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FHAES: Fire History Analysis and Exploration System

1. us114001 fhx 1a 1571 n us204001 fhx 142 1572 143 1573 us205001 fhx 144 1574 us206001 fhx n BE alle di us208001 fhx DA e E TA us209001 fhx 149 i 1579 150 IIUIA 1580 us210001 fhx us212001 fhx us213001 fhx usach001 fhx 197 usach002 fhx wo usach003 fhx wo usach004 fhx usach005 fhx T usach006 fhx usach007 fhx usach009 fhx 151 ci 1581 152 cl 1582 153 oleo TITTI 1583 11154 cl lt 1584 155 Pase 1 157 158 llas 160 161 162 163 164 165 166 167 168 1585 1586 1587 1588 1589 1590 1591 1592 1593 1594 1595 1596 1597 1598 1599 169 solo wW usach010 fhx v 25 l Lala 1600 v Order None i Analysis results gt File Viewer Fe File summary o j Map g Figure 3 2 The left panel shows the FHX files that are currently loaded and the right tabbed panel contains details about the selected file and results of the fire history analyses Note that the file list contains one file us101001 fhx that has been determined to contain errors and three that contain no fire events The File viewer tab is open and contains a view of the erroneous file us1
2. 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 7 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 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 6 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
3. 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
4. 1 250 000 25 Lowest elev 270m 26 Highest elev 27 Slope 28 Aspect 29 Area sampled 30 Substrate type Till sandy clay and silty sand 31 Begin comments BELOW this line 32 Principal Investigator s Yves Bergeron Jacques Brisson 33 End comments ABOVE this line 35 FHX2 FORMAT 36 1573 45 3 37 676382883011400066669996777758882299996366662 38 026305112911677733332224877642225564455055559 39 7760766595238231 4589456182398978451 8904367894 40 4l RR A E 1573 A E EE EAA EE E E 1574 2 1 E E E Ti Miles 1818 e Merle II 1819 IO lilas loa 1820 22 IO hala Mili 1821 soa Urania a eee HE 1822 296 lontana Mea IT 1823 2971 A A sli LT 1824 298 lino reia less ee 1825 299 In leer FU Pease 1826 300 lara a RIA aa 1827 301 reia aa IT 1828 302 lea lia IT 1829 203 luciana lese IT 1830 341 Een less a Ill 1831 s 305 AA le ra ITI 1832 A 306 lisina H lies 1833 307 1834 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 Data entry 17 Symbol Described as Interpreted as Period or dot Left curly bracket Right curly bracket Right bracket Left bracket Bar or Pipe Dorma
5. 6 Weibull Mean 2 2 2222 oo on 25 5 1 7 Weibull Median 2222 CC un n nn 25 5 1 8 2 Weibull Modal 2 too 2 was aa area a er la 25 5 1 9 Weibull Standard Deviation sacc seare on nn nn 26 5 1 10 Weibull Fire Frequency LL 26 571 11 Weibull Skewness s a cei ae man a ke a a a 26 5 1 12 Exceedance Intervals LL 26 5 2 SEASONality ra it ae km hun ee Pe re 26 5 3 Binary summary matrices e 26 5 4 Binary comparison matrices Le 26 5 5 Similarity and dissimilarity matrices 2 0 0 e 26 6 Sample Size Analysis 29 6 1 Introduction va LA deli eS ei RE i A ARA 29 6 2 Performing analysis a T a aa a Ta e Paa 30 6 3 Analysis results 3 03 ak A ea A ek eS 31 6 4 Interpreting results 00 31 7 Superposed Epoch Analysis 33 8 Fire History Charts 35 8 1 Ch rt components si ELITE A II 36 8 2 Modifying the Chatta 36 8 3 Exporting Charts 0 0 dob bee otk SOA el E la perda N 37 Il Developers guide 39 9 Developing FHAES 41 9 1 Source Code tali als ne io A Re AOA ei id RI aa de i se A 41 9 2 Development environment LL 41 9 3 Dependencies sica oil a e ip rota Goda ee E 42 9 4 Multimedia resources 0 43 9 5 LOGGING sc dad ia ai ot Bete BO ei e ese De a 43 9 6 Preferences vuo rai wee een Geb Gee Wee Re re ARIA 44 9 7 Build SER PEO hatte dele OM Rac ee ae ea Bete eh iy BS 44 9 7 1 Windows installer aaa aaa 45 9 12 Mac package ion muha a a A A a 45 9 7 3 Linux Debpackage i iii ao an ee a ee
6. FHX2 software for analyzing temporal and spatial patterns in fire regimes from tree rings Tree Ring Research 57 115 124 Jansma E Brewer P Zandhuis l 2010 TRiDaS 1 1 The tree ring data standard Dendrochronologia 28 99 130 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 For FHAES version 2 0 x Compiled September 9 2014
7. Fire History Analysis and Exploration System Once installed you can then launch Eclipse To access the FHAES source code you will need to install the Subversive plugin to Eclipse As of Eclipse v3 5 this can be done by going to Help gt Install new software Select the main Update site in the Work with box then locate the Subversive SVN Team Provider plugin under Collaboration If you are using an earlier version of Eclipse you may need to add a specific Subversive update site See the Subversive website http www eclipse org subversive for more details Once installed you will need to restart Eclipse Next you will need to install the m2e Maven plugin to Eclipse This can also be installed by going to Help gt Install new software however you may need to add the Maven update site as this plugin is not currently available in the main Eclipse repository You can do this by click the Add button and using the URL http m2eclipse sonatype org sites m2e Once again you will need to restart Eclipse before continuing Next you need to get the FHAES source code Go to File New gt Project then in the dialog select SVN gt Project from SVN There are two methods of accessing the FHAES repository anonymously in which case you will have read only access or with a username provided by the FHAES development team Anonymous users will need to add a repository in the form http svn code sf net p fhaes code and full users
