 1995 2000 2005

Time
Missing dates with red bars

Q75 : Do the three stations cover the same time period? Do they have
the same missing dates? Does every date have at least one observation
(from at least one of the stations)? Jump to A75 •

To answer this, we use the is.na logical function to determine whether

an observation is a missing value, and the which function to identify
these positions in the series. We then use these indices to print the
times, extracted by the time function.
(miss.2 <- which(is.na(tana.2.ppt)))

## [1] 2216 2217 2218 2219 2220 2221 2247 2248 2249 2275 2276 2277 2278
## [14] 2279 2280 2306 2307 2308 2309 2310 2336 2337 2338 2339 2340 2341
## [27] 2367 2368 2369 2370 2371 2397 2398 2399 2400 2401 2402 2428 2429
## [40] 2430 2431 2432 2433 2459 2460 2461 2462 2463 2489 2490 2491 2492
## [53] 2493 2494 2520 2521 2522 2523 2524 2550 2551 2552 2553 2554 2555

(time.miss.2 <- time(tana.2.ppt)[miss.2])

## [1] 2006.068 2006.071 2006.074 2006.077 2006.079 2006.082 2006.153

## [8] 2006.156 2006.159 2006.230 2006.233 2006.236 2006.238 2006.241
## [15] 2006.244 2006.315 2006.318 2006.321 2006.323 2006.326 2006.397
## [22] 2006.400 2006.403 2006.405 2006.408 2006.411 2006.482 2006.485
## [29] 2006.488 2006.490 2006.493 2006.564 2006.567 2006.570 2006.573
## [36] 2006.575 2006.578 2006.649 2006.652 2006.655 2006.658 2006.660
## [43] 2006.663 2006.734 2006.737 2006.740 2006.742 2006.745 2006.816
## [50] 2006.819 2006.822 2006.825 2006.827 2006.830 2006.901 2006.904
## [57] 2006.907 2006.910 2006.912 2006.984 2006.986 2006.989 2006.992
## [64] 2006.995 2006.997

miss.3 <- which(is.na(tana.3.ppt))

time.miss.3 <- time(tana.3.ppt)[miss.3]
miss.1 <- which(is.na(tana.ppt))
time.miss.1 <- time(tana.ppt)[miss.1]

The intersect set operator gives the sets where two time series share
the same missing dates.
length(miss.12 <- intersect(time.miss.1, time.miss.2))

## [1] 0

length(miss.13 <- intersect(time.miss.1, time.miss.3))

## [1] 96

length(miss.23 <- intersect(time.miss.2, time.miss.3))

123
## [1] 64

rm(miss.1, miss.2, miss.3, time.miss.1, time.miss.2, time.miss.3)

Task 92 : Find the common period of the three time series, and plot
them on one graph. •
This is the same procedures as in §6, i.e., using the ts.intersect func-
tion to create a “multiple time series” object of class mts:
t3 <- ts.intersect(tana.ppt, tana.2.ppt, tana.3.ppt)
str(t3)

## Time-Series [1:2555, 1:3] from 2000 to 2007: 0 0 0 0 ...

## - attr(*, "dimnames")=List of 2
## ..$ : NULL
## ..$ : chr [1:3] "tana.ppt" "tana.2.ppt" "tana.3.ppt"

class(t3)

## [1] "mts" "ts" "matrix"

plot(t3, main="Lake Tana rainfall, 3 stations")

Lake Tana rainfall, 3 stations

120
100
80
tana.ppt
60
40
20
0
60
tana.2.ppt
40
20
0
60
50
tana.3.ppt
40
30
20
10
0

2000 2001 2002 2003 2004 2005 2006 2007

Time

7.5 Answers

A70 : After deletion there are five NA (missing) values. The median and mean
change slightly because of the deleted values. Return to Q70 •

A71 : Fairly well, especially when the missing value was in a linear section of
the graph (steady increase or decrease in depth). However, for March 1997 it
missed the high-water stand substantially; this is because that point happens
to be a local extremum and not in a linear section of the curve. Return to Q71

