By Elaine Kennedy Sutherland, Peter W. Brewer,
Donald A. Falk and M. Elena Vel´asquez.
For FHAES version 2.0.2
Elaine Kennedy Sutherland
Missoula Forestry Sciences Lab
800 Block East Beckwith
Missoula, MT 59801 USA.
esutherland@fs.fed.us
Compiled using L
A
T
E
X 2
ε
Thursday 21
st
December, 2017
Permission is granted to copy, distribute and/or modify this document under the terms of the GNU Free Documentation License, Version 1.3
or any later version published by the Free Software Foundation; with no Invariant Sections, no Front-Cover Texts, and no Back-Cover Texts.
A copy of the license is included in the appendix entitled “GNU Free Documentation License” (pages 53–56).
FHAES
Fire History Analysis and Exploration System
By Elaine Kennedy Sutherland, Peter W. Brewer,
Donald A. Falk and M. Elena Vel´asquez.
Compiled: Thursday 21
st
December, 2017
Thursday 21
st
December, 2017
Contents
Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
1 Introduction 3
1.1 What is FHAES? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
1.2 Comparing FHAES and FHX2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
1.3 Where can I get help? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
1.4 How do I cite FHAES? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
2 Installation 5
2.1 Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
2.2 How to install FHAES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
2.3 How to uninstall FHAES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
2.4 Source code and development . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
3 Getting started 7
3.1 Main screen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
3.2 Data and analysis tabs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
3.2.1 File viewer tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
3.2.2 File summary tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
3.2.3 Analysis tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
3.2.4 Map tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
3.2.5 Chart tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
3.3 Data manipulation and tools . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
3.3.1 Merge selected files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
3.3.2 Create composite file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
3.3.3 Create event file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
3.3.4 Spatial join on selected files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
3.3.5 Create site summary shapefile . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
4 Data entry 13
4.1 Introduction to FHX data files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
4.2 Fire History Recorder . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
4.3 Metadata . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
4.4 Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
4.4.1 Events . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
4.4.2 Recorder years . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
4.5 Summary and Graphs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
4.6 Correcting erroneous files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
4.7 FHX2 restrictions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
4.8 Limitations of the FHX format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
5 Analyses 23
5.1 Descriptive summaries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
5.2 Interval analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
5.2.1 Total intervals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
5.2.2 Mean fire interval . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
5.2.3 Median fire interval . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
Thursday 21
st
December, 2017
iv CONTENTS
5.2.4 Standard deviation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
5.2.5 Fire frequency . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
5.2.6 Coefficient of Variation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
5.2.7 Skewness . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
5.2.8 Kurtosis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
5.2.9 Minimum and maximum fire intervals . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
5.2.10 Weibull Distribution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
5.2.11 Weibull Mean . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
5.2.12 Weibull Median . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
5.2.13 Weibull Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
5.2.14 Weibull Standard Deviation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
5.2.15 Weibull Skewness . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
5.2.16 Exceedance Intervals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
5.3 Seasonality . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
5.4 Binary summary matrices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
5.5 Binary comparison matrices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
5.6 Similarity and dissimilarity matrices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
6 Sample Size Analysis 33
6.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
6.2 Performing analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
6.3 Analysis results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
6.4 Interpreting results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
7 Superposed Epoch Analysis 37
7.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
7.2 Input files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
7.3 Window, Simulation, and Statistics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
7.4 Segmentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
7.5 Historical note . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
7.6 Analytical background . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
8 Fire History Charts 41
8.1 Chart components . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
8.2 Modifying the chart . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
8.2.1 Generic options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
8.2.2 Index plot options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
8.2.3 Chronology plot options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
8.2.4 Composite plot options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
8.3 Categories and sorting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
8.4 Exporting charts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
8.5 Clarification of component widths . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
A Recorder Years 45
B GNU General Public License 47
B.1 Preamble . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
B.2 Terms and Conditions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
C GNU Free Documentation License 53
C.1 Preamble . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
C.2 Terms and conditions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
D Trademark notices 57
References 59
Thursday 21
st
December, 2017
Preface
FHAES (Fire History Analysis and Exploration System) is a tool used to analyze fire history based on fire scar chronologies
developed from tree rings. FHAES has also been used to analyze chronologies of other disturbance events: any envi-
ronmental event that results in a distinct anatomical marker in the rings. FHAES is a reimplementation and expansion
of many functions of the FHX2 program (Grissino-Mayer, 2001). In FHAES the user can enter or revise fire event data
(FHX files), evaluate sample size, summarize (compile) site files, create shapefiles, draw fire charts, perform statistical
analysis, and evaluate the relationship between fire occurrence and presumed driving processes (e.g., climate conditions)
using superposed epoch analysis.
FHAES is written in Java and builds on a variety of open source libraries. Downloads are available for several operating
systems including Windows, OS X, Linux and UNIX. FHAES is open source software (see the details of the license on
pages 47–51), so you are encouraged to inspect and edit the code. Please contact the authors if you’ll like to find out
how you can contribute to the FHAES project.
The development of FHAES is guided by the scientific steering committee: Elaine Kennedy Sutherland; Tom Swetnam;
Donald Falk; Peter Brown; Henri Grissino-Mayer. FHAES is programmed by Peter Brewer and Elena Vel´asquez with
support from Elaine Kennedy Sutherland and Donald Falk.
We acknowledge the contributions of NOAA’s Paleoclimatic Division, Boulder, Colorado in early coordination and devel-
opment of this project. We mention with gratitude the contributions of the late Michael Hartman who set up NOAA’s
International Multiproxy Paleofire Database, and worked to integrate this project with it. We also acknowledge the im-
portant role played by Wendy Gross, who programmed FHAES’ original FHChart module and set up the original FHAES
website on FRAMES. Thanks also to the late Richard Holmes for his pioneering work on many of the analytical routines
that have been reimplemented in FHAES. Finally we’d like to thank the students of the University of Wisconsin-Platteville
(especially Joshua Brogan) along with Evan Larson, Kun Tian and Omar Meqdadi for their work on the data entry and
chart modules. An up-to-date list of all contributing programmers can be found in the ‘About’ dialog in the software.
We hope that you find FHAES useful and look forward to hearing your feedback.
Elaine Kennedy Sutherland
USDA Forest Service
Rocky Mountain Research Station
Peter W. Brewer
University of Arizona
Laboratory of Tree-Ring Research
Donald A. Falk
University of Arizona
School of Natural Resources and the Environment
and Laboratory of Tree-Ring Research
M. Elena Vel´asquez
Boise State University
Department of Mathematics
Thursday 21
st
December, 2017
Chapter 1
Introduction
1.1 What is FHAES?
FHAES (Fire History Analysis and Exploration System) is a software tool to evaluate fire regime properties such as
frequency, seasonality, extent, and fire/climate relationships from indicators of fire on trees. FHAES can also be used
to calculate similar properties for other events that create unique signatures in a time series, like light rings from insect
infestations or frost rings resulting from volcanic eruptions. FHAES accepts input data recording fire events in the Fire
History Exchange (FHX) format similar to FHX2 (Grissino-Mayer, 2001). The techniques of fire history analysis that
FHAES is built on assumes the user applied dendrochronological cross-dating methods to determine calendar year dates
of annual tree rings and the characteristics of fire scars (Baisan and Swetnam, 1990; Dieterich and Swetnam, 1984; Fritts,
1976; Holmes, 1983; Stokes and Smiley, 1968).
1.2 Comparing FHAES and FHX2
FHX2 (Grissino-Mayer, 2001) has long been the standard for fire history analysis. Copyrighted by Henri D. Grissino-
Mayer, it is a mix of Pascal and Fortran. It runs on Microsoft Windows operating systems, XP or earlier, and will run on
other operating systems by using a DOS emulator.
FHAES is a comprehensive reimplementation of most of FHX2’s functions. It is written as an open source, cross-platform,
GUI application. FHAES will run on all modern operating systems (including 32 and 64 bit versions) and takes advantage
of improvements in memory to analyze larger and longer datasets. In addition to reimplementing most functionality
provided by FHX2, FHAES also includes additional features that you may find useful.
We hope that those of you familiar with FHX2 will find transitioning to FHAES quite simple. It is, however, important
to understand that results produced by FHAES will not be identical in some cases to those produced by FHX2. For
instance there are differences in the precision of floating point numbers (especially for provided numbers like π) between
Pascal and Java. There are also different—yet equally valid—methods for performing certain calculations. For example,
Henri Grissino-Mayer generously provided the source code from FHX2 for us to consult when we were coding FHAES.
Unfortunately, the code for the Weibull function in FHX2 is a closed source binary (compiled Fortran code) so we had no
way to determine its precise implementation. Within FHAES, however, all functions are open source and can be inspected
by anyone interested in how the calculations are performed.
We are confident that the results produced by FHAES are identical, equivalent or more precise than those provided by
FHX2. If, however, you feel that you have an example dataset which illustrates a degradation in the results produced by
FHAES over FHX2, then we urge you to contact the authors so we can, with your assistance, investigate thoroughly.
Not every facet of FHX2 has been replicated in FHAES. While much of the output has been formatted as text and in
spreadsheets, not all the earlier output tables are available at this time. That can change, with user input. There is no
test for differences between two time periods or two subsamples of a site (“spatial differences”). If users express that
some component of FHX2 was important to their work and is now missing from FHAES, please let us know and we’ll do
our best to redevelop it in FHAES (fhaeshelp@gmail.com).
Thursday 21
st
December, 2017
4 FHAES: Fire History Analysis and Exploration System
1.3 Where can I get help?
This manual is the main source for information about FHAES and how to run it. The most up-to-date version of this
manual is available from http://help.fhaes.org, or if you prefer to download a copy from http://help.fhaes.
org/pdf/. If you would like a copy of the manual as it was at the release of a specific version of FHAES you can append
the version number to the URL (e.g. http://help.fhaes.org/2.0.0/ or http://help.fhaes.org/2.0.0/pdf/).
Please note that we intend to continue improving the manual over the coming months and years. Improvements will
include better descriptions of the analyses and how to interpret them as well as documentation for future new features.
Keep in mind if you choose to download a PDF version of the manual you will not be viewing the latest version. We
therefore suggest you periodically check the URLs above - especially when you install a new release.
If you can’t find the answer to your questions in the manual, you can email the developers at fhaeshelp@gmail.com
or through the contact form on the FHAES website. Another source is the ITRDB forum mailing list, especially if your
question is in regards to an academic issue (rather than FHAES itself) as many of the world’s leading dendropyrologists
are members.
1.4 How do I cite FHAES?
When you have used FHAES in your research please cite as you would any other academic publication. There are two
distinct products that you can cite: the software itself; and this manual. When citing the software you should include
the precise version of FHAES that you have used. Each official release of FHAES has it’s own DOI number which can
be found within the Help About dialog. Depending on your citation style, a typical citation will be:
Brewer, P.W., Vel´asquez, M.E., Sutherland, E.K. and Falk, D.A. (201X) Fire History Analysis and Exploration
System (FHAES) version X.X [computer software]. http://www.fhaes.org. DOI:10.5281/zenodo.XXXXX.
The citation for this user manual should be:
Sutherland, E.K., Brewer, P.W., Falk, D.A. and Vel´asquez, M.E. (2015) Fire History Analysis and Exploration
System (FHAES) user manual. [compiled on 21/12/2017]. http://www.fhaes.org.
Thursday 21
st
December, 2017
Chapter 2
Installation
2.1 Requirements
FHAES will run on any relatively modern operating system although testing is concentrated on the most recent releases.
On Windows, FHAES will run on all versions back to XP. On OS X, FHAES will run on Lion (v10.7) and later, as well as
64-bit Macs running Snow Leopard (v10.6). On Ubuntu, FHAES will run on Precise Pangolin (v12.04) and later. On all
other operating systems FHAES will run on anything that supports Java 7 or later, however, we highly recommend using
Java 8 for FHAES (and for any other Java application) because Java 7 has passed its end-of-life and security updates are
no longer released. Note that the Windows, OS X and Ubuntu packages come bundled with Java (or use the operating
system’s internal dependency manager) so there is no need to install Java separately.
2.2 How to install FHAES
Installation packages for FHAES are available for Windows, MacOS X, Linux and Unix. For users of other operating
systems FHAES can be run from an executable JAR file.
First, download the relevant installation file for your operating system: http://download.fhaes.org/
Windows – Run the installation program and follow the instructions
1
.Once installed, FHAES can be launched via
the Start menu.
Mac OS X – Download then mount the DMG file, and then drag FHAES into your applications folder. Depending
on your security settings OS X may block the launch of FHAES because it is not signed by an Apple-generated
certificate. In this case you will need to go to System Preferences Security and approve FHAES to be run.
Ubuntu Linux – A Deb file is available which was designed for use on Ubuntu distributions but should work on any
Debian based system. Install using your favorite package management system. On Ubuntu, the package will add a
FHAES shortcut to your applications menu. Alternatively you can start FHAES from the command line by typing
fhaes.
Unix – This binary installer script is designed to run on most Unix and Linux distributions. Simply make the script
executable and run from the command line. Note that this package does not include Java so you must ensure a
suitable version of Java (Java 7 or later) is already installed.
Other operating systems – Make sure you have Java 7 or later installed, then download the FHAES JAR file to
your hard disk. You can run FHAES from the command line by typing:
java -jar fhaes.jar
.
1
Some anti-virus programs may show warning messages that FHAES is not a widely known and may potentially be dangerous to install.
Such messages are not the result of a detected flaw in the software but simply an indication that it hasn’t been installed by thousands of
users! You will, however, notice that the application is signed with a valid security certificate owned by the lead developer at the University of
Arizona. This certificate shows the application hasn’t been altered by anyone outside of the FHAES development team, therefore if you trust
us you can ignore your anti-virus program’s warnings.
Thursday 21
st
December, 2017
6 FHAES: Fire History Analysis and Exploration System
2.3 How to uninstall FHAES
We understand that FHAES will never suit the requirements of all users, but as an open source product, we would
really appreciate feedback as to why it didn’t meet your needs. Without this feedback it is difficult to prioritize future
development.
For Windows users, FHAES can be uninstalled using the standard add/remove programs feature in control panel. Mac
users should simply delete the application from their applications folder. Linux users should use their prefered package
management tool.
2.4 Source code and development
FHAES is open source and we warmly welcome contributions from members of the community. If you would like to
inspect the source code or directly contribute to the development of FHAES please go to the FHAES Github page
https://github.com/petebrew/fhaes for further information. The main readme file displayed there contains details
of how to download the code into an Integrated Development Environment (IDE). The Github environment encourages
you to fork the code, make changes in your own version of the repository and then send pull requests to the main
development team. This is an easy and efficient way for new users to get aquainted with the code.
The Github pages also contain the issue system used to track bugs and feature requests, view progress towards the next
milestone/release as well as recent code changes via the ‘pulse’ page.
If you would like to discuss how you can contribute to FHAES please contact the main FHAES developers at fhaeshelp@
gmail.com.
Thursday 21
st
December, 2017
Chapter 3
Getting started
If you have not yet done so, please install FHAES using the instructions on page 5 for your particular operating system.
Once you launch FHAES you will be greeted by the FHAES home screen and ‘quick-start’ menu (figure 3.1). From here
you can:
Create a new FHX file – Details about creating new FHX data files and general information about the structure of
FHX files are in chapter 4. The data entry form is also accessible from the toolbar and file menu.
Load existing FHX file(s) – Load existing data files using the equivalent button on the toolbar or from the file menu
1
.
Files can be loaded in the main screen by dragging and dropping them from your operating system’s file manager.
There is a routine in FHAES that checks FHX files for formatting errors and tells the user where in the file the
format is wrong
2
.
Run Superposed Epoch Analysis (SEA) – SEA analyses are performed in a separate window. Full details are in
chapter 7.
Figure 3.1: The FHAES home screen displayed on startup. Begin using FHAES by selecting either ‘Create new FHX file’ or ’Load
existing FHX file(s)’.
1
If you do not have any FHX data files but would like to test FHAES, use one of the sample files provided on the FHAES site or you can
download data from NOAA’s International Multiproxy Paleofire Database http://www.ncdc.noaa.gov/paleo/impd/
2
If you come across problems with missing ‘non-English’ characters in FHX files loaded in FHAES see 4.7 for further assistance.
Thursday 21
st
December, 2017
8
Figure 3.2: The left panel shows the FHX files currently loaded and the right tabbed panel shows details about the selected file.
Note that the file list includes one file (us101001.fhx) that was checked and found to have formatting errors, and three files with
no fire events. The ‘File viewer’ tab is open and shows a view of the erroneous file us101001.fhx. FHAES is highlighting the error
in the file and is explaining the error in the message at the top of the screen.
Thursday 21
st
December, 2017
Getting started 9
3.1 Main screen
The main screen is divided into two main parts: the file list on the left and the main tab panels on the right. The file list
on the left shows all the FHX files currently loaded in FHAES and the main data and analysis tab panels on the right
show information about these files and the analyses performed.