8. International Multiproxy Paleofire Database http www ncdc noaa gov paleo impd or create one or more new FHX files figure 3 1 There is also a small sample dataset available from the FHAES software download page 10 FHAES Fire History Analysis and Exploration System If you already have FHX files these can be loaded by using the open file icon on the toolbar through the File gt Open menu or by dragging and dropping files from your operating system s file manager application onto the file list panel 3 1 1 Analysis options Once files are loaded or created you will be presented with the Analysis options dialog TIP You should always run the analysis even if you aren t interested in performing it because several of the tools in FHAES cannot function without the analysis results The dialog is split into three groups of fields 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 gt only fire events upper case letters in the input files gt 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
9. The graph tab figure 4 4 shows similar information in a graphical form The colour 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 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 With the ever increasing speed and amounts of memory in modern computers such limitations were not necessary when developing FHAES FHAES can therefore read and edit all data files produced by the original FHX2 application however a little care must be taken if you intend to use files created by FHAES in FHX2 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 Data entry 21 5 0 2L2 22 3 N E amp ooc0000000 00 DDD Or oo ols ooorororoooorowrorrwoon oooroooHrooo0o00on r oronwoom 2223 Figure 4 3 The FHR
10. Windows installer Maven generates the Windows executable for the Tellervo application through the launch4j plugin Windows users however expect an installer that will create menu entries and add uninstall options to the control panel An installer is also required to install the user manual The best open source tool for creating Windows installer scripts is NSIS see http nsis sourceforge net This is an extremely flexible scripting system that does all we need If you have NSIS installed the Maven package goal should create the Windows installer automatically We use the Maven antrun plugin to run the makensis executable This script is stored in Native BuildResources WinBuild The Maven resource plugin moves it into the target folder and replaces the version numbering for use in filenames etc 9 7 2 Mac package The Maven osxappbundle plugin is able to produce both app and dmg files Unfortunately the libraries for producing dmg files are proprietary to Apple When Maven is run on Windows or Linux it is therefore only able to produce a zipped app file and not dmg Note an antrun plugin is used to remove duplicate libraries from the final package 9 7 3 Linux Deb package A Linux Debian package is produced using the JDeb Maven plugin If Maven does its job properly it should all just work as part of the standard maven package phase In addition to the configuration in the pom xml there are three files that are used to
11. a 45 9 8 Code SIGNING ran er EE p A a a e ea 45 9 8 1 Signing Java jars LL 46 9 8 2 Signing Windows executables 0 46 9 8 3 Signing OSX executables 0 0 46 9 9 Developing graphical interfaces 000 46 9 10 Writing documentation 2 ut a ar E ee e l 47 9 11 Making a new release a bb an u eee ae ee 47 Ill Appendices 49 A GNU General Public License 51 CONTENTS v A 2 Terms and Conditions 52 B GNU Free Documentation License 57 B 1 Preamble cirie elia Sia Re UPA eee ite i a Ob a a 57 B 2 Terms and conditions sha A a5 222 Ae eG Ae te A idas ae 57 References 61 Index 63 Preface FHAES Fire History Analysis and Exploration System is a revision of the original FHX2 program written by Dr Henri Grissino Mayer designed for the analysis of chronologies of fire scars developed from tree ring data and can be used to analyze chronologies of other disturbance events The original FHX2 program was written in Pascal and Fortran and uses proprietary graphics software It provides the means to enter and store fire history data graph and plot these data statistically analyze the fire chronologies and evaluate the relationship between fire occurrence and climate condition This program has been widely used and considered to be the standard for fire history analysis but will only run on Microsoft Windows operating systems XP or earlier or for higher versions by using a DOS emulator This revised system now renamed FHAE