124
•

A72 : The three interpolators are very similar for the gaps in linear sections
of the graph; however for the extremum of March 1997 there are substantial
differences; both spline interpolators are much closer (about 30 cm) to the true
value. Return to Q72 •

A73 : For gaps in the linear sections of the graph, both interpolators per-
formed reasonably well. However, with longer gaps around extrema, as in
early 1988, both underestimate the extremes. Akima splines performed better
than linear interpolation. Return to Q73 •

A74 : The interpolators reproduce the overall trend in groundwater depth

during the missing year (slightly decreasing); the spline has a very attenuated
seasonality as well. But the strong seasonal effect is completely missing. Re-
turn to Q74 •

A75 : The stations all end in December 2006, but they start in 1981 (Bahir
Dar), 1987 (Dangila), and 2000 (Wete Abay). The first and second stations have
no missing dates in common, whereas the third station has some of the same
missing dates as the other two stations. Return to Q75 •

8 Simulation

To simulate a time series is to generate a series with defined statistical

characteristics. This requires a model (§4) with a stochastic (random)
component; the simulation uses random-number generation from vari-
ous probability distributions. R is particularly strong in this area.
Simulations are used to generate many probable “states of nature”; these
are then used as inputs to decision-theoretical models. For example,
simulating hundreds of years of rainfall, according to a calibrated model,
allows direct evaluation of the probability of an extreme event such as
prolonged drought.
Simulation of climatic time series is a key element of synthetic weather
generation [19].

8.1 AR models

In §4.4.1 we constructed AR(1) and AR(2) models of the groundwater

levels, after accounting for trend and seasonality. We can simulate the
process with these models, to see how well they reproduce the series.
The arima.sim function simulates AR, MA, ARMA and ARIMA models.
In this case we specify only an AR component.
The arima.sim function also has an optional sd argument to specify the
white noise.

125
Task 93 : Simulate three realizations of fifteen years of groundwater
level remainders with the AR(1) model from §4.4.1, and compare with
the actual series. •
Recall that the fitted AR(1) model is in object ar.gw.r.1; the coefficients
are in field ar of that object, and the red-noise (residual) variance in field
var.pred:
par(mfrow=c(4,1))
for (i in 1:3) {
plot(arima.sim(model=list(ar=ar.gw.r.1$ar), n=12*15,
rand.gen=rnorm, sd=sqrt(ar.gw.r.1$var.pred)),
main=paste("Simulated AR(1) process",i), ylab="modelled")
abline(h=0, lty=2)
}
plot(window(gw.r, 1989, 1989+15),
main="Remainders 1989 -- 2004", ylab="actual")
abline(h=0, lty=2)
par(mfrow=c(1,1))

126
Simulated AR(1) process 1

3
2
1
modelled

0
−1
−2
−3

0 50 100 150

Time

Simulated AR(1) process 2

3
2
1
modelled

0
−1
−2

0 50 100 150

Time

Simulated AR(1) process 3

3
2
1
modelled

0
−1
−2

0 50 100 150

Time

Remainders 1989 −− 2004

3
2
1
actual

0
−1
−2

1990 1995 2000

Time

Q76 : How well do the simulations reproduce the structure of the actual
series? Jump to A76 •

127
Task 94 : Repeat for the fitted AR(2) model. •
The fitted AR(2) model is in object ar.gw.r.
par(mfrow=c(4,1))
for (i in 1:3) {
plot(arima.sim(model=list(ar=ar.gw.r$ar), n=12*15,
rand.gen=rnorm, sd=sqrt(ar.gw.r$var.pred)),
main=paste("Simulated AR(2) process",i), ylab="modelled")
abline(h=0, lty=2)
}
plot(window(gw.r, 1989, 1989+15),
main="Remainders 1989 -- 2004", ylab="actual")
abline(h=0, lty=2)
par(mfrow=c(1,1))