FHAES uses the TRiCYCLE dendro converter library (Brewer et al., 2011) which makes use of the Tree Ring Data
Standard (TRiDaS – Jansma et al., 2010) to load files you have chosen and checks they are valid. FHX files that are
determined to be invalid are indicated by a red cross icon in the file list, while valid files are denoted by a green tick .
Files marked with an amber exclamation mark are technically valid FHX files but contain no valid event data (FHX
demography files for instance) and are therefore excluded from analyses although they can still be charted. Erroneous
files can be corrected by double clicking the appropriate file in the list and then using the FHAES data entry screen to
find and change the error(s), and re-save the file (see pages 13–18).
You can re-order the files using the drop down menu at the bottom of the left panel. The order of the files in the list
will be reflected by the order of the analysis results.
3.2 Data and analysis tabs
In the following sections, we describe the processes available in the right panel’s tabs of the main screen.
3.2.1 File viewer tab
The ‘File viewer’ tab displays the contents of the currently selected file in the file list (see figure 3.2). If this file is
erroneous (i.e. it is marked by a red cross symbol) then a message is shown at the top of the screen. Where possible,
FHAES will also highlight the line where the error exists. You can edit existing files by right clicking and choosing ’edit’,
or by using the equivalent toolbar or menu options.
3.2.2 File summary tab
The ‘File summary’ tab contains a report summarising the contents of the file currently selected in the file list. Note
that only files with a green or amber marker will have a file summary. The summary includes details about: how many
samples there are in the file; dates for the start and end of each sample; number of events; average number of years for
each fire event etc. This text report is similar to the basic summary output produced by FHX2.
3.2.3 Analysis tab
The ‘Analysis’ tab shows the ‘Analysis options’ dialog where you define the parameters you’d like to use for your assessment
of fire interval statistics and fire seasons, and for setting up numeric data matrices for further analyses outside of FHAES.
Full details are in chapter 5.
3.2.4 Map tab
The ‘Map’ tab contains an interactive map displaying the latitude and longitude of sites in currently loaded files, if it was
given in the header information. You can choose between a variety of background styles, zoom to the current map pins,
and also turn the pin labels on or off using the buttons at the top of the page.
Please note that the latitude and longitude fields in FHX files are free-text and can therefore be in many formats. While
FHAES will do its best to parse these fields to ascertain the coordinates, this may fail - in which case you will be warned.
Please also note that in addition to lat/long fields, FHX-formatted files can contain location information in UTM and
township/range fields. Because there is no field in FHX files to record the UTM zone (essential for the UTM easting
and northing values to make sense), UTM information is disregarded by FHAES. Due to the huge potential variability of
townshop/range data and the very limited use of these fields in FHX, they are also disregarded by FHAES. We strongly
Thursday 21
st
December, 2017
10 FHAES: Fire History Analysis and Exploration System
recommend using standardized WGS84 decimal latitude and longitude in your FHX files. Note you can use the FHAES
data entry metadata tab to standardize coordinates.
FHAES uses the latitude and longitude fields in all spatial analyses. For further information see sections 3.3.4 and 3.3.5.
3.2.5 Chart tab
The ‘Chart’ tab displays a standard fire history chart for the currently selected file. There are many options for altering
the content and style of the chart. See chapter 8 for a full description.
3.3 Data manipulation and tools
FHAES includes a number of tools for manipulating and processing your fire history data. These are available from
various buttons on the toolbar and from the ‘Data’ and ‘Tools’ menus on the main screen. Because of their complexity,
the Sample Size Analysis and tools are described in their own chapters (chapters 6 and 7 respectively). Descriptions
and instructions for all other tools are provided below:
3.3.1 Merge selected files
The ‘merge selected files’ tool enables you to combine the data from two or more FHX files into a single file. It
maintains all the samples from each input file as separate series within the output file. Note that because the tool
requires two or more files, it will only be enabled once you select two or more files from the file list. When you launch
the tool you will be asked whether to merge all years or just a subset of years. Once you have made your choice you
will then be asked where you’d like to save the resulting FHX file, and whether you’d like to immediately add it to your
existing project.
3.3.2 Create composite file
The ‘create composite file’ tool is similar to the merge tool, with the exception that all samples from a file are combined
into a single series in the output. The output file therefore contains only one series per input file, labeled with the site
code. Like the merge tool, a dialog will open asking whether the output file should be restricted to a specified range of
years, or whether to include all years. However, you will also be asked to specify how the composite should be calculated.
When creating a composite you might wish to only include broadly represented (“major”) events in your datasets. The
composite filter enables you to create a site composite composed using either a minimum number of events in a given
year or the minimum percentage of series sharing the event in a given year for it to be included. For example, the filter
for minimum number of events might be set at (for a given year) at least two fires among all the series indicate a fire
to be included in the composite as a fire. Alternatively, the filter could be set at (for a given year) a minimum of 25%
of the series indicate a fire to be included in the composite. The filter dialog also requires you to specify the minimum
number of samples or recording samples in a year.
Note that events in composite files are always recorded as having an unknown seasonality because FHX files cannot
represent events with multiple seasons within a single year.
3.3.3 Create event file
The ‘create event file’ tool produces a simple single column text file containing a list of years recording events. The
file is typically used as an input to Superposed Epoch Analysis (see chapter 7) but may also be of use for other analyses.
The tool is run on one or more selected files from the file list, and like the composite tool, it also asks the user to specify
a year range, and options for how to filter the input files into a composite.
Thursday 21
st
December, 2017
Getting started 11
3.3.4 Spatial join on selected files
The ‘spatial join’ tool provides a method for creating event, composite and merge files based on location. It is only
available when two or more files are selected in the file list. The tool works by clustering together files based upon the
lat/long location fields provided in the FHX file header. It gives you the option to specify a threshold in kilometres lower
than which sites are combined together. This is useful when doing regional analyses when you have multiple sites located
close to each other recording similar fire histories. By combining these together you can simplify the comparison between
these sites and those located further away.
When you specify your distance threshold, the tool will automatically create groups of sites list on the left of the dialog.
You can click on each in turn to examine which sites have been included in each group. Files with no location information
(or whose location information has not been successfully parsed) are located in a final miscellaneous group. By double
clicking on the group names you can rename them to suit your needs. The tool also includes a separate map tab to show
the spatial relationship between the groups. Each group is given a unique color.
The other parameter that needs to be set before continuing is what sort of output file you’d like to create: event;
composite; or merge files. Once you’ve chosen your output file type and selected save you will be asked to chosen an
output folder location. The files will be named according to the names you gave each group.
3.3.5 Create site summary shapefile
The ‘create site summary shapefile’ tool enables you to save the results of the ‘binary site summary’ table in Shapefile
format for further visualization and analysis in GIS applications such as ArcGIS and QGIS. The resulting shapefile is
typically viewed in conjunction with a temporal GIS plugin such as the Time Slider facility in ArcGIS or the Time
Manager plugin to QGIS
3
.
Figure 3.3: The screenshot of the export to shapefile dialog.
The export to shapefile dialog (figure 3.3) asks the user to provide an export filename, to specify the style of attribute
table to use and to select the years you’d like to include. There are two attribute table styles, which you will find most
convenient will depend on the GIS tool you are using.
The first creates a shapefile with just one map marker pin (row) per site but the associated attribute table contains
multiple fields, one for each year requested. Because the shapefile format only supports a limited number of fields you
can only include data for 255 years in your file. An example of the associated attribute table as displayed by QGIS is
shown on the left in figure 3.4.
The second style creates multiple map markers (rows) for each site, one for each requested year. So if you select 200
years you will end up with a shapefile containing 200 markers in the same location for each site in your dataset. The
associated attribute table will have just two fields, one containing the year and the other the data value. An illustration
3
http://anitagraser.com/projects/time-manager/
Thursday 21
st
December, 2017
12 FHAES: Fire History Analysis and Exploration System
Figure 3.4: Examples of the attribute tables associated with the shapefiles exported by FHAES. On the left is the table produced
when the output style was set to ‘one marker per site with multiple year attributes’, whereas the right shows the output style when
set to ‘multiple markers per site, one for each year’.
of this is shown on the right in figure 3.4. There are no hard coded limits to the number of sites or years you can include
using this style. However, if you do select a very large dataset you may find that your GIS becomes sluggish. In this case
you would be best to import your data into a spatial database and ensure the relevant indexes have been configured.
Thursday 21
st
December, 2017
Chapter 4
Data entry
4.1 Introduction to FHX (Fire History Exchange) data files
The FHX data format is the data standard used to archive fire-scar based fire history data in the International Multi-
proxy Paleofire Database hosted by NOAA
1
. Although the file extensions are .fhx, they are actually text files formatted
specifically for storing fire history information. While we recommend using the data entry tool in FHAES, with a good
understanding of the format it is also possible to edit FHX files using standard text editing software.
The information recorded with FHX files includes an optional (yet highly recommended) header for storing metadata
about the site and the samples, followed by the data (see figure 4.1 for an example data file). The data include the
sample identification code and information regarding the beginning and ending year, years when the sample was and was
not fire scar susceptible, and years when a fire scar or other indicator was recorded. The sample data are not numeric as
is typical in dendrochronological data files, they are categorical and describe the status of each tree ring for the entire
series. There are different characters for the beginning year depending on whether the sample included the pith (the true
inside year). There are also different characters for the last year of the series, indicating whether the sample still had
bark, or if the outside was bare wood that could potentially have eroded (and not included the last year of life). The
position of a fire scar or other indicator in an annual ring relative to its earlywood or latewood is sometimes visible. This
provides evidence of when the wildfire burned relative to the tree growth season.
An important concept in fire history analysis is “recording years” and in subsequent sections of this manual you will read
many references to it. Whether particular rings are in recording status matters because it affects the analysis statistics,
including mean, mode, variance, and many other descriptors. A recording year might be simply defined as a year when a
tree could record a fire. Most analysts consider this to be the years after the first scar. After a tree is injured by a fire
and the bark later falls away, the tree is considered ”fire-susceptible,” because wood is exposed and is in recording status.
This biological response and physical condition translates into an FHX series being in non-recording status in pre-injury
years and recording status in post-injury years. Once scarred, the tree is in recording status for the rest of its life, with
some exceptions. There will be more about this issue in section A, below.
A complete list of the characters used for recording these data is shown in table 4.1.
The data for each sample are arranged by column, with each row corresponding to a year—beginning with the earliest year
of any sample in the entire data set and ending with the latest year in the entire data set. This may seem unusual, but
the nature of the data drives it. Fire scar data series can be several centuries or even millennia long. If the data format
were reversed—that is, each year was represented by a column rather than a row—then there could be many hundreds
of columns in a file. Viewing and managing many columns of data is far more unwieldy in most software compared to
viewing and managing many rows of data.
Further information about the FHX file format can be found on the NOAA Paleoclimate website
2
1
http://www.ncdc.noaa.gov/data-access/paleoclimatology-data/datasets/fire-history
2
http://www.ncdc.noaa.gov/paleo/impd/tree_event_info.html
Thursday 21
st
December, 2017
14 FHAES: Fire History Analysis and Exploration System
Header / Metadata
Data
Figure 4.1: An example FHX data file with header/metadata at top followed by data section. Note the file has been split and
truncated (indicated by the line numbers on the left) to show the detail of the most interesting part of the file.
Thursday 21
st
December, 2017
Data entry 15
Symbol Described as Interpreted as
. Period or dot (Can indicate two things:)
- Space holder in data matrix before sample starts or after sample
ends
- Dated tree rings if sample is not recording for some period (typically
before the first event in a series)
{ Left curly bracket Beginning of sample’s tree-ring series, if pith is not present
} Right curly bracket End of sample’s tree-ring series, if no bark is present
[ Right bracket Pith date of a sample; not always present
] Left bracket Bark date of a sample; not always present
| Bar or Pipe Recorder year. Tree is capable of recording fires but no fire was
detected. Typically starts the year after the first fire event. See
appendix A
D,d Dormant season The injury occurred between after cambial growth ceased or before
it began; during the cambial “dormant” season
E,e Early earlywood The injury occurred during the first third of tree ring growth.
M,m Middle earlywood The injury occurred in the middle third of the tree ring growth.
L,l Late earlywood Cambium was injured late in earlywood development.
A,a Latewood The injury was apparent in the latest stage of cambial growth that
year.
U,u Undetermined The position of the injury either was not or could not be determined.
Table 4.1: Symbols that indicate the status of each tree ring in a sample series. Brackets indicate beginning and ending years but
are different depending on whether the pith or bark are present. Upper case letters designate years with fire scars, while lower case
letters show years when indicators of fire other than scars–like resin ducts and growth releases–were present. Periods (dots) are
used to fill the years before the tree was first scarred, or during periods when it is uncertain that the tree was recording fires (for
example, a pocket of rot has obscured some rings).
4.2 Fire History Recorder
The purpose of the data entry module (FHRecorder) in FHAES is to create and edit FHX files. Please note that it is
designed for editing standard data series files recording information about individual trees (as outlined above) and not
for the very similarly formatted ‘composite’ files (see section 3.3.2) that represent data for multiple trees and/or sites.
There should be no need for you to manually edit composite files and FHRecorder will warn you of this.
When creating a file we strongly advise you to record the metadata as fully as possible. If all the information is not
available at first, fill out as much as possible and plan to obtain it and revise the file later. Because the original FHX
metadata format did not provide a field to record UTM zone, if you have the UTM coordinates, record the zone used in
the comment field and fill out the latitude and longitude field. We strongly recommend that you use the latitude and
longitude fields as the primary means for recording locality information.
To create a new file you can click the icon on the toolbar, or by going to File New. If you’d like to edit an existing
file open it in FHAES as normal, then double click the entry in the file list, or select the file and click the edit button
on the toolbar.
The main data entry screen has four tabs: data; metadata (see figure 4.2); summary; and graphs. These are described
in detail in the following sections.
4.3 Metadata
The metadata tab provides a straightforward method for filling out the fields that make up the FHX header and at the
bottom of the tab is space to enter comments. Next to each field is a help tip button which gives you a short description
of the field and the sort of data you should be entering. This information is also provided below:
Township, Range, Section, Quarter Section – Township, range, section and quarter section fields have been used
historically in the USA to record the locations using the Public Land Survey System. If used, the township and
range fields are required at a minimum, with the section and quarter section values optionally used depending on
Thursday 21
st
December, 2017
16 FHAES: Fire History Analysis and Exploration System
Figure 4.2: The main data entry dialog showing a file containing multiple series. The details of the selected series (666) are shown
on the right. We can see it contains fire scars in the early earlywood portion of the 1892, 1922 and 1962 rings.
the precision and size of area being defined. These fields are not used by FHAES in spatial analysis, the latitude
and longitude fields should be used instead.
Site name – Human readable name for the site. To be compatible with FHX2 this field should be no more than 70
characters long.
Site code – Short code used to identify the site. By convention and for use in FHX2, this should be 3 characters long,
but can be longer if you only intend to use the file in FHAES.
Collection date – Date or dates when the samples included in this file were collected. It is best to use the ISO 8601
standard so that dates are recorded YYYY-MM-DD e.g. 2000-12-25.
Collector(s) name(s) – The name or names of those in the field that collected the samples represented in this file.
Dater(s) name(s) – Name or names of those who provided the dendrochronological placement for these samples.
Latin name(s) – Latin names of the trees from which these samples were taken. If more than one species is included
in this file separate them with commas and then provide further information in the comments field.
Common name(s) – Common/vernacular names for the species in this file. As for latin names if more than one species
is included then separate with commas.
Habitat type – Habitat type at this site. Please use standardized naming systems applicable to the region wherever
possible.
Country – Country where this site is located.
State – State where this sample is located.
County – County where this sample is located.
Park – Park (e.g. National Park) where this site is located.
Forest – Name of forest where this site is located.
Ranger district – The Ranger district that covers this site.
Thursday 21
st
December, 2017
Data entry 17
UTM easting –Warning Deprecated – UTM easting value for the site. The FHX specification does not provide a facility
for recording the UTM zone so UTM data is ignored by FHAES. The latitude and longitude fields should be used
instead.
UTM northing –Warning Deprecated – UTM northing value for the site. The FHX specification does not provide a
facility for recording the UTM zone so UTM data is ignored by FHAES. The latitude and longitude fields should
be used instead.
Latitude – Latitude value for the location of this site. Although this is a free text field and any formatting is valid, we
strongly recommend using decimal degrees. Existing free text values can be parsed and converted using the convert
button.
Longitude – Longitude value for the location of this site. Although this is a free text field and any formatting is valid,
we strongly recommend using decimal degrees. Existing free text values can be parsed and converted using the
convert button.
Topographic map – Reference to the topographic map covering the site.
Highest elevation – Highest elevation of the site. Please also specify units.
Lowest elevation – Lowest elevation of the site. Please also specify units.
Slope angle – Angle of the slope of the site either as a description, or as a value in degrees.
Slope aspect – General aspect of the site, typically recorded as compass direction.