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13. 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 52 FHAES Fire History Analysis and Exploration System 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 A 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 Li censees 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 unmodifie
14. 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 copy and pasted into other applications such as spreadsheet 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 Fire History Analysis and Exploration System Function Family pdf Asymptotic term Logisti Sigmoidal ogistic igmoida a E 1 be ez i x ax Michaelis Menten Growth saturation a b a Modified exponential Exponential aez a b d Modified Michaelis Menten Growth saturation Tr c a Weibull Sigmoidal a beca a Table 6 1 Description of the different curve fitting functions used to calculate the asymptote Chapter 7 Superposed Epoch Analysis Chapter 8 Fire History Charts FHAES includes the tools necessary to produce publication quality fire history charts These charts provide a powerful method for illustrasting the fire regime of a site or region T
15. 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 inconjunction with a temporal GIS plugin such as the Time Slider facility in ArcGIS or the Time Manager plugin to QGIS 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 14 FHAES Fire History Analysis and Exploration System y Lo Generate shapefile YO Attribute table style One marker per site with multiple year attributes 8 Multiple markers per site one for each year Years to include Available Selected 1759 1760 1761 gt 1762 1763 1764 1765 LY l OK Cancel Figure 3 3 The screenshot of the export to shapefile dialog 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
16. during periods when it is uncertain that the tree was recording fires for example a pocket of rot has obscured some rings 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 For 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 gt icon on the toolbar or by going to File gt 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 12 edit button on the toolbar The main data entry screen has four tabs data metadata see figure 4 2 summary and graphs 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 value
17. from the FHAES application menu Help gt Error log viewer 44 FHAES Fire History Analysis and Exploration System To alter the way these appenders are configured you need to edit the log4j xml file See the Log4J documen tation for further information Using the logging framework is very simple Just define a Logger as a static variable in your class like this 7 private final static Logger log LoggerFactory getLogger MyClass class where MyClass is the name of the current class Then you can log messages simply by calling log warn My message log debug My message etc Before managed logging was introduced to FHAES debugging was often handled through the use of Sys tem out and System err messages To ensure that these messages are not lost we use another package called SysOutOverSLF4J This redirects messages sent to System out and System err to the logging system This is a temporary solution so when working on older classes please take the time to transition these older calls to the proper logging calls We can then remove the need for SysOutOverSLF4J 9 6 Preferences It is helpful to remember certain user preferences e g last folder opened etc so that they don t have to do tasks repeatedly This is achieved through the use of the FHAESPreferences class This stores preferences in a specific place on the users computer depending on the operating system they are using For instance in Windows preferences are stored i
18. 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 the same 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 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 ever decreasing sub sample of series within a data file Multiple simulations are run by randomly picking series from the file to simulate the reduction in tree sample size 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 an
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20. release Making a new release should be a relatively quick and simply process but there are still a few things to remember Make sure this documentation is up to date Update the logging appenders to an appropriate level so that the user is not swamped by debug messages Increment the build version number s in the pom xml of FHAES and any of the other modules as applicable v Check the code in Eclipse and eliminate as many warnings as possible Make sure the developers metadata is correct in the pom xml Add any new developers that have joined the project since the last release Run Maven deploy on the secondary packages Run Maven package on the FHAES project itself Test Make sure all packages are working on the major operating systems being supported vY vV VvV sy Copy the packages to the website and change the most recent build number on the website This will inform users of the new release the next time they load FHAES Part Ill Appendices Appendix A GNU General Public License FHAES is released under the GNU General Public License GPL version 3 Copyright 2014 FHAES Team 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 WARRAN