128
Simulated AR(2) process 1

2
1
0
modelled

−1
−2
−3

0 50 100 150

Time

Simulated AR(2) process 2

3
2
1
modelled

0
−1
−2
−3

0 50 100 150

Time

Simulated AR(2) process 3

2
1
modelled

0
−1
−2

0 50 100 150

Time

Remainders 1989 −− 2004

3
2
1
actual

0
−1
−2

1990 1995 2000

Time

Q77 : How well do the AR(2) simulations reproduce the structure of the
actual series? Jump to A77 •

129
8.2 Answers

A76 : The AR(1) simulations seem somewhat noisier than that actual series.
The scale seems correct. Return to Q76 •

A77 : The AR(2) simulations seem to match the actual series better. Return
to Q77 •

130
References
[1] Hiroshi Akima. A new method of interpolation and smooth curve
fitting based on local procedures. Journal of the ACM, 17(4):589–
602, 1970. 112
[2] D Bates. Fitting linear mixed models in R. R News, 5(1):27–30, 2005.
63
[3] David Birkes and Yadolah Dodge. Alternative methods of regression.
John Wiley & Sons, Inc., New York, 1993. 72
[4] George E. P. Box. Time series analysis: forecasting and control.
John Wiley & Sons, Inc., fifth edition / edition, 2016. ISBN 978-
1-118-67492-5. URL http://ebookcentral.proquest.com/lib/
cornell/detail.action?docID=2064681. 1
[5] George E.P. Box, Gwilym M. Jenkins, and Gregory C. Reinsel. Time
series analysis: forecasting, and control. Prentice-Hall, Englewood
Cliffs, NJ, 3rd edition, 1994. 76
[6] William S. Cleveland and Susan J. Devlin. Locally weighted regres-
sion: an approach to regression analysis by local fitting. Jour-
nal of the American Statistical Association, 83(403):596–610, Sep
1988. ISSN 0162-1459, 1537-274X. doi: 10.1080/01621459.1988.
10478639. 32
[7] JC Davis. Statistics and data analysis in geology. John Wiley & Sons,
New York, 3rd edition, 2002. 1
[8] Peter J. Diggle. Time series: a biostatistical introduction. Oxford
Statistical Science Series; 5. Oxford Science Publications, Oxford,
1989. 1
[9] John Fox. An R and S-Plus Companion to Applied Regression. Sage
Publications, Thousand Oaks, CA, USA, 2002. 15
[10] Keith W. Hipel and A. Ian McLeod. Time series modelling of water
resources and environmental systems. Number 45 in Developments
in Water Science. Elsevier, 1994. ISBN 9780444892706. URL http:
//www.stats.uwo.ca/faculty/aim/1994Book/. 1, 72, 98
[11] Robert M. Hirsch, James M Slack, and Richard A Smith. Techniques
of trend analysis for monthly water quality data. Water Resources
Research, 18(1):107–121, 1982. 72, 73
[12] R Ihaka and R Gentleman. R: A language for data analysis and graph-
ics. Journal of Computational and Graphical Statistics, 5(3):299–314,
1996. 1
[13] Andrew V. Metcalfe and Paul S.P. Cowpertwait. Introductory Time
Series with R. Use R! Springer, 2009. DOI: 10.1007/978-0-387-88698-
5. 1
[14] R Development Core Team. R: A language and environment for sta-
tistical computing. R Foundation for Statistical Computing, Vienna,