Area sampled – Total area sampled. Please also specify units. Should be 10 characters or less to remain compatible
with FHX2.
Substrate – Description of the substrate at this site.
Sample count – This field is automatically set by FHAES depending on the number of samples entered in the data
screen.
Note that all fields are free-text with no formatting restrictions (see section 4.8) but it is best to be consistent and
standardize wherever possible . For example, we strongly suggest for the latitude and longitude fields you restrict yourself
to using standard WGS84 decimal degrees. If you do have coordinates in other styles you may like to try the conversion
buttons to standardize your data. It will successfully convert many commonly used styles of coordinates including those
in degrees, minutes and seconds.
The metadata tab includes a checkbox to enforce original FHX2 field length requirements. The original FHX2 program
included limits for the length of each field. Although FHAES does not have these same limitations (see section 4.7), if
you intend to use the file in FHX2 as well as FHAES you should tick the checkbox here. Fields that do not meet the
FHX2 specification are highlighted in red and a warning appears at the top of the screen. Note this checkbox enforces a
length limit on sample names too.
4.4 Data
The main data tab is where you enter details about your samples and events. The panel on the left shows a list of series
within the file. Series can be added and removed using the plus and cross buttons respectively. The order of the series
can also be changed, either automatically by choosing sort criteria, or manually by using the up and down buttons. The
order of the series in this list will be reflected in the order they appear in the FHX file, and therefore the order they will
appear in analysis outputs and charts.
When you add a new series, you will be asked: to give the series a name; to specify the start and end years for the
sequence; and to indicate whether the sample has pith and/or bark (see section 4.8 for an explanation of cases where
pith/bark information is disregarded). In FHAES, the series name can be as long as the user wishes unless the ‘Force
FHX2 requirements’ checkbox has been selected on the metadata page. In this case you will be restricted to eight
characters to ensure the file can be successfully read in the original FHX2 program. See section 4.7 for more information.
Thursday 21
st
December, 2017
18 FHAES: Fire History Analysis and Exploration System
4.4.1 Events
To add events to the series, first select the sample in the list. The panels on the right will show the details about
the selected series and list any existing events currently associated with it. The series name, year range, pith and bark
information are displayed and can be edited at the top of the screen. You can add events by clicking the add event
button. In the event table you can then specify: whether the event is a fire or other injury; the year the event was
recorded and what season it was recorded in. Note that events will automatically be ordered into chronological sequence.
Once the recording years table (described below) has been populated also note that you will not be able to add events
that fall outside of the year range(s) that describe when the tree was ‘recording’. For instance if you need to add an
event prior to your first defined event you will need to extend the recording years backwards in time before the event
table will accept the earlier year.
4.4.2 Recorder years
Once you have entered the events for your sample, you can then specify the recorder years (see appendix A) i.e. the
years in which the tree was susceptible to fire (sensu Romme, 1980). Typically this will be from the first event until the
end of the sample. If the recording years are not correct you can automatically re-populate the table using the button
above the table. This option allows you to override the recording years to: from first event to the end of the sample;
or from beginning to the end of the sample. The second case is used occasionally by some researchers when working
with certain ecosystems and species where it is considered that trees record fires regardless of whether they have already
sustained an injury or not.
In some samples there may be periods when the sample reverts to ‘non-recording’ status in the middle of the series. For
instance in a tree injured by fire and therefore considered to be in ‘recording’ status the edges of the scar may close
together until the cambium is reconnected. At this point the tree would be considered by many researchers to be in
‘non-recording’ status again until another cambium-injuring fire was to occur. In such cases you can add multiple ranges
for ‘recording’ with gaps covering the ‘non-recording’ years to reflect this.
4.5 Summary and Graphs
The remaining two tabs in the data entry window provide an overview of the data file which can be helpful to verify that
the data entry has been done correctly. The summary tab (figure 4.3) provides a table summarising the samples on a
year-by-year basis. For each year the number of events, the number of samples and the percentage scarred samples are
shown, along with the distribution of events by season. The final column of the table includes a color bar summarising
the seasonality of the events recorded. The color bar can be customised with the button at the top of the screen. This
enables the user to change colors as well as merge together seasons into a single color bar. This is done by dragging and
dropping the seasons together into a single group.
The summary table can be exported to a CSV file using the relevant button at the top of the screen. It can also be copy
and pasted into various spreadsheet applications.
The graph tab (figure 4.4) shows similar information in a graphical form. The color bar is replicated horizontally at the
top of the screen, with the number of events and samples shown at the bottom. One good use for the bottom graph is
to check for single events located immediately before or after a large number of events. This may be an indication that
an event has been added a year too early or late.
4.6 Correcting erroneous files
If you edit an FHX file which includes one or more errors (i.e. is marked by a red icon ), FHAES will display a file
correction screen (see figure 4.5). This shows the original file on the left with the error highlighted, and then the same
file on the right with the correction the FHAES suggests. Check that the correction suggested by FHAES is valid and if
not you can manually edit the text. (It is helpful to have a copy of the original data nearby for reference.) When you
are satisfied that the file is now valid, click save and the file will open in the standard data entry screen. If the changes
you’ve made mean the file is still invalid, the file correction screen will refresh with the remaining errors highlighted.
Thursday 21
st
December, 2017
20 FHAES: Fire History Analysis and Exploration System
Figure 4.5: Screenshot of the file correction screen that is displayed when an erroneous FHX file is edited. Note the original file is
shown on the left with the error highlighted and explained, while the right of the screen shows the same file with the suggested
corrections.
4.7 FHX2 restrictions
The original FHX2 application enforces a number of limitations on field sizes and amount of data. This was in response
to the relatively limited computer resources available at the time the program was originally written. Because modern
computers have much more memory and speed, we didn’t have such limitations when developing FHAES, and FHX files
produced by FHAES can be slightly different than those produced by the original FHX2 application. While FHAES can
read and edit all data files produced by FHX2, not all FHX data files produced by FHAES can be read by FHX2. Care
must be taken if you intend to use files created by FHAES in FHX2. We have tried to make this easy: on the metadata
page of FHRecorder there is a checkbox that instructs FHAES to enforce the original FHX2 format requirements. With
this checked, the FHX2 field length limits are displayed and any fields exceeding these limits highlighted. Any fields not
meeting the restrictions must be truncated before the file can be saved.
Here are some of the limitations in FHX2 that are not present in FHAES: the length of series names (limited to 8
characters); the number of series in a file (up to 254); and range of years (501BC-2020AD although earlier releases were
501BC-2006AD). It is also worth noting the difference in handling of BC dates in FHAES and FHX2. FHX2 uses the
astronomical dating system which includes the year zero. This means that all year numbers prior to 1AD are offset by
one e.g. 1AD=1; 1BC=0; 2BC=1 etc. FHAES on the other hand uses Gregorian year numbering, thus skipping the
non-existent year 0. Care should therefore be taken when moving datasets containing BC data between the two programs.
A further limitation of FHX2 is only apparent when entering characters other than those used in English. FHX2 requires
that data files use Extended ASCII (also known as Cp437, IBM437, ISO-8859-1 and others) character encoding with
unsupported characters replaced by question marks. Even though FHX2 uses extended ASCII internally, the data entry
interface only allows basic ASCII characters. A file saved with popular western accented characters (e.g. ´a `e ˆı ¨o etc) will
display correctly in FHX2 but despite it not being possible to enter these characters manually in the program.
By contrast FHAES uses the UTF-8 character encoding which supports characters from virtually all languages. When the
checkbox on the metadata page is set to force FHX2 compliance, FHAES will save to a file with ISO-8859-1, maintaining
all characters supported by this older encoding. If unsupported characters are entered in the metadata the user is warned.
When loading FHX files in FHAES, the default behaviour is for FHAES to attempt to automatically detect the character
encoding and use it accordingly. Unfortunately in some circumstances there is no way to definitively detect encodings
without knowing the language and context of the text stored. In cases where FHAES incorrectly detects the encoding and
you know the correct one, you can override the encoding used by using the Preferences Character encoding preferences
Thursday 21
st
December, 2017
Data entry 21
menu. We recommend editing and saving ‘exotically’ encoded files in FHAES to ensure they are saved in UTF-8 for ease
of use and sharing.
4.8 Limitations of the FHX format
Even though the field and data length restrictions of FHX2 outlined in section 4.7 have been removed in FHAES, the
FHX format still has a number of fundamental limitations for the accurate description of fire history data. The primary
issues are outlined below:
No standardisation of metadata – The metadata fields that are present in FHX files are all free text with
no restrictions on how information should be added or formatted. The clearest example of this is the latitude
and longitude fields. They can be written in a wide number of formats and styles: either decimal degrees; degrees
minutes and seconds; degrees and decimal minutes; direction characters variably as +,-,N,S,E or W; space delimited;
apostrophe delimited. The list is almost endless. To make use of this information in FHAES or in any other software,
the coordinates, and other metadata fields must be interpretable without manual user intervention.
Single data point per sample per year – The format only allows for only one data point (piece of information)
to be recorded about each sample in any year. This causes problems, for instance when a tree begins or ends with
an event as it means the pith/bark status cannot also be recorded
3
. Perhaps more importantly, it means that fire
scars and other injuries cannot be coded in the same years which creates significant problems for those attempting
to do analysis comparing, say, fire and insect outbreaks in the same stand.
Metadata applies to all series in the file – The metadata header is limited by the fact that it applies to all
series within the file. If the file contains data from different species there is no mechanism for for defining which
species applies to a given series, although the user can list the species in the header or a comment line. There
is a similar issue with coordinates as it’s routine now to record each tree location with a GPS rather than more
general coordinates for entire sites. Likewise for slope, aspect, collection date, substrate type etc, users may prefer
to record these on a tree-by-tree rather than site-by-site basis. Having ready access to this data would be extremely
useful for charting and spatial analysis.
Pre-defined categories of events with no flexibility – The analytical routines within FHAES are agnostic with
regards the type of events being processed. However, the pre-defined nature of the event categories in the FHX
format means that users may find it difficult to adapt their data when using FHAES for novel analyses. As indicated
elsewhere in this manual, the analyses performed in FHAES are not limited to fire histories but could be used for a
wide variety of similar event types. These pre-defined event categories also do not allow for the recording of more
general (textual) observations about particular rings.
Separation of dendro and fire history data – Fire history research is often conducted alongside traditional
dendrochronological research. The separation of ring-width and fire event data into different data files means
duplicatation of metadata management. Combining all this data into a single file would be more efficient and
would also facilitate analyses that combine ring-width and event data, for instance growth releases following fire
events.
Dated and undated series – Although fire history research is conducted overwhelmingly on trees that are absolutely
dated via standard dendrochronological methods, it is conceivable that researchers may want to use FHAES on
samples for which this is not the case. For example research may be carried out on wood sourced from archaeological
or palaeoecological contexts. In these cases the samples may be dated within a relative dating framework; dated
with uncertainty (e.g. via radiocarbon analysis); or not-dated at all. It would be preferable if this information was
included alongside the fire history data.
To overcome these issues, the long-term aim is to support the Tree Ring Data Standard (Jansma et al., 2010) within
FHAES while maintaining the ability to read existing FHX data files. In the meantime we recommend you maintain
extensive notes to go with your FHX files. These can then be used to upgrade your existing FHX files in future once
TRiDaS is fully supported.
3
In cases like this the event information supersedes the pith/bark status so data series may in some circumstances begin and/or end with
events rather than brackets. When this happens we must assume pith and/or bark are absent.
Thursday 21
st
December, 2017
Thursday 21
st
December, 2017
Chapter 5
Analyses
This chapter describes the analysis results tables presented on the ‘Analysis’ tab of the main window. The majority of
these results tables are available only once the main analysis has been run. Some of the results also require two or more
files to be loaded.
Most statistical calculations within FHAES are done using the standard Apache Commons Math library
1
. The main
exceptions are the calculations associated with the Weibull distribution which are not available in any known open source
libraries. These have been programmed within FHAES by Elena Velasquez. As with all the FHAES code, the code for
these calculations can be inspected and scrutinized (see section 2.4 for further information).
Once files are loaded or created and you switch to the ‘Analysis’ tab you will be shown the ‘Run Analysis’ button. Clicking
this will show the ‘Analysis options’ dialog where you can define the parameters you’d like to use for your analyses, after
which FHAES will then perform the analyses.
Figure 5.1: The analysis options dialog allows the user to define the parameters used when running fire history analyses. Note that
options that have unavailable or not yet implemented are greyed out.
The dialog is split into three panels: analysis options; filters and years; and seasons. Each of the fields includes a help
tip button to provide you with more information after what the parameter means and it’s implications for the analysis.
This information is also reproduced below:
Event type for analysis – Select whether to perform analyses on:
1
https://commons.apache.org/proper/commons-math/
Thursday 21
st
December, 2017
24 FHAES: Fire History Analysis and Exploration System
only fire events (upper case letters in the input files)
only other indicators (lower case letters)
both fire events and other indicators
Note that choosing one of the first two options may remove one or more of your input files from the analyses if
they do not contain enough of the specified event types.
Label results by – Select how you would like to label the input files in your results tables and charts. Note that FHAES
will default to file name if you pick site name or code and a file is missing the relevant header information.
Interval analysis type – Select whether you want to perform analyses based separately upon each sample in your file
or by combining samples within a file into a composite. Note if you select ‘composite’ then you may like to set
composite filter options as well.
Include intervals after last event – Indicate whether you’d like to treat the time period from the final event marker
until the end of the series as an interval in the interval analyses.
Alpha value – The alpha value or error is the maximum probability that a given return interval will be significantly short
or long. The default alpha value for this two-tailed test is 0.125.
Year range – the default option is that the analyses are calculated across the entire range of years in your input files, or
you may specify a more restricted time period.
Composite fire threshold – Specify how the composite of your samples should be filtered during analyses (number or
percentage). If you choose ‘number of fires’ equals 1 for a given year then all fire events will be included in the
composite; if number of fires is larger than one then only years with at least that many fires in a given year will
be included in the composite. The ’percentage of fires’ value ranges from 1 to 99. The larger the filter, the more
that extensive events in the record are emphasized.
First season combination – In the seasons analysis, scar positions relative to the earlywood, latewood, or between
growth rings (or grouped) are compared for differences based on some hypothesis. A common hypothesis would
be that most fires occurred in the typical wildland fire season for the locale (first season combination) and rarely
occurred in the second season combination.
Second season combination – The second season combination are scar positions being compared to the first season.
The analysis options dialog will open automatically each time you load FHX files. If you want to repeat analyses without
confirming or changing options each time you can choose to use the same options without confirmation for the rest of
the session. The next time you load FHAES it will remember your preferred analysis options, although you will be shown
the options dialog and asked to confirm them again. Once you confirm your analysis options FHAES will perform the
calculations and populate the tabs on the home screen (see figure 3.2).
Once the analyses have been performed, a categorized list shows all the available analysis results on the right, while the
table on the left shows the currently selected result. Analyses not available will be greyed out (e.g. when only one FHX
file was loaded and the listed analysis requires multiple files for comparison). There is a full description of each analysis
in chapter 5 as well as through the online help system you can access by pressing the help button.
To view the analysis results simply select the analysis type from the categorical list on the right and they will be shown in
the table on the left. You can copy and paste values from this table into your preferred spreadsheet or statistical package
using the edit menu, toolbar buttons, or right-click popup menu. You can also save single tables by right- clicking the
required table in the results tree on the right. Additionally, certain tables can be saved in other formats. For example
the popup menu for ‘Binary site summary’ will allow you to save as a GIS Shapefile (see page 11 for more information).
To save all analysis results at once, you can go to File Save Save analysis results or use the save button on the
toolbar. You have the option of specifying ZIP or XLSX format; the former will give you a ZIP file containing each table
as a CSV text file and the latter will give you a single Microsoft Excel workbook with each table as a separate worksheet.
5.1 Descriptive summaries
The descriptive summaries provide basic summaries of either all the loaded files or the currently selected file depending
of the analysis selected.
Thursday 21
st
December, 2017
Analyses 25
Series-by-series summary – This summary table has a row for each series found in each of the currently loaded files.
It includes a number of columns of file-wise metadata extracted including: filename; site name and code; sampling
date; latitude; longitude; state and country. It also includes series specific metadata including: series name; first
year; last year; pith presence; and bark presence. The final two columns contain a summary of event years with
and without associated seasonality information as a simple space delimited list.
Current file annual summary – The current file annual summary provides a basic descriptive summary by year of the
currently selected file. It contains a row for each year present in the file and has columns for: sample depth;
recording depth; number of events; percentage of recording trees with an event. The percentage of events column
has a value of −99.0 as a ‘nodata’ value when there are no recording trees.
Current file event summary – The event summary table provides a summary of events in the currently selected file.
The table has three columns: trees recording; number of years; and years. The table groups the years in which n
trees record an event, and provides a count and sorted list of these years. It provides the user with a quick tool for
seeing which fire years are most (and least) commonly represented in the file.