21. 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 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 in some cases will not be identical to those produced by FHX2 For instance there are differences in the precision of floating point numbers especially for provided numbers like 7 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 work from when we were re 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
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23. 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 7 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 6 for more information 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 w
24. 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 3In 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 Data entry 23 To overcome these issues the long term aim is to support the Tree Ring Data Standard TRiDaS Jansma et al 2010 within FHAES while maintaining the ability to read existing FHX data files In the mean time 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 Chapter 5 Analyses 5 1 Interval analysis The Interval analysis tables shows the results of a variety of analyses for each data file A description and formula for each is shown below 5 1 1 Coefficient of Variation 5 1 2 Skewness 5 13 Kurtosis _ 6I 7 120702 313 443 Ta4 y2 DESEE 5 1 whe
25. 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 that 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 6 FHAES Fire History Analysis and Exploration System 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 1 3 Where can get help This manual is the main source for information about FHAES and how to run it If you can t find the answer to your questions here 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 with regards an academic issue as many of the world s leading dendropyrologists are members Although right now the manual is more about which buttons to push to make the program work we will continue to add descriptive information and examples Chapter 2 Installation 2 1 Require
26. will need to use svn ssh svn code sf net p fhaes code FHAES is comprised of a number of projects which are stored as seperate folders within the trunk folder in in Sourceforge This enables us to work and package different aspects of the system separately For instance the graphics module can be built and run separately from the main stats modules You will need to set up separate projects in Eclipse for each of these modules FHUtil gt FHRecorder FHChart p gt FHSampleSize FHAES The FHAES project is the main application that most users use to access the functionality of the other modules Although FHAES depends upon the other modules mentioned above the Maven configuration should retrieve these modules from our Maven repository if you don t intend to work with them This means you shouldn t need to configure all modules in Eclipse to get up and running To launch FHAES from within Eclipse you will need to go to Run gt Run Java application Create a new run configuration with the main class set to org fhaes gui MainWindow 9 3 Dependencies FHAES is built with Maven One of the main benefits of Maven is that it handles dependencies efficiently All the libraries that FHAES relies upon are configured within the Maven pom xml file and installed seamlessly as part of the build process Maven handles transient dependencies i e dependencies of dependencies auto matically Therefore if a developer knows he needs th
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28. you will need to make changes 46 FHAES Fire History Analysis and Exploration System 9 8 1 Signing Java jars The Java jars are signed using a Java utility called jarsigner that comes with your JDK so there is nothing to install The pom xml is currently hard coded to access the certificate and key files stored on the lead FHAES development machine You will need to alter these settings accordingly 9 8 2 Signing Windows executables Windows executables are typically signed using the Windows only Microsoft utility signcode On Linux and OSX there is an open source equivalent called osslsigncode which can be downloaded from Sourceforge and compiled You may also be able to find third party binaries for your operating system The FHAES pom xml file has been configured to run osslsigncode with the location and naming of the certificate and key files hard coded Change these to match the certificate you are using If you are using signcode instead of osslsigncode you should find that the parameters are very similar You should hopefully be able to modify them without too much difficulty Please note that both signcode and osslsigncode need the certificate in a different format to jarsigner You can use openssl to do this conversion and there are many tutorials online which describe how 9 8 3 Signing OSX executables With the inclusion of the GateKeeper technology in OSX 10 7 code signing has become almost essential in OSX The jar wrapped