131
Austria, 2004. URL http://www.R-project.org. ISBN 3-900051-
07-0. 1
[15] Jose D. Salas. Analysis and modeling of hydrologic time series.
In David R. Maidment, editor, Handbook of hydrology, pages 19.1–
19.72. McGraw-Hill, New York, 1993. 1, 107
[16] Robert H. Shumway and David S. Stoffer. Time series analysis and
its applications : with R examples. Springer, New York, 2nd edition,
2006. 1
[17] R Development Core Team. R Data Import/Export. The R Founda-
tion for Statistical Computing, Vienna, version 2.9.0 (2009-04-17)
edition, 2009. URL http://cran.r-project.org/doc/manuals/
R-data.pdf. 12
[18] WN Venables and BD Ripley. Modern applied statistics with S.
Springer-Verlag, New York, fourth edition, 2002. 1
[19] D S Wilks and R L Wilby. The weather generation game: a review of
stochastic weather models. Progress in Physical Geography, 23(3):
329–357, 1999. 125
[20] Daniel S. Wilks. Statistical methods in the atmospheric sciences. In-
ternational Geophysics Series 59. Academic Press, New York, 1995.
1, 79, 82

132
Index of R Concepts
[[]] operator, 25 IND argument (by function), 25
[] operator, 10, 78, 110 index.return argument (sort function),
$ operator, 44 51
~ operator, 25 intersect, 123
is.na, 14, 123
abline, 99
acf, 42, 45, 47, 63, 79, 89, 90 Kendall package, 72, 74, 98
aggregate, 26, 28
akima package, 112 lag, 41, 78
anova, 65 lag.plot, 40, 77
approx, 110, 115 lags argument (lag.plot function), 40
ar, 81, 82, 84 lm, 60, 63, 78
arima, 83, 84, 92 lowess, 32, 34
arima.sim, 125
MannKendall (package:Kendall), 72
as.numeric, 18, 24
match, 27
as.vector, 99
max, 18, 25, 28, 105
aspline (package:akima), 111, 112, 115
mean, 28
attributes, 3
median, 25, 28
boxplot, 25 min, 25, 28
by, 25 mts class, 55, 101, 124

c, 6, 16 NA constant, 109
car package, 15 na.action, 110
ccf, 103, 105 na.contiguous, 20
corAR1 (nlme package), 63 na.exclude, 110
correlation argument (gls function), 63 na.omit, 73, 99, 110
corStruct class, 63 nfrequency argument (aggregate func-
cycle, 4, 10, 24 tion), 28
nlme package, 63
deltat, 5
diff, 7, 8 pacf, 46, 64, 90
plot, 5, 17, 18, 36, 71
end, 3 plot.stl, 36
end argument (window function), 18 plot.ts, 5, 101
excel_sheets (readxl package), 12 plot.type argument (spectrum function),
extend argument (window function), 18 106
points, 17
file.show, 2, 12 predict, 68, 94
filter, 29 predict.Arima, 94
fitted, 85 predict.lm, 68
floor, 24, 117 print, 4
frequency, 5, 34, 86 print.ts, 4
FUN argument (aggregate function), 28
FUN argument (by function), 25 quantile, 25

geterrmessage, 110 read.csv, 13, 14

gls (nlme package), 63, 64, 96 read.table, 13
GuelphP dataset, 74, 98 read_excel (readxl package), 12

133
readxl package, 12
recode, 15
require, 15
rule argument (approx function), 115, 116

s.window argument (stl function), 34, 35,

37, 38
sample, 108
scan, 2
SeasonalMannKendall (package:Kendall),
72
set.seed, 108, 115
sort, 14, 51, 115
spans argument (spectrum function), 49
spectrum, 48, 106
spline, 112
stack, 15
start, 3
start argument (window function), 18
stats package, 112
stl, 34, 35, 44, 57, 110
stl class, 55
str, 3, 105
subset, 66
sum, 14, 18, 28
summary, 24, 25

t.window argument (stl function), 35, 38

time, 4, 10, 24, 110, 123
try, 110
ts, 3–5, 17, 122
ts.intersect, 101, 124
ts.plot, 37
ts.union, 101
tsdiag, 92

unique, 14

v graphics argument, 99

which, 9, 117, 123

which argument (plot function), 71
which.max, 9, 105
which.min, 9
window, 6, 18, 85, 117

xout argument (approx function), 111

xout argument (aspline function), 112

134

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