Note that the current file annual and file event summary tables are not saved to the analysis results file but this
option may be available in a later version of FHAES. For the present we suggest performing a copy-and-paste of
the current file tables to a text or spreadsheet file.
5.2 Interval analysis
The Interval analysis tables provide the results of several analyses for each data file. Interpretation of the results will
depend on whether you chose to perform the interval analysis on the composite or by sample. If you specify “composite”,
FHAES creates a composite (summary) fire chronology for the site and calculates the intervals (and analyses) between
fires for that composite chronology. Say the time period you are analyzing is 1600–1900, and the earliest fire scar was
1625 and the most recent was 1889. The results are interpreted as the mean (or median) intervals between fires occurring
anywhere in the area sampled. If you specify “sample”, FHAES calculates a set of fire interval statistics describing how
often fire could be expected to return to each original point or sample. The composite chronology intervals are likely to
be shorter than those of the sample intervals because fire will probably occur at least somewhere in the sample area more
often than it will burn at each sampling point.
The fire interval statistics are given for two probability distributions, the normal and the Weibull. Often, sets of fire
intervals have more short intervals than long ones and are better described by the Weibull distribution than the normal.
A description and formula for each statistic or parameter are shown below.
5.2.1 Total intervals
This is the number of intervals between fires, notated as n. The number of intervals will be one less than the number of
fires (so n = F − 1).
5.2.2 Mean fire interval
The mean fire interval
¯
I is the arithmetic mean of the intervals in a series, where I
j
is the Jth interval in years. Fire
intervals are in units of years/fire. Note that the mean of a distribution can be influenced by outliers (extreme small or
large values) or asymmetrical distributions. Because fire interval distributions are often strongly right-skewed,
¯
I can be
”pulled” to the right by occasional long intervals. The median fire interval (below) provides a potential solution to this
issue.
¯
I =
n
j=1
I
j
n
(5.1)
Thursday 21
st
December, 2017
26 FHAES: Fire History Analysis and Exploration System
5.2.3 Median fire interval
The median fire interval is the middle value of all intervals in a series when the intervals are rank ordered by size. When
there is an even number of intervals, the median is calculated by convention as the arithmetic midpoint between the two
adjacent middle values. Median fire intervals are often used as a measure of central tendency because the median is
less sensitive than the arithmetic mean to outliers or highly skewed distributions.In fire history the median fire interval is
considered a robust estimator of the fire regime.
5.2.4 Standard deviation
Standard deviation is the square root of the variance in a sample, and is used in calculating measures of departure from
the mean, such as calculating confidence intervals. FHAES calculates the sample standard deviation (SD-sub-N), because
the intervals evaluated are an unknown subset of the complete population of intervals.
SD =
n
j=1
(I
j
−
¯
I)
2
n − 1
(5.2)
5.2.5 Fire frequency
Frequency in a discrete series is the number of events per unit time. In the case of fire history, frequency is the number
of fires, F , divided by the total number of years in a series. Fire frequency is in units of fires per unit time (year, decade,
century).
5.2.6 Coefficient of Variation
The coefficient of variation (CV ) is the standard deviation of a sample normalized by (that is, divided by) the sample
mean. The CV is useful for comparing the relative variation between samples that may have different means, since
it provides the standard deviation as a proportion of the mean. The CV is unitless since the units divide out in the
numerator and denominator. Here the denominator is the mean fire interval,
¯
I.
CV =
SD
¯
I
(5.3)
5.2.7 Skewness
Skewness is a measure of the symmetry of a distribution around the mean. A skewed distribution has more values below
(“left-skewed”) or above (“right-skewed”) the modal value. Thus by definition, skewed distributions are asymmetric and
thus are non-normally distributed. Fire interval distributions are commonly right-skewed, meaning that there are more
long intervals above the mode than short intervals below the mode. In right-skewed distributions, the mean is higher than
the mode or median. Skewness is hence an indicator of whether the mean fire interval is a robust indicator of central
tendency. Skewness is the third moment of the frequency distribution, given as:
γ
2
=
(I
j
−
¯
I)
3
N
(5.4)
5.2.8 Kurtosis
Kurtosis is sometimes referred to as the “fourth moment” of variation about the mean, which is how much of the data
is in the tails of the distribution compared to centrally distributed. Distributions with high kurtosis are “heavy tailed”
Thursday 21
st
December, 2017
Analyses 27
(i.e., more of the data are divergent from the mean) compares to a normal distribution. In fire history this could indicate
a greater than expected prevalence of short or long intervals compared to a standard normal distribution.
kurtosis =
N
i=1
(Y
i
−
¯
Y )
4
/N
s
4
(5.5)
5.2.9 Minimum and maximum fire intervals
These are simply the shortest and longest fire intervals (in years) observed in the dataset. Note that these extreme values
may not represent the distribution of all intervals well, because a single small or large value could be very divergent from
the rest of the distribution.
5.2.10 Weibull Distribution
The Weibull function is a flexible probability distribution that can represent a wide range of non-normal data. Because
of its flexibility and relative tractability, it has been extensively adapted for statistical analysis in fire history (Falk,
2004; Grissino-Mayer, 1995, 1999; Johnson, 1992; Johnson and Van Wagner, 1985) The Weibull distribution is a “stress
accumulation” statistical model; thus, under some circumstances the probability of an event (e.g. a fire) increases with
time as a result of some accumulating stress (e.g. fuels as a function of time since fire).
The underlying reason that the Weibull is used in fire history analysis is that many fire regime properties (e.g. fire intervals
or frequency) are not normally distributed. For example, fire interval distributions are nearly universally right-tailed (i.e.
skewed) with a heavy tail (i.e., data have occasional outliers of very long intervals), so they cannot be approximated by
a normal curve (Falk, 2004; Grissino-Mayer, 1995, 1999). The Weibull distribution is used to model a set of empirical
data (for example, a frequency distribution or histogram of fire intervals).Empirical distributions (e.g. from a fire history
collection) may be “noisy”, i.e. they may not be smoothly distributed. Fitting a modeled probability distribution to
empirical data allows the data to be quantified and analyzed; this is the real strength of probability modeling in fire
history.
There are several forms of the Weibull function. FHAES models the two-parameter Weibull distribution, with parameters
for shape and scale respectively, by iteratively fitting the distribution to a set of empirical data such as fire intervals. The
shape parameter (κ) regulates departures of the Weibull distribution from normality. When κ > 1, the Weibull probability
distribution is modal and approximately normal at κ = 3; as κ becomes smaller, the mode of the distribution drifts toward
0, and the distribution becomes strongly right-skewed (i.e., a long right tail, typical of fire interval distributions). At
κ = 1, the Weibull distribution reduces to a negative exponential, and for κ < 1, the Weibull approaches
1
x
, a rectangular
hyperbola. Values of κ are non-negative, i.e.:
κ(0, ∞) (5.6)
For a Weibull distribution with a given shape parameter κ, the scale parameter (λ) stretches or compresses the distribution.
Lower values of λ are more compressed about the mode, meaning that most of the values are close to the center.
Distributions with high λ are more dispersed into the tails. λ is also a non-negative parameter:
λ(0, ∞) (5.7)
5.2.11 Weibull Mean
The mean of a fitted Weibull distribution can be calculated from the parameters κ and λ, which are estimated during
the model fitting process. The Weibull mean is:
λΓ (1 +
1
k
) (5.8)
where Γ is the Gamma distribution evaluated for (1 +
1
k
). For fire intervals, the Weibull Mean Probability Interval is a
modelled analogue to the mean fire interval calculated from empirical data.
Thursday 21
st
December, 2017
28 FHAES: Fire History Analysis and Exploration System
5.2.12 Weibull Median
As noted above (Sec. 5.2.3), median values are used throughout statistics to represent central tendency in non-normal or
asymmetric distributions. This holds true for fire history, where interval distributions are often right-skewed. The median
of a Weibull distribution is defined as the value for which half of the probability distribution is below, and half above,
that value.The Weibull median probability interval (I
W M
) is considered a robust estimator of central tendency and can
also be calculated as:
λ(ln(2))
1
k
(5.9)
5.2.13 Weibull Mode
The mode of a distribution is defined as the most common value, for data that are integers or compiled into bins. For a
modeled probability distribution, the mode represents the frequency peak in the probability density function (pdf). The
mode would thus represent the most common (probable) range of values for data set. In fire history, this would represent
the most common fire interval.
The mode of a Weibull distribution is calculated using the parameters κ and :
λ(
k−1
k
)
1
k
k > 1
0 k = 1
(5.10)
5.2.14 Weibull Standard Deviation
If needed, the standard deviation of a Weibull distribution can be estimated using the parameters κ and , and the gamma
distribution:
λ
2
Γ(1 +
2
k
) − (Γ(1 +
1
k
))
2
(5.11)
Note that this formula takes into account the skewness and dispersion of the data, and is thus preferred to a standard
deviation calculated with an assumption of normality.
5.2.15 Weibull Skewness
Similarly, the skewness of a fitted Weibull distribution is estimated using the model parameters:
Γ (1 +
3
k
)λ
3
− 3µσ
2
− µ
3
σ
3
(5.12)
5.2.16 Exceedance Intervals
Exceedence intervals are values of a distribution for which of a value smaller (or larger) than that value has a probability
of p. For example, If the upper 95% exceedence value of a fire interval distrubiton is 75 years, this indicates that 95% of
all fire intervals are less than 75 years, and only 5 percent larger. Exceedence intervals are widely used in hydrology and
climatology, e.g. to estimate the probability of an event of a given magnitude. This statistic is also highly useful in fire
regime analysis for indicating the probability of short or long intervals.
In FHAES, exceedence intervals are displayed in the output table as: lower exceedance interval; upper exceedance interval;
significantly short interval upper bound; and significantly long interval lower bound. Exceedence intervals are estimated
using the probability density function (pdf) of the fitted Weibull distribution.
Thursday 21
st
December, 2017
Analyses 29
5.3 Seasonality
Careful dating of fire scars often allows information about when fires burned relative to the growth of individual tree
rings to be estimated in the laboratory. The edges of the scar—the scar margins—can occur between rings or extend
into xylem cells of an annual ring. Ring position is only an approximate proxy for actual calendar seasonality, since the
time of formation earlywood or latewood of a ring varies by species, location, and year. If the phenology of a sampled
species is known, then ring position can be translated into an estimate (of unknown accuracy) of calendar seasonality.
In FHAES, seasonality analysis summarizes the ring position of each fire scar (if entred by the user), and then summary
statistics for the frequency distribution of fire scars by ring position.
5.4 Binary summary matrices
Binary matrices are a convenient way to summarize the occurrence (or non-occurrence) of fire across multiple plots over
a period of record. In essence, binary data condense a fire record into a presence/absence (1,0) matrix with dimensions
of years (rows) x plots or trees (columns). Binary matrices can include all events, or the input data can be filtered to
include only years or plots meeting certain criteria. Binary matrices are also a convenient way to tabulate fire occurrence
over a study area.
In FHAES, the binary summary matrices provide summaries of presence or absence of events, including fire, other injuries,
or both. If an event is recorded then the matrix for that plot or tree x year cell takes a value of 1, whereas if the event
is not recorded despite the fact the trees were capable of recording then the matrix includes a value of 0. If there are no
data for that particular year (as occurs if the tree-ring record doesn’t extend to that particular year, or other non-recording
years) then a value of -1 is recorded in the matrix.
FHAES produces three types of binary summary matrices:
Binary site summary – a single summary binary matrix for the entire file, with one column per file (in other words, a
vector of years x 1).
Binary tree summary – a binary summary of the fire record but divided into individual trees (columns). In addition to
the normal header row containing the site name, code or filename, the matrix has a second header row containing
the tree code. Thus the dimensions of this matrix is years x trees.
NTP matrix – the NTP matrix contains three columns per file: one for the number of fires; one for the number of
trees; and a third for the percentage of trees that were scarred. The dimensions of the NTP matrix is years x 3.
5.5 Binary comparison matrices
FHAES generates a set of matrices that compare the fire record at two or more sites. These comparison matrices are the
foundation of similarity analysis in fire history.
For any pair of sites in a given year, there are four possible outcomes:
Both sites record fire – this is referred to as the a case.
Only one site records fire – these are the b or c cases, where b or c are assigned each to one of the sites.
Neither site records fire, called the d case.
For every year common to the two sites, the number of a, b, c, and d cases is compiled, along with the number of years
of common record. FHAES then outputs these results in a series of files that report the number of years with each of the
four outcomes. If multiple sites are selected for analysis, the resulting triangular matrices will have the same number of
rows and columns, which will correspond to the number of sites, but the analyses are only for each pairwise comparison.
The FHAES matrix files are:
A – number of years in which both sites record fire (1,1)
B – number of years only one of the two sites record fire (1,0)
C – number of years in which only the other site records fire (0,1)
Thursday 21
st
December, 2017
30 FHAES: Fire History Analysis and Exploration System
D – number of years in which neither site record fires (0,0)
L – number of common years between each pair of sites
5.6 Similarity and dissimilarity matrices
FHAES calculates indices of multivariate similarity using the five binary output files summarized above. The similarity
index used in FHAES is the Jaccard index, a widely-used statistic in ecological analysis.Using the four cases in a binary
comparison, Jaccard similarity is computed as:
SJ = [A / (A + B + C)]where A, B, and C are the number of cases compiled in the comparison files. The motivation
of the Jaccard index is to calculate the number of times to sites both have fire in the same year (A), and then express
that as a proportion of all years in which fire occurred in one or the other sites, or both (A + B + C ). Note that Jaccard
does not use the D case in which neither site records fire. This is a suitable property for fire history analysis, as even in
high-frequency systems most years at a given location are non-fire years unless the ”site” is a very large area.
The Jaccard index returns values from 0 to 1 inclusive: J(0, 1).
Jaccard dissimilarity (or ”distance”) is 1-SJ; in other words, when SJ = 1 two sites are completely different, and when
SJ = 0 they are identical.
The general form for a probability-corrected similarity index is:
Sp =
P (z) − P (e)
1 − P (e)
(5.13)
Where Sp is the pth index, P (z) is the probability of agreement between two pairs, and P (e) is the expected probability
of agreement based on chance.
Site j
Outcomes 1 0
Site i 1 a (1,1) b (1,0)
0 c (0,1) d (0,0)
This method can be illustrated with Cohen’s index (S
COH
), in which both (1,1) and (0,0) cases a and d are considered
‘agreement’, P (a) =
a+d
N
, where N = a + b + c + d. P (e) is computed as the joint probability of sites i and j having a
‘1’; hence,
P (1i) =
a + b
N
, (5.14)
P (1j) =
a + c
N
(5.15)
P (e) = P (1i) × P (1j) (5.16)
Consider a comparison between a pair of sampling units with the following outcome:
Site j
Outcomes 1 0
Site i 1 8 (1,1) 4 (1,0)
0 5 (0,1) 83 (0,0)
Thursday 21
st
December, 2017
Analyses 31
Hence a = 8, b = 4, c = 5, d = 83, and N = 100. Then:
P (z) =
8 + 83
100
= 0.920
P (1i) =
8 + 4
100
= 0.120
P (1j) =
8 + 5
100
= 0.130
P (e) = 0.12 × 0.13 = 0.016
S
COH
=
0.920 − 0.016
1 − 0.016
= 0.919
Note that similarity in this case is dominated by the d (0,0) case. This represents a common outcome for rare events
where d >> a.
In the previous example, when both the a and d cases are considered ‘agreement’, the index can be dominated by d case
when events (a) are rare. An alternative approach for rare events is to calculate similarity based on the positive outcomes
only, e.g. in our context, event years, the a (1,1), b(1,0), and c (0,1) cases. Let R = (a + b + c), the union of event
years; then pairwise similarity is calculated as:
Sp =
P (a) − P (e∗)
1 − P (e∗)
(5.17)
Where P (a) =
a
L
, the probability of the a case given a fire in either site, P (1∗
i
) =
a+b
R
, P (1∗
j
) =
a+c
R
, and P (e∗) =
P (1∗
i
) × P (1∗
j
), the probability of joint 1s occurring by chance in an event year. In the example given:
L = a + b + c = 8 + 4 + 5 = 17
P (a) =
8
17
= 0.471
P (1∗
i
) =
8 + 4
17
= 0.706
P (1∗
j
) =
8 + 5
17
= 0.765
P (e) = 0.706 × 0.765 = 0.540
S∗ =
0.471 − 0.540
1 − 0.540
= −0.15
This index reflects only the distribution of the event cases a, b, and c. The outcome is negative if (b + c) > a, and
positive if a > (b + c), which complicates interpretation. To avoid this outcome the index can be expressed as 1 + S,
which occurs on 0,1; in this case, S∗ = 0.85.