29. 01001 fhx FHAES is highlighting the error in the file and is explaining the error in the message at the top of the screen 3 1 2 File list 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 check they are valid FHX files that are determined to be invalid are indicated by a red cross icon Y 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 Erroneous files can be corrected by double clicking the appropriate file in the list and then using the FHAES data entry screen see pages 15 20 The file list can be sorted using the drop down menu at the bottom of the screen This can be helpful as the order of the files in the list will also be reflected in the order the analysis results will be presented The following sections describe the contents of the various tabs in the right hand panel of the main screen 3 1 3 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 has been determined to be invalid i e it is marked by red cross symbol then a message is shown at the top of the screen Where possible FHAES will also highlight th
30. 10 9 000 9 000 0 000 0 000 8 846 8 898 154 1611 1810 22 000 22 000 0 000 0 000 21 624 21 749 154 1711 1910 32 000 32 000 0 000 0 000 31 453 31 636 154 1800 1999 20 500 20 500 0 000 0 000 20 149 20 267 153 1511 1710 9 000 9 000 0 000 0 000 8 846 8 898 153 1611 1810 22 000 22 000 0 000 0 000 21 624 21 749 153 1711 1910 32 000 32 000 0 000 0 000 31 453 31 636 v Reset 44 Run analysis a Ze Simulations Asymptote Figure 6 1 The screenshot of the sample size analysis tool The screen includes the analysis parameters on the left and the results on the right 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 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 12 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 anal
31. 3 2 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 Ihttp www ncdc noaa gov data access paleoclimatology data datasets fire history http www ncdc noaa gov paleo impd tree_event_info html 16 FHAES Fire History Analysis and Exploration System 1 Name of site Mesic mainland sites around Lake Duparquet 2 Site code DMM 3 Collection date Summer 1985 and 1986 4 Collectors Y Bergeron J Brisson D Lemieux F Tetrault 5 Crossdaters Y Bergeron J Brisson D Lemieux F Tetrault B Suran 6 Number samples 45 7 Species name Thuja occidentalis Pinus banksiana Pinus resinosa 8 Common name Eastern white cedar jack pine red pine 9 Habitat type Mesic shoreline 10 Country Canada 11 State Quebec 12 County Abitibi Temiscamingue 13 Park Monument L Duparquet Research and Teaching Forest 14 National Forest 15 Ranger district 16 Township Header Metadata y Range 18 Section 19 Quarter section 20 UTM easting 630000m 21 UTM northing 5370000m 22 Latitude 48 28 N 23 Longitude 7917W 24 Topographic map Rouyn Noranda 32 D
32. 4 Attribute table style1 Features total 8 filtered 8 selected 0 JOY gs Attribute table style2 Features total 1816 filtered 1816 selected 0 x 9 1 y LITE NES IIS Bl ZJE Se Ss Sa 85 18 9 B 1759 1760 1761 1762 1763 1764 1765 name A year i value ca045001 1981 0 ca045001 1982 0 ca045001 1983 0 ca045001 1984 0 1 1 1 1 1 ca045001 ca050001 ca054001 ca070001 ca077001 ca045001 1985 ca050001 1759 ca050001 1760 ca050001 1761 ca050001 1762 ca050001 1763 E y ca083001 ca088001 ca090001 HRA gt E ShowaAllFeatures la 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 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 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 l
33. AES app You can then verify that the signing worked by doing Z codesign display verbose 4 FHAES app 9 9 Developing graphical interfaces The graphical interfaces in FHAES have mostly been designed using the Google WindowBuilder Pro tool with Eclipse Unlike other graphical design tools WindowBuilder has the benefit of being able to parse most hand written layout code so it is possible to manually edit the layouts if you prefer However most of the interfaces are built using the MigLayout layout manager which can be a little tricky to code by hand Developing FHAES 47 9 10 Writing documentation The documentation in FHAES is written in the well established typesetting language ATEX 2e TEX is a great tool for producing high quality documentation with a good structure and style Unlike standard WYSIWYG what you see is what you get word processing applications like Microsoft Word ATEX uses simple plain text code to layout a document so that it is often described as WYSIWYM what you see is what you mean The style of a TEX document is handled separated enabling the author to concentrate on content By removing the possibility for authors to tinker with font sizes etc ATEX forces you to create clear well structured documents For further details see http en wikibooks org wiki LaTeX ATEX has fantastic cross referencing and citation functionality built in Please follow the lead of the existing documentation 9 11 Making a new