Thursday 21
st
December, 2017
Thursday 21
st
December, 2017
Chapter 6
Sample Size Analysis
6.1 Introduction
Like all areas of paleoecological research, fire history relies on analysis of remnant evidence. While such evidence can
provide a long time perspective on ecological processes, individual evidence generally represents an incomplete picture
of the events and conditions at the time of its creation. In the case of fire history, fire scar formation and retention
reflect a combination of deterministic and stochastic processes. Fire is not necessarily the cause of cambial injury in every
scarred tree, even where fires have burned. Fire intensity (heat output per unit area) can be highly variable within stands
due to variation in fuel mass and continuity, as well as fine-scale variation in winds, humidity, and topography. Tree
characteristics (such as diameter, bark thickness and rooting depth) can also vary within stands, making some trees more
susceptible to scarring than others. Once scarred, a variety of contingent factors affect the retention and preservation of
lesions, including subsequent burning, mechanical injury, wood decomposition, and mobilization of resin into xylem cells
in a zone from the heartwood to the injured surface. The net result of these factors is that individual trees provide an
incomplete record of fire occurrence, even at the stand scale.
To counteract the limitations of records provided by individual trees, fire historians and ecologists typically composite
the records from multiple trees in a stand or other scale of interest. In most fire regimes, records from individual trees
overlap to some extent; i.e., there are some fires in common among trees, whereas other events may be detected on
some trees but not others. Thus, as the number of trees sampled increases, additional fire dates are usually detected,
but at a decreasing rate (Falk, 2004). This pattern is formally analogous to the “collector’s curve” used in estimating
species richness from a number of sample plots. For a given area, the number of species detected (s) is a function of
the number of samples (trees or plots). As n increases, s generally increases at a decreasing rate, causing the collector’s
curve to flatten out with additional samples.
The sample size analysis tool is designed to ask a similar question for characterization of fire history in a study area. Have
we sampled enough trees to capture the main fire dates, and to characterize properties of the fire regime (frequency,
interval distribution, etc.)? If our sample size is too small, can we estimate how many more samples would be required
to provide a reliable estimate of the site fire history?
Although the sample size analysis tool is designed to explore the effect of sample size on the observation of fire frequency,
it is equally capable of exploring other event data such as insect infestations. The tool calculates the mean number
of events per century observed in an increasing sub-sample of series within a data file. Multiple simulations are run by
randomly picking series from the file to simulate the accumulation of trees in the total sample.
The sample size analysis tool in FHAES is a reimplementation of the original SSIZ tool written by Richard Holmes
under the direction of Tom Swetnam at the Laboratory of Tree Ring Research, University of Arizona. The FHAES
implementation of SSIZ removes the limitations in simulation number, sample size, and time span imposed by the
original SSIZ program while dramatically speeding up analyses.
6.2 Performing analysis
The sample size analysis tool is launched from the tools menu or via the equivalent button on the FHAES toolbar. The
screen (figure 6.1) is split into two halves: the left containing the analysis parameters; and the right the analysis results.
The parameters required by the tool are outlined below:
Thursday 21
st
December, 2017
34 FHAES: Fire History Analysis and Exploration System
Figure 6.1: Screenshot of the sample size analysis tool. The screen includes the analysis parameters on the left and the results on
the right.
Input file – provide an FHX format file containing the data you would like to analyse. If you would like to analyse data
across multiple files you will need to use the ‘Merge files’ tool in FHAES first (see page 10).
Event type – you can choose to analyse: just fire events (in which case all lower case events are ignored in the FHX
data file); just injuries (in which case upper case events are ignored); or fires and injuries together.
Simulations – here you specify the number of simulations or repetitions on the analysis you’d like to run for each stage
of the analysis. The more simulations you run the smaller the confidence intervals, however the longer the analysis
will take.
Seed number – the random selection of series is in fact pseudo-random. This means that when an analysis is done with
the sample parameters and seed number the results will be identical
1
. The seed number should be a large integer
and can be left as the default value unless you specifically want to generate results from a different randomised
pool of series.
Resampling – FHAES supports resampling both with and without replacement. When ’sample with replacement’ is
chosen, each random selection of a series is done from the entire dataset which means that one series can be
included multiple times. Conversely when sampling without replacement, each series can only appear in the
random pool once.
Threshold – the threshold parameters determine how many times an event must be recorded in the file to be considered
a true event for sample size analysis. The threshold can be determined either as an absolute number, or as a
percentage within the dataset (either as a percentage of all trees or as a percentage of only those that are in
recording status). If the threshold is set to >= 1 fire then all events within the dataset are used including those
that are only represented by a single series. Often researchers prefer to exclude events recorded by just one tree as
they can be indicative of very localised fires that have not played a significant role in the region. There is also the
option of specifying an upper threshold to remove very large events from the dataset.
Common years – this option enables users to limit the analysis to only the years in common to all series within the file.
This can be useful, for example, when a single series in the file extends beyond the temporal coverage of all the
remaining series in the file. If all years are considered in such an analysis, then the events recorded by the long
series may skew the analysis.
1
This should be the case when run on different computers running the same major version number of Java; however it can only be
guaranteed when run on exactly the same system.
Thursday 21
st
December, 2017
Sample Size Analysis 35
Include series with no events – this option enables the user to choose whether to include or exclude series which do
not include events. By excluding series with no events the user can interpret the result of the asymptote analysis
as indicating the number of samples with evidence of fires required to adequately characterise the fire history of
the study region. If non-event series are included, then the asymptote is indicative of the number of trees required
to characterise the regime of the study area using samples from both scarred and non-scarred trees. This could be
useful, for instance, if you are studying insect oubreaks where trees are sampled without any visible injury. Note
that if you are running analyses on a subset of a series (either due to the common years option being enabled, or
through segmentation) then a series will be excluded if there are no events within the time period being analysed,
regardless of whether it has events elsewhere in the dataset.
Segmentation – segmentation parameters enable you to run sample size analysis on one or more time periods in the
file. You can manually specify the start and end years for each segment by clicking the ‘add’ button and typing
the values in the table. Alternatively you can use the ‘auto populate’ button to generate equally sized segments.
The dialog asks for the first year you’d like analysed, the length of each segment and the lag between the start of
each segment. For instance with a start year of 1600, a length of 100 and a lag of 50, the segments would run:
1600–1699; 1650–1749; 1700–1799 etc.
Plot variable – FHAES allows the user to select the output variable of interest, in units of centennial fire frequency
(i.e., fires per 100 years). This variable is easily converted to other units (e.g. annual fire frequency, fire interval)
as needed for analysis. FHAES provides fire frequency based on the (a) arithmetic mean, (b) arithmetic median,
(c) fitted Weibull distribution mean, and (d) fitted Weibull distribution median. The dark red line is the central
value of the variable; the shaded area indicates the 95th and 99th percentile confidence intervals (these are also
provided in the output table).
Once you have entered your parameters, press the ‘run analysis’ button at the bottom of the screen or on the toolbar.
Note that if you have chosen a very large number of simulations and have many series in your data file, the analysis may
take several minutes to run.
6.3 Analysis results
The results of the analysis are shown in the tables and graph on the right hand side of the screen. Note that the plot
variable can be changed even after the analysis is run, by using the ”Plot” pull-down button.
The options on the chart enable you to visualise the the different measures calculated during the analysis. If you ran the
analysis on multiple segments you can choose which segment to view. The chart can be exported to in both PNG and
PDF formats by right clicking, and can also be copied and pasted into other applications. Some basic properties of the
chart can be altered through the right click properties option.
Once you have run your analysis you may prefer to hide the parameters panel by clicking the collapse
button on the vertical divider in the middle of the screen. Likewise, the amount of space given to the chart
and tables can be altered by dragging the horizontal divider.
Below the chart, the raw data produced by the analysis are shown in tables. These tables can be copied and pasted
into other applications such as spreadsheet or statistical programs for further analysis. They can also be exported to tab
delimited text files. Both options are accessed via a right click menu. Alternatively you can use the option in the file
menu or the equivalent button on the toolbar to save the results to disk.
6.4 Interpreting results
FHAES calculates the response variable (fires per century) as if this were estimated from a single tree selected at random
from the FHX file. The program then picks a second tree and re-calculates fire frequency, then a third, and so on until the
number of trees sampled is equal to the total sample size in the file. If the user has chosen sampling with replacement,
then any tree may be chosen more than once; Scheiner and Gurevitch (2001) and Legendre and Legendre (2012) are
good guides on this issue.
The overall shape of the resampling curve is invariably a downwardly-inflected (that is, saturating) function, rising rapidly
at low sample sizes and flattening out as sample size increases. This occurs because with small number of trees, the
probability that any given tree will contribute a new event is high, but as numbers accumulate, the probability of a unique
Thursday 21
st
December, 2017
36 FHAES: Fire History Analysis and Exploration System
event declines. This “flattening” of the sample size curve is evidence that the study area has been adequately sampled, or
in other words, the fire frequency of the study area has been accurately estimated. The different mathematical variables
(mean, mean, fitted Weibull mean or median) generally have similar behavior, although the confidence intervals may vary.
Thursday 21
st
December, 2017
Chapter 7
Superposed Epoch Analysis
7.1 Introduction
Section in progress
Superposed Epoch Analysis (SEA) is a statistical procedure used to evaluate the temporal relationships between the
occurrence of key events and the high or low values in a time series of information related to the event (Prager and
Hoenig, 1992). For example, Wilson et al. (2010) used SEA to evaluate how volcanic eruptions influenced annual climate
indices for several years after eruptions. The most common application of SEA in dendrochronology has been to assess
how climate variability (e.g., Palmer Drought Severity Index; Palmer, 1965) influenced fire occurrence in the years before
and during fire; for example, Baisan and Swetnam (1997); Brown and Schoettle (2008); Flatley et al. (2013).
Figure 7.1: Screenshot of the jSEA analysis tool. The screen includes the analysis parameters on the left and the results on the
right.
Thursday 21
st
December, 2017
38 FHAES: Fire History Analysis and Exploration System
7.2 Input files
SEA requires two data files as input: a discrete time series and a list of key events. Both files should be provided as
comma delimited (CSV) text files. Any header lines or comments should begin with an asterisk to ensure the comments
are ignored by the input routine.
The key event list should be a simple single column of integer (whole numbers) years. You can create an event file from
any FHX data file using the ‘create event file’ option in the Data menu of the main FHAES window. Alternatively you
can use a text editor to create a comma delimited file of key event years. The year can be positive or negative, depending
on its relative relationship to beginning of the Common Era (CE). The last line should end with an End Of Line character
(EOL). FHAES does this automatically.
The time series file should contain two columns. The first column contains the year (as an integer) and the second the
data value (as a decimal). The year and the data value can be positive or negative. The rows of the file should be in
sequence, the oldest at the beginning and the most recent at the end. The separator between the year and value can be
spaces, tabs, or commas. The last line should end in an EOL.
If you need to view or edit the files to ensure they meet these criteria, use a text editor.
7.3 Window, Simulation, and Statistics
The main parameters for the SEA are found in the ‘Window, Simulations and Statistics’ panel of the jSEA dialog (see
figure 7.1). An explanation of each parameter is given below:
Years to analyse – Specify the time period over which the analysis should be performed. By default this will be all the
years in the data file, but can be restricted to a subset if desired. Note this is separate to segmentation of the time
periods handled in the segmentation panel.
Lags prior to event – Specify how many years prior to the event in question should be analysed.
Lags following the event – Specify how many years following the event in question should be analysed.
Include incomplete epoch – An incomplete epoch occurs when there is an event near the beginning or end of the time
series. In this case, the window of analysis around the event overlaps the beginning or end of the series.
Simulations – Number of simulations to run. Increasing the number of simulations increases the analysis time.
Seed number – The analysis requires a pseudo-random component which is seeded with the seed number (a large
integer value). Running analyses with the same seed number enables produces the same results. You can leave the
seed as the default number unless you specifically want to generate results from a different randomised pool.
p-value – The cutoff value to use for statistical significance.
7.4 Segmentation
SEA can be performed independently on segments of the dataset. This is useful, for example, when comparing two time
periods with different regimes.
You can manually specify the start and end years for each segment by clicking the ‘add’ button and typing the values
in the table. Alternatively you can use the ‘auto populate’ button to generate equally sized segments. The dialog asks
for the first year you’d like analysed, the length of each segment and the lag between the start of each segment. For
instance with a start year of 1600, a length of 100 and a lag of 50, the segments would run: 1600–1699; 1650–1749;
1700–1799 etc.
7.5 Historical note
In dendrochronological research, SEA was originally calculated using the FORTRAN program EVENT written in 1994 by
Richard Holmes at the direction of Thomas Swetnam (Laboratory of Tree-Ring Research, University of Arizona). The
Thursday 21
st
December, 2017
Superposed Epoch Analysis 39
last version of EVENT (6.02) was released in 2001 and is available from the Dendro Program Library (DPL; Holmes,
1983). Superposed epoch analysis has been more commonly performed in the past 20 years using FHX2 (Grissino-Mayer,
2001). FHX2 performs SEA using a module called FHEVENT which until March, 2016 has been the original version
of EVENT. This original version did not adjust the range of the series to match the range of the event series. If the
series has a broader range than that of the events, numbers chosen during the Monte Carlo randomization procedure can
include numbers outside the event range, introducing error. Later versions of EVENT (6.02) removes values outside the
common ranges of the event and time series.
7.6 Analytical background
SEA compares the climate conditions during event years to the prevailing climate conditions during a defined period of
time in which the events occur. SEA uses Monte Carlo randomization to establish confidence intervals of climate during
analysis period. The mean and variance of climate in the event years is then compared to the climatic confidence interval.
SEA compiles values for the climate time series in each event year (t = 0), and then for any prior or subsequent years
selected in the input screen. For example, an investigator interested in antecedent climate conditions to fire years might
include 4 years prior to a fire year (t = -1, -2...-4).
SEA compiles these event year and antecedent year values for each event, and creates a matrix in which the mean and
variance in all event years is calculated, as is the mean and variance of antecedent years; this is the process of ”super-
position” which gives the procedure its name. In dendrochronology, we align multiple events of some kind, and then
examine the temporal antecedent (and subsequent, if appropriate) conditions common to these events. FHAES plots
histogram bars to indicate the mean climate values of the superposed event or antecedent years.
To determine the confidence intervals of the background climate series, SEA selects sets of years at random from the full
time series. This procedure is iterated as directed by the user to establish 95th and 99th confidence intervals of the full
climate time series. In practice, the variance in confidence intervals stabilizes at roughly 2x the length of the series, which
can be used as a starting guide to the number of iterations required. Given the speed of modern computing systems,
there is little cost to running a larger number of iterations for CI calculation.
SEA tests a null hypothesis of no difference between the climate values in the event years compared to a random draw
of climate values in the overall climate series. In other words, SEA asks whether the association between a set of key
events and an continuous variable is stronger than would be expected if events were located randomly in the time series.
If values of the continuous series are significantly different in events years, H0 is rejected.
Thursday 21
st
December, 2017
Thursday 21
st
December, 2017
Chapter 8
Fire History Charts
FHAES includes the tools necessary to produce publication quality fire history charts. These charts provide a powerful
method for illustrating the fire regime of a site or region.
Charts are produced on a file-by-file basis and are available on the ‘chart’ tab of the main screen.
Figure 8.1: A typical fire history chart produced by FHAES. The chart has three optional components: fire index plot (top); fire
chronology plot (middle); and fire composite plot (bottom).
8.1 Chart components
There are three components to a fire history chart, each or which can be included or removed as desired. The first (shown
at the top of figure 8.1) is the fire index plot. This includes a histogram showing the sample depth for each year (i.e.
how many trees are recording the fire history in each year) and a bar chart illustrating what percentage of these trees
record a scar event.
The second component is the fire chronology plot. This shows a bar for each sample in the file illustrating the timeline
for the tree e.g. the start and end year for each sample and all fire events. Through the use of various symbols the plot
illustrates whether the tree is recording fire histories or not; when a tree records a fire scar or injury; and whether the
sample starts and ends with pith and bark or not. Figure 8.2 shows the symbols used by this plot for each feature.
Thursday 21
st
December, 2017
42 FHAES: Fire History Analysis and Exploration System
The third and final component is the fire composite plot. This shows whether the samples in the site or region as a
whole record a fire event depending on certain threshold criteria set in the plot preferences. When the criteria are met,
a line is marked on the plot for that year. The criteria can be set so that only years where greater than a specified
percentage of trees record an event are marked. It is also possible to require a minimum number of samples so that
events recorded by small number of trees when the sample depth is very low are not shown. These criteria are set by
going to Edit Filter Options Composite Axis Filters.
Figure 8.2: Legend for fire chronology plots.
Each of the chart components can be displayed or hidden by toggling them on and off using the toolbar buttons, through
the chart menu, via the right click popup menu or via the chart properties dialog described below.
8.2 Modifying the chart
The main features of the chart can be altered through the chart properties dialog. This can be accessed through the
toolbar, menu or by right-click popup menu. The dialog is split into four tabs: Generic options; Index plot; Chronology
plot; and Composite plot (see figure 8.3). Options that alter the general appearance of the entire plot are located on the
generic options tab, while the remaining tabs alter options specific to the three main parts of the chart.