34. FHAES Fire History Analysis and Exploration System IENE Free as in Freedom By Elaine Kennedy Sutherland Peter W Brewer and Henri Grissino Mayer For FHAES version 2 0 x Elaine Kennedy Sutherland Missoula Forestry Sciences Lab 800 Block East Beckwith Missoula MT 59801 USA e esutherland fs fed us Compiled September 9 2014 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 57 60 FHAES Fire History Analysis and Exploration System By Elaine Kennedy Sutherland Peter W Brewer and Henri Grissino Mayer Compiled September 9 2014 Contents Preface eu cv fee iI OR ERR A BU NRE Da PBS SS User Guide 1 Introduction 1 1 Whats FHAES 2 00 25 44 228 4464 Boye bebe hog meet LI 1 2 Comparing FHAES and FHAS 2 20 25 pio aa id a wath a er 1 3 Where can get helpf i i mena ay Fh ee WE a ad ea aa 2 Installation 2 1 REQUIFEMENTS it de tt te lS OU ok oe ad A a Cn ne de ee on aa 2 2 How to install FHAAES 4 4 2 es BAR Hoe A a ee Roose bane Fe a 2 3 How to uninstall FHAES 2 4 2 eee 0 2 e En ee 3 Getting started 3 1 Main sereen 2 84 Sas ee a ee hoe eh et ats Pee ae eh Ag
35. Fire does not cause the cambial damage that leads to lesion formation in every tree in a stand exposed to fire 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 damage 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 create composite records comprised of the recorded fires from multiple trees in a stand or other scale of interest In most fire regimes the records from individual trees overlap to some extent i e there are some fires in common between 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
36. LAR 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 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 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 Appendix B 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 Docu
37. S Fire History Analysis and Exploration System is completely re written in Java and builds upon a variety of open source libraries Downloads are available for Windows Mac OSX and Linux FHAES is open source software see the details of the license on pages 51 56 so you are welcome to inspect and edit the code Please contact the authors if you ll like to find out how you can contribute We wish to acknowledge the contributions of NOAA s Paleoclimatic Division Boulder Colorado in early coordination and development 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 coordinate this project with it We also acknowledge the important role of Wendy Gross who programmed the FHChart module and who also set up the original FHAES website on FRAMES Also thanks to Evan Larson and Kun Tian who have supervised the development of the FHRecorder module by students at the University of Wisconsin Platteville 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 Brewer University of Arizona Laboratory of Tree Ring Research Henri Grissino Mayer University of Tennessee Department of Geography Maria Elena Velasquez Boise State University Department of Mathematics Donald A Falk University of Arizona School of Natural Resour
38. S L Analysis OPtlONS 00 2 00 Saeed ia ey Bees pe Gh ae Bee a 3 12 Files 4 6 2222 2 2 2 Oe tee ee we DE eee bee be es 3 1 3 Pile viewer tabs 2 2 8 RE we ee eh ee ae ae ed ie eh 3 14 SUMMA tab a aie Oe ee A BELA 3 1 57 Mabtab 2 22 BOE a ee pal ae ae AS 3 1 6 gt Analysissresults tab 2 ig 2 2 2 een eB Se 3 2 Ori HOt tate an et ok Lee NE 3 2 1 Merge selected files 3 2 2 Create composite file u 2 3 ii pe ani e Eee Rae Bae a 32 3 Createvevent files Vitis ir We ee DI See Be ee a l 3 2 4 Spatial join on selected files 3 2 5 Create site summary shapefile 00 4 Data entry 4 1 Introduction to FHX data files 4 2 Fire History Recorder sig aan a Ta E e e eh 4 3 Metadata nuclei A ELE ii e aaa ee se ne te Set 4 4 Data lh rt det BARE RAE Meee ye eye oe Bd oe de ALAM EVENTS fie e AS ak Te a A Men tel E RE ud 442 Recorder years rei A E A ea ee A ae 4 5 Summary and Graphs a is 42 2 4 3 dla sea ROR al dii la AA rd do ae da 4 6 FEIX2 restrictions aaa ee a o alia io A en A ad 4 7 Limitations of the FHX format aaa aaa a a 5 Analyses 5 1 Interval analysis 3 4 5 2 4 2 4 ua PM e eM ee ae 5 1 1 Coefficient of Variation 2 oo nn 5 1 2 Skewness re oa wey OE ei dR a A are he as dana a w 0 NNN A 1 Preamblerv pf roca i GEA iano nane ie iv CONTENTS 5 134 Kurtosis 3 dii lei ea 25 5 1 4 Weibull Scale Parameter 000 25 5 1 5 Weibull Shape Parameter 2 2 2 Emo nn nn 25 5 1
39. TY without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE See the GNU General Public License for more details A 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 right
40. ack 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 e g from the Ubuntu command line sudo dpkg remove fhaes Chapter 3 Getting started If you have not yet done so please install FHAES using the instructions for your particular operating system on page 7 3 1 Main screen Once you launch FHAES you will be greeted by the standard FHAES home screen Now load You enter new FHX format data by using the data entry module in FHAES This is accessed by using the icon on the toolbar or by using the File gt New menu Further information about the structure of FHX files and data entry is available in chapter 4 d gS FHAES Fire History Analysis and Exploration System DEORE Eile Edit Tools Help x La A DEI wh BG Xx Ones A x gt v MB FHA vs u m ae Create a new FHX file L Load existing FHX file s Order None analysis results Fie Viewer File summary map Figure 3 1 The FHAES home screen that it displayed on startup To begin using FHAES select either Create new FHX file or Load existing FHX file s If you do not have any FHX data files but would like to test FHAES you can download data from NOAA s