The options specified in the chart properties dialog are remembered between sessions. If at any time you’d like to revert
to the default settings you can press the ‘revert to defaults’ button at the bottom of the dialog.
8.2.1 Generic options
The top panel sets the font family to use throughout the chart, as well as whether to include a legend and title. The
title can be styled and the title text itself can be overriden (the default coming from the metadata of the FHX file).
The next panel specifies details about the x-axis (timeline) primarily what time period the chart should cover. This
defaults to the full extent of the data file. The font size for the timeline labels can also be altered.
The ‘Ticks and Vertical Guides’ panel allows the user to enable/disable these features as well as control their style. Major
and minor ticks are the small graticule lines displayed on the timeline axis. Here the interval for each can be defined.
Vertical guides are lines that are drawn across the entire chart to help align the reader. The interval is fixed to that of
the major tick, and the style, width and color of the guide can be set.
The ‘Highlighted Years’ panel allows the user to annotate the chart with extra guide lines to help illustrate a year (or
years) of interest. When enabled, years can be added and removed using the plus and cross buttons, and Like the standard
periodic vertical guides, the highlighted year lines can also be styled.
Thursday 21
st
December, 2017
Fire History Charts 43
Figure 8.3: The chart properties dialog provides many options for modifying the content and style of fire history charts
8.2.2 Index plot options
The Index Plot tab provides options for tailoring the index plot panel at the top of the chart. The index plot can be
enabled/disabled using the checkbox at the top of the panel and the height of the index plot panel can be set here too.
The ‘Components’ panel allows the user to specify what data values to include. Typically the index plot contains a
histogram of sample depth and a line chart of percent scarred. In FHAES you have the option of specifying whether the
sample depth histogram is based on complete sample depth or recording sample depth (i.e. only count samples that are
in recording status). FHAES also has the option of adding a sample threshold line. This is a simple horizontal line at the
specified sample depth. This is typically used to indicate the point at which the sample depth becomes significant, the
value being derived from an sample size analysis (see chapter 6). The remaining panels enable the user to style the axis
titles.
8.2.3 Chronology plot options
The chronology plot tab provides options of tailoring the central sample-by-sample fire history plot. The top panel gives
options for showing/hiding and styling the labels as well as which series to plot.
The next panel provides options for showing/hiding different features. For instance if your data file has both fire and
other injuries, but you are only interested in seeing fire events, the injury markers can be hidden.
The bottom panel provides the ability to style series categories. This panel is only relevant if you enable sorting by
categories (see section 8.3).
8.2.4 Composite plot options
The final tab controls the style of the bottom composite plot. The top panel provides options for basic chart size and
title label style while the next panel provides options for how the composite years are calculated. The composite filter
used here is the same as that provided for the ‘create composite file’ tool described in section 3.3.2.
Thursday 21
st
December, 2017
44 FHAES: Fire History Analysis and Exploration System
The bottom panel styles the year labels on the composite plot. Years can either be displayed in long (e.g. 1996) or short
(e.g. ’96) style, and can be displayed horizontally, vertically or angled depending on preference.
8.3 Categories and sorting
The series within the chronology plot are by default displayed in the order in which they are recorded in the file. There
are a number of other options in the Chart Sort series by menu including: name (alphabetically); first fire year; start
year; end year; category; and order in file. These options are also available in the Chart Properties dialog.
The sort by category option enables you to group series into defined categories e.g. species, slope aspect, sub-groups
etc. Unfortunately the FHX file format does not provide for sample-by-sample metadata (see section 4.8 for further
information) so there is no way to define these categories programmatically. To define these categories manually, go you
Chart Edit categories. Click the ‘add new category’ button against each sample and enter the category name. When
you are done, click the save button.
This category information is saved to a CSV text file next to your original FHX data file. The format of this file is
very simple and self-explanatory so if you have your metadata stored in a structured format elsewhere (e.g. database or
spreadsheet) you should be able to generate the category files for each of your FHX files quite easily.
8.4 Exporting charts
Once you are happy with your chart you can export to one of three image files for use in publications and reports. The
PNG format is a raster image format which is suitable for inserting into word processing documents and basic reports.
It is however not very suitable for high quality journal publications. In this case you should use either the PDF or SVG
vector formats. The nature of these formats means that can be scaled to any size with not loss of quality. Both formats
are widely supported by vector editing programs which provide you with the ability to further tailor the charts beyond
what FHAES offers.
To export the current chart go to File Export chart Export current chart as... then in the file dialog specify the
filename and the file format you’d like to use.
Alternatively you can export charts for all the files you currently have loaded by going to File Export chart Bulk
export to choosing the format you would like to use. You then need to specify a folder where the exported charts should
be saved. The charts will be named the same as the input FHX files but with the .pdf, .svg or .png extensions according
to the format you specified.
8.5 Clarification of component widths
One aspect of the chart drawing that may cause confusion—especially for charts with few years—is the width of some
of the chart components.
The width of the percentage scar columns, chronology event markers and composite plot columns are all fixed regardless
of x-axis scale. This is to ensure a clear and uniform-looking chart whether it decades or millennia of data are drawn.
These data points are plotted to coincide with the tick-marks on the x-axis. If two data points are shown in adjacent
years, then there will be a small gap (depending on the scale of the x-axis) between them.
The horizontal lines for each sample in the chronology plot, as well as the blue sample/recorder depth line in the index
plot are in contrast, drawn continuously with no gaps. This gives the sample/recorder depth line a ‘saw-tooth’ style plot.
Thursday 21
st
December, 2017
Appendix A
Recorder Years
The issue of what constitutes a ‘recorder year’ is actually quite complex. Some researchers feel that a tree can only ever
be in recording status after it has been injured by fire. Others feel that this is not necessarily the case depending on the
species and ecosystem you are working with.
Within FHX data files the issue is confused by two factors. The first is that the design of the format means that only one
character can be used per year for each sample. It is therefore not possible to explicity specify if a year in which there
is an injury whether the tree was in recording status or not. Likewise you can’t specify the recording status as well as
indicating the inner/outer rings, or pith/bark. The second issue is that the dot symbol has multiple meanings depending
on the context:
Filler symbol before the first ring
Filler symbol after the last ring
A dateable ring prior to the first scar (i.e. prior to recording status)
An eroded ring (or commonly a succession of such rings) before the intial scar when fire cannot be determined to
be present or absent
An eroded ring (or commonly a succession of such rings) after the intial scar when fire cannot be determined to
be present or absent
The standard way to decide if a year is interpreted as ‘recording’ or not in FHAES is described in figure A.1. This flow
chart assumes you are at the beginning or within a series (i.e. it doesn’t describe handling the initial filler symbols). This
method is the same as the convention used within FHX2. The chart assumes you the analysis is being carried out with
the event type set to ‘fires’ or ‘fires and injuries’. If the event type is set to ‘injuries’ then the case of the characters
should be inverted.
The modular way in which FHAES has been developed has led to one portion of FHAES using a different, more simplistic
method of determining whether a sample is ‘recording’ or not. The FHMatrix module used in the calculation of the binary
comparison and similarity/dissimilarity matrices (see sections 5.5 and 5.6) relies upon this simpler method. This method
does not consider any year prior to the first fire year as recording. All fire and injury events are considered recording years,
but all dot, pith, bark, inner ring and outer ring symbols are regarded as non-recording. The method is more transparent
than the standard method but may be at odds with some researchers concepts of a recording year given the departure
from the traditional concept used in FHX2. It is therefore important to understand these differences when interpreting
binary comparison and similarity/dissimilarity matrices, especially if your data files contain recording years before the first
fire event.
Thursday 21
st
December, 2017
46
Figure A.1: A flow chart illustrating how FHAES (with the exception of the FHMatrix module) determines if a tree is in recording
status or not. Note the chart assumes you are at the beginning or within a series and therefore does not describe the handling of
the initial filler dot symbols. The chart is only applicable as drawn for analyses where the event type is set to ‘fires’ or ‘fires and
injuries’. If the event type is set to ‘injuries’ then the flow chart should be interpreted with the case of all characters inverted, i.e.
replace ‘Upper case’ with ’Lower case’ and vice versa.
Thursday 21
st
December, 2017
Appendix B
GNU General Public License
FHAES is released under the GNU General Public License (GPL) version 3.
Copyright © 2015 Elaine Kennedy Sutherland, Peter W. Brewer, Donald A. Falk and M. Elena Vel´asquez.
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License
as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
License for more details.
B.1 Preamble
Copyright © 2007 Free Software Foundation, Inc. http://fsf.org/
Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed.
The GNU General Public License is a free, copyleft license for software and other kinds of works.
The licenses for most software and other practical works are designed to take away your freedom to share and change the works. By contrast,
the GNU General Public License is intended to guarantee your freedom to share and change all versions of a program–to make sure it remains
free software for all its users. We, the Free Software Foundation, use the GNU General Public License for most of our software; it applies also
to any other work released this way by its authors. You can apply it to your programs, too.
When we speak of free software, we are referring to freedom, not price. Our General Public Licenses are designed to make sure that you have
the freedom to distribute copies of free software (and charge for them if you wish), that you receive source code or can get it if you want it,
that you can change the software or use pieces of it in new free programs, and that you know you can do these things.
To protect your rights, we need to prevent others from denying you these rights or asking you to surrender the rights. Therefore, you have
certain responsibilities if you distribute copies of the software, or if you modify it: responsibilities to respect the freedom of others.
For example, if you distribute copies of such a program, whether gratis or for a fee, you must pass on to the recipients the same freedoms that
you received. You must make sure that they, too, receive or can get the source code. And you must show them these terms so they know
their rights.
Developers that use the GNU GPL protect your rights with two steps: (1) assert copyright on the software, and (2) offer you this License
giving you legal permission to copy, distribute and/or modify it.
For the developers’ and authors’ protection, the GPL clearly explains that there is no warranty for this free software. For both users’ and
authors’ sake, the GPL requires that modified versions be marked as changed, so that their problems will not be attributed erroneously to
authors of previous versions.
Some devices are designed to deny users access to install or run modified versions of the software inside them, although the manufacturer can
do so. This is fundamentally incompatible with the aim of protecting users’ freedom to change the software. The systematic pattern of such
abuse occurs in the area of products for individuals to use, which is precisely where it is most unacceptable. Therefore, we have designed this
version of the GPL to prohibit the practice for those products. If such problems arise substantially in other domains, we stand ready to extend
this provision to those domains in future versions of the GPL, as needed to protect the freedom of users.
Finally, every program is threatened constantly by software patents. States should not allow patents to restrict development and use of software
on general-purpose computers, but in those that do, we wish to avoid the special danger that patents applied to a free program could make
it effectively proprietary. To prevent this, the GPL assures that patents cannot be used to render the program non-free.
The precise terms and conditions for copying, distribution and modification follow.
Thursday 21
st
December, 2017
48 FHAES: Fire History Analysis and Exploration System
B.2 Terms and Conditions
0. Definitions.
“This License” refers to version 3 of the GNU General Public License.
“Copyright” also means copyright-like laws that apply to other kinds of works, such as semiconductor masks.
“The Program” refers to any copyrightable work licensed under this License. Each licensee is addressed as “you”. “Licensees” and
“recipients” may be individuals or organizations.
To “modify” a work means to copy from or adapt all or part of the work in a fashion requiring copyright permission, other than the
making of an exact copy. The resulting work is called a “modified version” of the earlier work or a work “based on” the earlier work.
A “covered work” means either the unmodified Program or a work based on the Program.
To “propagate” a work means to do anything with it that, without permission, would make you directly or secondarily liable for
infringement under applicable copyright law, except executing it on a computer or modifying a private copy. Propagation includes
copying, distribution (with or without modification), making available to the public, and in some countries other activities as well.
To “convey” a work means any kind of propagation that enables other parties to make or receive copies. Mere interaction with a user
through a computer network, with no transfer of a copy, is not conveying.
An interactive user interface displays “Appropriate Legal Notices” to the extent that it includes a convenient and prominently visible
feature that (1) displays an appropriate copyright notice, and (2) tells the user that there is no warranty for the work (except to the
extent that warranties are provided), that licensees may convey the work under this License, and how to view a copy of this License. If
the interface presents a list of user commands or options, such as a menu, a prominent item in the list meets this criterion.
1. Source Code.
The “source code” for a work means the preferred form of the work for making modifications to it. “Object code” means any non-source
form of a work.
A “Standard Interface” means an interface that either is an official standard defined by a recognized standards body, or, in the case of
interfaces specified for a particular programming language, one that is widely used among developers working in that language.
The “System Libraries” of an executable work include anything, other than the work as a whole, that (a) is included in the normal form
of packaging a Major Component, but which is not part of that Major Component, and (b) serves only to enable use of the work with
that Major Component, or to implement a Standard Interface for which an implementation is available to the public in source code
form. A “Major Component”, in this context, means a major essential component (kernel, window system, and so on) of the specific
operating system (if any) on which the executable work runs, or a compiler used to produce the work, or an object code interpreter
used to run it.
The “Corresponding Source” for a work in object code form means all the source code needed to generate, install, and (for an executable
work) run the object code and to modify the work, including scripts to control those activities. However, it does not include the work’s
System Libraries, or general-purpose tools or generally available free programs which are used unmodified in performing those activities
but which are not part of the work. For example, Corresponding Source includes interface definition files associated with source files for
the work, and the source code for shared libraries and dynamically linked subprograms that the work is specifically designed to require,
such as by intimate data communication or control flow between those subprograms and other parts of the work.
The Corresponding Source need not include anything that users can regenerate automatically from other parts of the Corresponding
Source.
The Corresponding Source for a work in source code form is that same work.
2. Basic Permissions.
All rights granted under this License are granted for the term of copyright on the Program, and are irrevocable provided the stated
conditions are met. This License explicitly affirms your unlimited permission to run the unmodified Program. The output from running
a covered work is covered by this License only if the output, given its content, constitutes a covered work. This License acknowledges
your rights of fair use or other equivalent, as provided by copyright law.
You may make, run and propagate covered works that you do not convey, without conditions so long as your license otherwise remains
in force. You may convey covered works to others for the sole purpose of having them make modifications exclusively for you, or provide
you with facilities for running those works, provided that you comply with the terms of this License in conveying all material for which
you do not control copyright. Those thus making or running the covered works for you must do so exclusively on your behalf, under
your direction and control, on terms that prohibit them from making any copies of your copyrighted material outside their relationship
with you.
Conveying under any other circumstances is permitted solely under the conditions stated below. Sublicensing is not allowed; section
10 makes it unnecessary.
3. Protecting Users’ Legal Rights From Anti-Circumvention Law.
No covered work shall be deemed part of an effective technological measure under any applicable law fulfilling obligations under article 11
of the WIPO copyright treaty adopted on 20 December 1996, or similar laws prohibiting or restricting circumvention of such measures.
When you convey a covered work, you waive any legal power to forbid circumvention of technological measures to the extent such
circumvention is effected by exercising rights under this License with respect to the covered work, and you disclaim any intention to
limit operation or modification of the work as a means of enforcing, against the work’s users, your or third parties’ legal rights to forbid
circumvention of technological measures.
4. Conveying Verbatim Copies.
You may convey verbatim copies of the Program’s source code as you receive it, in any medium, provided that you conspicuously
and appropriately publish on each copy an appropriate copyright notice; keep intact all notices stating that this License and any non-
permissive terms added in accord with section 7 apply to the code; keep intact all notices of the absence of any warranty; and give all
recipients a copy of this License along with the Program.
You may charge any price or no price for each copy that you convey, and you may offer support or warranty protection for a fee.
5. Conveying Modified Source Versions.
You may convey a work based on the Program, or the modifications to produce it from the Program, in the form of source code under
the terms of section 4, provided that you also meet all of these conditions:
Thursday 21
st
December, 2017
GNU General Public License 49
(a) The work must carry prominent notices stating that you modified it, and giving a relevant date.
(b) The work must carry prominent notices stating that it is released under this License and any conditions added under section 7.
This requirement modifies the requirement in section 4 to “keep intact all notices”.
(c) You must license the entire work, as a whole, under this License to anyone who comes into possession of a copy. This License
will therefore apply, along with any applicable section 7 additional terms, to the whole of the work, and all its parts, regardless
of how they are packaged. This License gives no permission to license the work in any other way, but it does not invalidate such
permission if you have separately received it.
(d) If the work has interactive user interfaces, each must display Appropriate Legal Notices; however, if the Program has interactive
interfaces that do not display Appropriate Legal Notices, your work need not make them do so.
A compilation of a covered work with other separate and independent works, which are not by their nature extensions of the covered
work, and which are not combined with it such as to form a larger program, in or on a volume of a storage or distribution medium, is
called an “aggregate” if the compilation and its resulting copyright are not used to limit the access or legal rights of the compilation’s
users beyond what the individual works permit. Inclusion of a covered work in an aggregate does not cause this License to apply to the
other parts of the aggregate.
6. Conveying Non-Source Forms.
You may convey a covered work in object code form under the terms of sections 4 and 5, provided that you also convey the machine-
readable Corresponding Source under the terms of this License, in one of these ways:
(a) Convey the object code in, or embodied in, a physical product (including a physical distribution medium), accompanied by the
Corresponding Source fixed on a durable physical medium customarily used for software interchange.
(b) Convey the object code in, or embodied in, a physical product (including a physical distribution medium), accompanied by a
written offer, valid for at least three years and valid for as long as you offer spare parts or customer support for that product
model, to give anyone who possesses the object code either (1) a copy of the Corresponding Source for all the software in the
product that is covered by this License, on a durable physical medium customarily used for software interchange, for a price no
more than your reasonable cost of physically performing this conveying of source, or (2) access to copy the Corresponding Source
from a network server at no charge.
(c) Convey individual copies of the object code with a copy of the written offer to provide the Corresponding Source. This alternative
is allowed only occasionally and noncommercially, and only if you received the object code with such an offer, in accord with
subsection 6b.
(d) Convey the object code by offering access from a designated place (gratis or for a charge), and offer equivalent access to the
Corresponding Source in the same way through the same place at no further charge. You need not require recipients to copy the
Corresponding Source along with the object code. If the place to copy the object code is a network server, the Corresponding
Source may be on a different server (operated by you or a third party) that supports equivalent copying facilities, provided you
maintain clear directions next to the object code saying where to find the Corresponding Source. Regardless of what server hosts
the Corresponding Source, you remain obligated to ensure that it is available for as long as needed to satisfy these requirements.
(e) Convey the object code using peer-to-peer transmission, provided you inform other peers where the object code and Corresponding
Source of the work are being offered to the general public at no charge under subsection 6d.
A separable portion of the object code, whose source code is excluded from the Corresponding Source as a System Library, need not
be included in conveying the object code work.
A “User Product” is either (1) a “consumer product”, which means any tangible personal property which is normally used for personal,
family, or household purposes, or (2) anything designed or sold for incorporation into a dwelling. In determining whether a product
is a consumer product, doubtful cases shall be resolved in favor of coverage. For a particular product received by a particular user,
“normally used” refers to a typical or common use of that class of product, regardless of the status of the particular user or of the way
in which the particular user actually uses, or expects or is expected to use, the product. A product is a consumer product regardless of
whether the product has substantial commercial, industrial or non-consumer uses, unless such uses represent the only significant mode
of use of the product.
“Installation Information” for a User Product means any methods, procedures, authorization keys, or other information required to
install and execute modified versions of a covered work in that User Product from a modified version of its Corresponding Source. The
information must suffice to ensure that the continued functioning of the modified object code is in no case prevented or interfered with
solely because modification has been made.
If you convey an object code work under this section in, or with, or specifically for use in, a User Product, and the conveying occurs
as part of a transaction in which the right of possession and use of the User Product is transferred to the recipient in perpetuity or
for a fixed term (regardless of how the transaction is characterized), the Corresponding Source conveyed under this section must be
accompanied by the Installation Information. But this requirement does not apply if neither you nor any third party retains the ability
to install modified object code on the User Product (for example, the work has been installed in ROM).
The requirement to provide Installation Information does not include a requirement to continue to provide support service, warranty,
or updates for a work that has been modified or installed by the recipient, or for the User Product in which it has been modified or
installed. Access to a network may be denied when the modification itself materially and adversely affects the operation of the network
or violates the rules and protocols for communication across the network.
Corresponding Source conveyed, and Installation Information provided, in accord with this section must be in a format that is publicly
documented (and with an implementation available to the public in source code form), and must require no special password or key
for unpacking, reading or copying.
7. Additional Terms.
“Additional permissions” are terms that supplement the terms of this License by making exceptions from one or more of its conditions.
Additional permissions that are applicable to the entire Program shall be treated as though they were included in this License, to
the extent that they are valid under applicable law. If additional permissions apply only to part of the Program, that part may be
used separately under those permissions, but the entire Program remains governed by this License without regard to the additional
permissions.
When you convey a copy of a covered work, you may at your option remove any additional permissions from that copy, or from any part
of it. (Additional permissions may be written to require their own removal in certain cases when you modify the work.) You may place
additional permissions on material, added by you to a covered work, for which you have or can give appropriate copyright permission.
Thursday 21
st
December, 2017
50 FHAES: Fire History Analysis and Exploration System
Notwithstanding any other provision of this License, for material you add to a covered work, you may (if authorized by the copyright
holders of that material) supplement the terms of this License with terms:
(a) Disclaiming warranty or limiting liability differently from the terms of sections 15 and 16 of this License; or
(b) Requiring preservation of specified reasonable legal notices or author attributions in that material or in the Appropriate Legal
Notices displayed by works containing it; or
(c) Prohibiting misrepresentation of the origin of that material, or requiring that modified versions of such material be marked in
reasonable ways as different from the original version; or
(d) Limiting the use for publicity purposes of names of licensors or authors of the material; or
(e) Declining to grant rights under trademark law for use of some trade names, trademarks, or service marks; or
(f) Requiring indemnification of licensors and authors of that material by anyone who conveys the material (or modified versions of
it) with contractual assumptions of liability to the recipient, for any liability that these contractual assumptions directly impose
on those licensors and authors.
All other non-permissive additional terms are considered “further restrictions” within the meaning of section 10. If the Program as you
received it, or any part of it, contains a notice stating that it is governed by this License along with a term that is a further restriction,
you may remove that term. If a license document contains a further restriction but permits relicensing or conveying under this License,
you may add to a covered work material governed by the terms of that license document, provided that the further restriction does not
survive such relicensing or conveying.
If you add terms to a covered work in accord with this section, you must place, in the relevant source files, a statement of the additional
terms that apply to those files, or a notice indicating where to find the applicable terms.
Additional terms, permissive or non-permissive, may be stated in the form of a separately written license, or stated as exceptions; the
above requirements apply either way.
8. Termination.
You may not propagate or modify a covered work except as expressly provided under this License. Any attempt otherwise to propagate
or modify it is void, and will automatically terminate your rights under this License (including any patent licenses granted under the
third paragraph of section 11).
However, if you cease all violation of this License, then your license from a particular copyright holder is reinstated (a) provisionally,
unless and until the copyright holder explicitly and finally terminates your license, and (b) permanently, if the copyright holder fails to
notify you of the violation by some reasonable means prior to 60 days after the cessation.
Moreover, your license from a particular copyright holder is reinstated permanently if the copyright holder notifies you of the violation
by some reasonable means, this is the first time you have received notice of violation of this License (for any work) from that copyright
holder, and you cure the violation prior to 30 days after your receipt of the notice.
Termination of your rights under this section does not terminate the licenses of parties who have received copies or rights from you
under this License. If your rights have been terminated and not permanently reinstated, you do not qualify to receive new licenses for
the same material under section 10.
9. Acceptance Not Required for Having Copies.
You are not required to accept this License in order to receive or run a copy of the Program. Ancillary propagation of a covered work
occurring solely as a consequence of using peer-to-peer transmission to receive a copy likewise does not require acceptance. However,
nothing other than this License grants you permission to propagate or modify any covered work. These actions infringe copyright if
you do not accept this License. Therefore, by modifying or propagating a covered work, you indicate your acceptance of this License
to do so.
10. Automatic Licensing of Downstream Recipients.
Each time you convey a covered work, the recipient automatically receives a license from the original licensors, to run, modify and
propagate that work, subject to this License. You are not responsible for enforcing compliance by third parties with this License.
An “entity transaction” is a transaction transferring control of an organization, or substantially all assets of one, or subdividing an
organization, or merging organizations. If propagation of a covered work results from an entity transaction, each party to that transaction
who receives a copy of the work also receives whatever licenses to the work the party’s predecessor in interest had or could give under
the previous paragraph, plus a right to possession of the Corresponding Source of the work from the predecessor in interest, if the
predecessor has it or can get it with reasonable efforts.
You may not impose any further restrictions on the exercise of the rights granted or affirmed under this License. For example, you may
not impose a license fee, royalty, or other charge for exercise of rights granted under this License, and you may not initiate litigation
(including a cross-claim or counterclaim in a lawsuit) alleging that any patent claim is infringed by making, using, selling, offering for
sale, or importing the Program or any portion of it.
11. Patents.
A “contributor” is a copyright holder who authorizes use under this License of the Program or a work on which the Program is based.
The work thus licensed is called the contributor’s “contributor version”.
A contributor’s “essential patent claims” are all patent claims owned or controlled by the contributor, whether already acquired or
hereafter acquired, that would be infringed by some manner, permitted by this License, of making, using, or selling its contributor
version, but do not include claims that would be infringed only as a consequence of further modification of the contributor version.
For purposes of this definition, “control” includes the right to grant patent sublicenses in a manner consistent with the requirements
of this License.
Each contributor grants you a non-exclusive, worldwide, royalty-free patent license under the contributor’s essential patent claims, to
make, use, sell, offer for sale, import and otherwise run, modify and propagate the contents of its contributor version.
In the following three paragraphs, a “patent license” is any express agreement or commitment, however denominated, not to enforce a
patent (such as an express permission to practice a patent or covenant not to sue for patent infringement). To “grant” such a patent
license to a party means to make such an agreement or commitment not to enforce a patent against the party.
If you convey a covered work, knowingly relying on a patent license, and the Corresponding Source of the work is not available for
anyone to copy, free of charge and under the terms of this License, through a publicly available network server or other readily accessible
Thursday 21
st
December, 2017
GNU General Public License 51
means, then you must either (1) cause the Corresponding Source to be so available, or (2) arrange to deprive yourself of the benefit
of the patent license for this particular work, or (3) arrange, in a manner consistent with the requirements of this License, to extend
the patent license to downstream recipients. “Knowingly relying” means you have actual knowledge that, but for the patent license,
your conveying the covered work in a country, or your recipient’s use of the covered work in a country, would infringe one or more
identifiable patents in that country that you have reason to believe are valid.
If, pursuant to or in connection with a single transaction or arrangement, you convey, or propagate by procuring conveyance of, a
covered work, and grant a patent license to some of the parties receiving the covered work authorizing them to use, propagate, modify
or convey a specific copy of the covered work, then the patent license you grant is automatically extended to all recipients of the
covered work and works based on it.
A patent license is “discriminatory” if it does not include within the scope of its coverage, prohibits the exercise of, or is conditioned
on the non-exercise of one or more of the rights that are specifically granted under this License. You may not convey a covered work
if you are a party to an arrangement with a third party that is in the business of distributing software, under which you make payment
to the third party based on the extent of your activity of conveying the work, and under which the third party grants, to any of the
parties who would receive the covered work from you, a discriminatory patent license (a) in connection with copies of the covered work
conveyed by you (or copies made from those copies), or (b) primarily for and in connection with specific products or compilations that
contain the covered work, unless you entered into that arrangement, or that patent license was granted, prior to 28 March 2007.
Nothing in this License shall be construed as excluding or limiting any implied license or other defenses to infringement that may
otherwise be available to you under applicable patent law.
12. No Surrender of Others’ Freedom.
If conditions are imposed on you (whether by court order, agreement or otherwise) that contradict the conditions of this License,
they do not excuse you from the conditions of this License. If you cannot convey a covered work so as to satisfy simultaneously your
obligations under this License and any other pertinent obligations, then as a consequence you may not convey it at all. For example, if
you agree to terms that obligate you to collect a royalty for further conveying from those to whom you convey the Program, the only
way you could satisfy both those terms and this License would be to refrain entirely from conveying the Program.
13. Use with the GNU Affero General Public License.
Notwithstanding any other provision of this License, you have permission to link or combine any covered work with a work licensed
under version 3 of the GNU Affero General Public License into a single combined work, and to convey the resulting work. The terms
of this License will continue to apply to the part which is the covered work, but the special requirements of the GNU Affero General
Public License, section 13, concerning interaction through a network will apply to the combination as such.
14. Revised Versions of this License.
The Free Software Foundation may publish revised and/or new versions of the GNU General Public License from time to time. Such
new versions will be similar in spirit to the present version, but may differ in detail to address new problems or concerns.
Each version is given a distinguishing version number. If the Program specifies that a certain numbered version of the GNU General
Public License “or any later version” applies to it, you have the option of following the terms and conditions either of that numbered
version or of any later version published by the Free Software Foundation. If the Program does not specify a version number of the
GNU General Public License, you may choose any version ever published by the Free Software Foundation.
If the Program specifies that a proxy can decide which future versions of the GNU General Public License can be used, that proxy’s
public statement of acceptance of a version permanently authorizes you to choose that version for the Program.
Later license versions may give you additional or different permissions. However, no additional obligations are imposed on any author
or copyright holder as a result of your choosing to follow a later version.
15. Disclaimer of Warranty.
THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN
OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM “AS
IS” WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO
THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU
ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
16. Limitation of Liability.
IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR
ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR
DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE
OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED
INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH
ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH
DAMAGES.
17. Interpretation of Sections 15 and 16.
If the disclaimer of warranty and limitation of liability provided above cannot be given local legal effect according to their terms,
reviewing courts shall apply local law that most closely approximates an absolute waiver of all civil liability in connection with the
Program, unless a warranty or assumption of liability accompanies a copy of the Program in return for a fee.
Thursday 21
st
December, 2017
Thursday 21
st
December, 2017
Appendix C
GNU Free Documentation License
This manual is released inder the GNU Free Documentation License (FDL) v1.3.
Permission is granted to copy, distribute and/or modify this document under the terms of the GNU Free Documentation
License, Version 1.3 or any later version published by the Free Software Foundation; with no Invariant Sections, no
Front-Cover Texts, and no Back-Cover Texts.
C.1 Preamble
Copyright © 2000, 2001, 2002, 2007, 2008 Free Software Foundation, Inc. http://fsf.org/
Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed.
The purpose of this License is to make a manual, textbook, or other functional and useful document “free” in the sense of freedom: to assure
everyone the effective freedom to copy and redistribute it, with or without modifying it, either commercially or noncommercially. Secondarily,
this License preserves for the author and publisher a way to get credit for their work, while not being considered responsible for modifications
made by others.
This License is a kind of “copyleft”, which means that derivative works of the document must themselves be free in the same sense. It
complements the GNU General Public License, which is a copyleft license designed for free software.
We have designed this License in order to use it for manuals for free software, because free software needs free documentation: a free program
should come with manuals providing the same freedoms that the software does. But this License is not limited to software manuals; it can be
used for any textual work, regardless of subject matter or whether it is published as a printed book. We recommend this License principally
for works whose purpose is instruction or reference.
C.2 Terms and conditions
1. Applicability and definitions
This License applies to any manual or other work, in any medium, that contains a notice placed by the copyright holder saying it can
be distributed under the terms of this License. Such a notice grants a world-wide, royalty-free license, unlimited in duration, to use
that work under the conditions stated herein. The “Document”, below, refers to any such manual or work. Any member of the public
is a licensee, and is addressed as “you”. You accept the license if you copy, modify or distribute the work in a way requiring permission
under copyright law.
A “Modified Version” of the Document means any work containing the Document or a portion of it, either copied verbatim, or with
modifications and/or translated into another language.
A “Secondary Section” is a named appendix or a front-matter section of the Document that deals exclusively with the relationship of
the publishers or authors of the Document to the Document’s overall subject (or to related matters) and contains nothing that could
fall directly within that overall subject. (Thus, if the Document is in part a textbook of mathematics, a Secondary Section may not
explain any mathematics.) The relationship could be a matter of historical connection with the subject or with related matters, or of
legal, commercial, philosophical, ethical or political position regarding them.
The “Invariant Sections” are certain Secondary Sections whose titles are designated, as being those of Invariant Sections, in the notice
that says that the Document is released under this License. If a section does not fit the above definition of Secondary then it is not
allowed to be designated as Invariant. The Document may contain zero Invariant Sections. If the Document does not identify any
Invariant Sections then there are none.
The “Cover Texts” are certain short passages of text that are listed, as Front-Cover Texts or Back-Cover Texts, in the notice that says
that the Document is released under this License. A Front-Cover Text may be at most 5 words, and a Back-Cover Text may be at
most 25 words.
Thursday 21
st
December, 2017
54 FHAES: Fire History Analysis and Exploration System
A “Transparent” copy of the Document means a machine-readable copy, represented in a format whose specification is available to
the general public, that is suitable for revising the document straightforwardly with generic text editors or (for images composed of
pixels) generic paint programs or (for drawings) some widely available drawing editor, and that is suitable for input to text formatters
or for automatic translation to a variety of formats suitable for input to text formatters. A copy made in an otherwise Transparent
file format whose markup, or absence of markup, has been arranged to thwart or discourage subsequent modification by readers is not
Transparent. An image format is not Transparent if used for any substantial amount of text. A copy that is not “Transparent” is called
“Opaque”.
Examples of suitable formats for Transparent copies include plain ASCII without markup, Texinfo input format, LaTeX input format,
SGML or XML using a publicly available DTD, and standard-conforming simple HTML, PostScript or PDF designed for human
modification. Examples of transparent image formats include PNG, XCF and JPG. Opaque formats include proprietary formats that
can be read and edited only by proprietary word processors, SGML or XML for which the DTD and/or processing tools are not generally
available, and the machine-generated HTML, PostScript or PDF produced by some word processors for output purposes only.
The “Title Page” means, for a printed book, the title page itself, plus such following pages as are needed to hold, legibly, the material
this License requires to appear in the title page. For works in formats which do not have any title page as such, “Title Page” means
the text near the most prominent appearance of the work’s title, preceding the beginning of the body of the text.
The “publisher” means any person or entity that distributes copies of the Document to the public.
A section “Entitled XYZ” means a named subunit of the Document whose title either is precisely XYZ or contains XYZ in parentheses
following text that translates XYZ in another language. (Here XYZ stands for a specific section name mentioned below, such as
“Acknowledgements”, “Dedications”, “Endorsements”, or “History”.) To “Preserve the Title” of such a section when you modify
the Document means that it remains a section “Entitled XYZ” according to this definition.
The Document may include Warranty Disclaimers next to the notice which states that this License applies to the Document. These
Warranty Disclaimers are considered to be included by reference in this License, but only as regards disclaiming warranties: any other
implication that these Warranty Disclaimers may have is void and has no effect on the meaning of this License.
2. Verbatim copying
You may copy and distribute the Document in any medium, either commercially or noncommercially, provided that this License, the
copyright notices, and the license notice saying this License applies to the Document are reproduced in all copies, and that you add no
other conditions whatsoever to those of this License. You may not use technical measures to obstruct or control the reading or further
copying of the copies you make or distribute. However, you may accept compensation in exchange for copies. If you distribute a large
enough number of copies you must also follow the conditions in section 3.
You may also lend copies, under the same conditions stated above, and you may publicly display copies.
3. Copying in quantity
If you publish printed copies (or copies in media that commonly have printed covers) of the Document, numbering more than 100,
and the Document’s license notice requires Cover Texts, you must enclose the copies in covers that carry, clearly and legibly, all these
Cover Texts: Front-Cover Texts on the front cover, and Back-Cover Texts on the back cover. Both covers must also clearly and legibly
identify you as the publisher of these copies. The front cover must present the full title with all words of the title equally prominent
and visible. You may add other material on the covers in addition. Copying with changes limited to the covers, as long as they preserve
the title of the Document and satisfy these conditions, can be treated as verbatim copying in other respects.
If the required texts for either cover are too voluminous to fit legibly, you should put the first ones listed (as many as fit reasonably)
on the actual cover, and continue the rest onto adjacent pages.
If you publish or distribute Opaque copies of the Document numbering more than 100, you must either include a machine-readable
Transparent copy along with each Opaque copy, or state in or with each Opaque copy a computer-network location from which the
general network-using public has access to download using public-standard network protocols a complete Transparent copy of the
Document, free of added material. If you use the latter option, you must take reasonably prudent steps, when you begin distribution
of Opaque copies in quantity, to ensure that this Transparent copy will remain thus accessible at the stated location until at least one
year after the last time you distribute an Opaque copy (directly or through your agents or retailers) of that edition to the public.
It is requested, but not required, that you contact the authors of the Document well before redistributing any large number of copies,
to give them a chance to provide you with an updated version of the Document.
4. Modifications
You may copy and distribute a Modified Version of the Document under the conditions of sections 2 and 3 above, provided that you
release the Modified Version under precisely this License, with the Modified Version filling the role of the Document, thus licensing
distribution and modification of the Modified Version to whoever possesses a copy of it. In addition, you must do these things in the
Modified Version:
A. Use in the Title Page (and on the covers, if any) a title distinct from that of the Document, and from those of previous versions
(which should, if there were any, be listed in the History section of the Document). You may use the same title as a previous
version if the original publisher of that version gives permission.
B. List on the Title Page, as authors, one or more persons or entities responsible for authorship of the modifications in the Modified
Version, together with at least five of the principal authors of the Document (all of its principal authors, if it has fewer than five),
unless they release you from this requirement.
C. State on the Title page the name of the publisher of the Modified Version, as the publisher.
D. Preserve all the copyright notices of the Document.
E. Add an appropriate copyright notice for your modifications adjacent to the other copyright notices.
F. Include, immediately after the copyright notices, a license notice giving the public permission to use the Modified Version under
the terms of this License, in the form shown in the Addendum below.
G. Preserve in that license notice the full lists of Invariant Sections and required Cover Texts given in the Document’s license notice.
H. Include an unaltered copy of this License.
I. Preserve the section Entitled “History”, Preserve its Title, and add to it an item stating at least the title, year, new authors, and
publisher of the Modified Version as given on the Title Page. If there is no section Entitled “History” in the Document, create
one stating the title, year, authors, and publisher of the Document as given on its Title Page, then add an item describing the
Modified Version as stated in the previous sentence.
Thursday 21
st
December, 2017
GNU Free Documentation License 55
J. Preserve the network location, if any, given in the Document for public access to a Transparent copy of the Document, and
likewise the network locations given in the Document for previous versions it was based on. These may be placed in the “History”
section. You may omit a network location for a work that was published at least four years before the Document itself, or if the
original publisher of the version it refers to gives permission.
K. For any section Entitled “Acknowledgements” or “Dedications”, Preserve the Title of the section, and preserve in the section all
the substance and tone of each of the contributor acknowledgements and/or dedications given therein.
L. Preserve all the Invariant Sections of the Document, unaltered in their text and in their titles. Section numbers or the equivalent
are not considered part of the section titles.
M. Delete any section Entitled “Endorsements”. Such a section may not be included in the Modified Version.
N. Do not retitle any existing section to be Entitled “Endorsements” or to conflict in title with any Invariant Section.
O. Preserve any Warranty Disclaimers.
If the Modified Version includes new front-matter sections or appendices that qualify as Secondary Sections and contain no material
copied from the Document, you may at your option designate some or all of these sections as invariant. To do this, add their titles to
the list of Invariant Sections in the Modified Version’s license notice. These titles must be distinct from any other section titles.
You may add a section Entitled “Endorsements”, provided it contains nothing but endorsements of your Modified Version by various
parties—for example, statements of peer review or that the text has been approved by an organization as the authoritative definition
of a standard.
You may add a passage of up to five words as a Front-Cover Text, and a passage of up to 25 words as a Back-Cover Text, to the end
of the list of Cover Texts in the Modified Version. Only one passage of Front-Cover Text and one of Back-Cover Text may be added
by (or through arrangements made by) any one entity. If the Document already includes a cover text for the same cover, previously
added by you or by arrangement made by the same entity you are acting on behalf of, you may not add another; but you may replace
the old one, on explicit permission from the previous publisher that added the old one.
The author(s) and publisher(s) of the Document do not by this License give permission to use their names for publicity for or to assert
or imply endorsement of any Modified Version.
5. Combining documents
You may combine the Document with other documents released under this License, under the terms defined in section 4 above for
modified versions, provided that you include in the combination all of the Invariant Sections of all of the original documents, unmodified,
and list them all as Invariant Sections of your combined work in its license notice, and that you preserve all their Warranty Disclaimers.
The combined work need only contain one copy of this License, and multiple identical Invariant Sections may be replaced with a single
copy. If there are multiple Invariant Sections with the same name but different contents, make the title of each such section unique by
adding at the end of it, in parentheses, the name of the original author or publisher of that section if known, or else a unique number.
Make the same adjustment to the section titles in the list of Invariant Sections in the license notice of the combined work.
In the combination, you must combine any sections Entitled “History” in the various original documents, forming one section Entitled
“History”; likewise combine any sections Entitled “Acknowledgements”, and any sections Entitled “Dedications”. You must delete all
sections Entitled “Endorsements”.
6. Collections of documents
You may make a collection consisting of the Document and other documents released under this License, and replace the individual
copies of this License in the various documents with a single copy that is included in the collection, provided that you follow the rules
of this License for verbatim copying of each of the documents in all other respects.
You may extract a single document from such a collection, and distribute it individually under this License, provided you insert a copy
of this License into the extracted document, and follow this License in all other respects regarding verbatim copying of that document.
7. Aggregation with independent works
A compilation of the Document or its derivatives with other separate and independent documents or works, in or on a volume of a
storage or distribution medium, is called an “aggregate” if the copyright resulting from the compilation is not used to limit the legal
rights of the compilation’s users beyond what the individual works permit. When the Document is included in an aggregate, this License
does not apply to the other works in the aggregate which are not themselves derivative works of the Document.
If the Cover Text requirement of section 3 is applicable to these copies of the Document, then if the Document is less than one half
of the entire aggregate, the Document’s Cover Texts may be placed on covers that bracket the Document within the aggregate, or the
electronic equivalent of covers if the Document is in electronic form. Otherwise they must appear on printed covers that bracket the
whole aggregate.
8. Translation
Translation is considered a kind of modification, so you may distribute translations of the Document under the terms of section 4.
Replacing Invariant Sections with translations requires special permission from their copyright holders, but you may include translations
of some or all Invariant Sections in addition to the original versions of these Invariant Sections. You may include a translation of this
License, and all the license notices in the Document, and any Warranty Disclaimers, provided that you also include the original English
version of this License and the original versions of those notices and disclaimers. In case of a disagreement between the translation and
the original version of this License or a notice or disclaimer, the original version will prevail.
If a section in the Document is Entitled “Acknowledgements”, “Dedications”, or “History”, the requirement (section 4) to Preserve its
Title (section 1) will typically require changing the actual title.
9. Termination
You may not copy, modify, sublicense, or distribute the Document except as expressly provided under this License. Any attempt
otherwise to copy, modify, sublicense, or distribute it is void, and will automatically terminate your rights under this License.
However, if you cease all violation of this License, then your license from a particular copyright holder is reinstated (a) provisionally,
unless and until the copyright holder explicitly and finally terminates your license, and (b) permanently, if the copyright holder fails to
notify you of the violation by some reasonable means prior to 60 days after the cessation.
Moreover, your license from a particular copyright holder is reinstated permanently if the copyright holder notifies you of the violation
by some reasonable means, this is the first time you have received notice of violation of this License (for any work) from that copyright
holder, and you cure the violation prior to 30 days after your receipt of the notice.
Thursday 21
st
December, 2017
56 FHAES: Fire History Analysis and Exploration System
Termination of your rights under this section does not terminate the licenses of parties who have received copies or rights from you
under this License. If your rights have been terminated and not permanently reinstated, receipt of a copy of some or all of the same
material does not give you any rights to use it.
10. Future revisions of this license
The Free Software Foundation may publish new, revised versions of the GNU Free Documentation License from time to time. Such
new versions will be similar in spirit to the present version, but may differ in detail to address new problems or concerns. See
http://www.gnu.org/copyleft/.
Each version of the License is given a distinguishing version number. If the Document specifies that a particular numbered version
of this License “or any later version” applies to it, you have the option of following the terms and conditions either of that specified
version or of any later version that has been published (not as a draft) by the Free Software Foundation. If the Document does not
specify a version number of this License, you may choose any version ever published (not as a draft) by the Free Software Foundation.
If the Document specifies that a proxy can decide which future versions of this License can be used, that proxy’s public statement of
acceptance of a version permanently authorizes you to choose that version for the Document.
11. Relicensing
“Massive Multiauthor Collaboration Site” (or “MMC Site”) means any World Wide Web server that publishes copyrightable works and
also provides prominent facilities for anybody to edit those works. A public wiki that anybody can edit is an example of such a server.
A “Massive Multiauthor Collaboration” (or “MMC”) contained in the site means any set of copyrightable works thus published on the
MMC site.
“CC-BY-SA” means the Creative Commons Attribution-Share Alike 3.0 license published by Creative Commons Corporation, a not-
for-profit corporation with a principal place of business in San Francisco, California, as well as future copyleft versions of that license
published by that same organization.
“Incorporate” means to publish or republish a Document, in whole or in part, as part of another Document.
An MMC is “eligible for relicensing” if it is licensed under this License, and if all works that were first published under this License
somewhere other than this MMC, and subsequently incorporated in whole or in part into the MMC, (1) had no cover texts or invariant
sections, and (2) were thus incorporated prior to November 1, 2008.
The operator of an MMC Site may republish an MMC contained in the site under CC-BY-SA on the same site at any time before
August 1, 2009, provided the MMC is eligible for relicensing.
Thursday 21
st
December, 2017
Appendix D
Trademark notices
Microsoft, Windows, MS-DOS and Excel are either registered trademarks or trademarks of Microsoft Corporation in the
United States and/or other countries.
Ubuntu is a registered trademark of Canonical Limited.
UNIX is a registered trademark of The Open Group.
Linux is a registered trademark of Linus Torvalds in the U.S. and other countries.
Oracle and Java are registered trademarks of Oracle and/or its affiliates.
Apple, Mac and OS X are trademarks of Apple Inc., registered in the U.S. and other countries.
Debian is a registered trademark owned by Software in the Public Interest, Inc.
Github is an exclusive trademark registered in the United States by GitHub, Inc.
Other names may be trademarks of their respective owners.
Thursday 21
st
December, 2017
Thursday 21
st
December, 2017
References
Baisan, C.H., Swetnam, T.W., 1990. Fire history on a desert mountain range: Rincon Mountain Wilderness, Arizona,
USA. Canadian Journal of Forest Research 20, 1559–1569.
Baisan, C.H., Swetnam, T.W., 1997. Interactions of fire regime and land-use history in the central Rio Grande Valley.
US Department of Agriculture, Forest Service Research Paper RM-RP-330 .
Brewer, P.W., Murphy, D., Jansma, E., 2011. TRiCYCLE: a universal conversion tool for digital tree-ring data. Tree-Ring
Research 67, 135–144.
Brown, P.M., Schoettle, A.W., 2008. Fire and stand history in two limber pine (Pinus flexilis) and Rocky Mountain
bristlecone pine (Pinus aristata) stands in Colorado. International Journal of Wildland Fire 17, 339–347.
Dieterich, J.H., Swetnam, T.W., 1984. Notes: Dendrochronology of a fire-scarred ponderosa pine. Forest Science 30,
238–247.
Falk, D.A., 2004. Scaling rules for fire regimes. Ph.D. thesis. University of Arizona. Tucson, Arizona.
Flatley, W.T., Lafon, C.W., Grissino-Mayer, H.D., LaForest, L.B., 2013. Fire history, related to climate and land use in
three southern appalachian landscapes in the eastern united states. Ecological Applications 23, 1250–1266.
Fritts, H.C., 1976. Tree rings and climate. Academic, San Diego, Calif.
Grissino-Mayer, H.D., 1995. Tree-ring reconstructions of climate and fire history at El Malpais National Monument, New
Mexico. Ph.D. thesis. The University of Arizona.
Grissino-Mayer, H.D., 1999. Modeling fire interval data from the american southwest with the weibull distribution.
International Journal of Wildland Fire 9, 37–50.
Grissino-Mayer, H.D., 2001. FHX2 - software for analyzing temporal and spatial patterns in fire regimes from tree rings.
Tree-Ring Research 57, 115–124.
Holmes, R.L., 1983. Computer-assisted quality control in tree-ring dating and measurement. Tree-Ring Bulletin 43,
69–78.
Jansma, E., Brewer, P.W., Zandhuis, I., 2010. TRiDaS 1.1: The tree-ring data standard. Dendrochronologia 28, 99–130.
Johnson, E., 1992 .
Johnson, E., Van Wagner, C., 1985. The theory and use of two fire history models. Canadian Journal of Forest Research
15, 214–220.
Legendre, P., Legendre, L.F.J., 2012. Numerical ecology. Elsevier, Amsterdam, The Netherlands.
Palmer, W.C., 1965. Meteorological drought. volume 30. US Department of Commerce, Weather Bureau Washington,
DC, USA.
Prager, M.H., Hoenig, J.M., 1992. Can we determine the significance of key-event effects on a recruitment time series?—a
power study of superposed epoch analysis. Transactions of the American Fisheries Society 121, 123–131.
Romme, W., 1980. Fire history terminology: Report of the ad hoc committee., in: Stokes, M., JH, D. (Eds.), Proceedings
of the Fire History Workshop, October 20-24, 1980, Tucson, Arizona, US Department of Agriculture General Technical
Report RM -81. pp. 135–137.
Thursday 21
st
December, 2017
60 REFERENCES
Scheiner, S.M., Gurevitch, J., 2001. Design and analysis of ecological experiments. Chapman & Hall, New York.
Stokes, M.A., Smiley, T.L., 1968. An introduction to tree-ring dating. University of Chicago Press, Chicago.
Wilson, R., Cook, E., D’Arrigo, R., Riedwyl, N., Evans, M.N., Tudhope, A., Allan, R., 2010. Reconstructing enso: the
influence of method, proxy data, climate forcing and teleconnections. Journal of Quaternary Science 25, 62–78.
Thursday 21
st
December, 2017
For FHAES version 2.0.2
Compiled Thursday 21
st
December, 2017