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42. arge 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 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 Multiproxy Paleofire Database hosted by NOAA 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 d
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48. ces and the Environment and Laboratory of Tree Ring Research Peter Brown Rocky Mountain Tree Ring Research Inc Fort Collins Colorado Connie Woodhouse University of Arizona School of Geography and Development Part User Guide 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 fire scars fire caused injuries on trees FHAES can also be used to calculate similar properties for other events that create unique signatures like light rings from insect infestations or frost rings resulting from volcanic eruptions As input FHAES requires data in the the Fire History Exchange FHX format similar to FHX2 Grissino Mayer 2001 The techniques of fire history analysis 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 Stokes and Smiley 1968 Fritts 1976 Holmes 1983 Dieterich and Swetnam 1984 Baisan and Swetnam 1990 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 and includes proprietary graphics software Golden Software Inc It runs on Microsoft Windows operating systems XP or earlier and will
49. cessed through the toolbar or the file menu Which format you choose depends on how you will use the chart The PNG image file can easily be embedded in word processing documents but because it is a raster file format the quality of the output will degrade if enlarged too much The PDF format is written as a vector file so can be enlarged to any size with no loss in quality The PDF format should therefore be used when publication quality output is required Part Il Developers guide Chapter 9 Developing FHAES FHAES is open source software and we actively encourage collaboration and assistance from others in the community There is always lots to do even for people with little or no programming experience Please get in touch with the development team as we d love to hear from you 9 1 Source code This section describes how to access the FHAES source code but as you are no doubt aware it is normal if not essential to use a integrated development environment for developing any more than the most simplistic applications If you plan to do any development work it is probably best to skip this section and move straight on to the Development environment section which includes instructions for accessing the source code directly from your IDE If however you just want to browse the source code please continue reading The FHAES source code is maintained in a Subversion repository at Sourceforge net The simplest way to see the source c
50. configure the final deb file In src deb control there is a control file which describes the runtime dependencies maintainer of the package description etc In Native BuildResources Lin Build are two files one a simple bash script that is used to launch FHAES on the users computer and the other a desktop file for configuring how it appears in the users menus All three of these files are automatically updated with the current version number so hopefully you shouldn t need to change anything 9 8 Code signing From Windows Vista and MacOSX 10 7 Lion onwards code signing has become important Windows ap plications that are not signed result in terrifying warning messages and in OSX by default they cannot even be run The idea behind code signing is that it provides some level of security for the user as code signing certificates can be revoked if an application is deemed to be malicious To sign an application you first need a code signing certificate In fact you need two one for Windows and Java and another for OSX as Apple only support certificates issued by themselves A generic Windows and Java certificate can be purchased from a variety of suppliers e g Verisign etc the Apple certificate must be purchased through the Apple Developer Connection Code signing the Java jars and Windows installers is handled within Maven The current set up in the Maven pom xml file is configured for Ubuntu Linux If you are developing on another platform
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52. d this License principally for works whose purpose is instruction or reference B 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
53. d time span imposed by the original SSIZ program while dramatically speeding up analyses FHAES also extends the the original SSIZ analysis to include the calculation of asymptotes as described by Falk 2004 This provides an indication of the number of samples required in a particular study region to ensure the fire history regime has been accurately characterised 30 FHAES Fire History Analysis and Exploration System de Sample Size Analysis SOTO File Au Input Input file ne pwb48 Downloads castn001 fhx ke 30 25 Simulations and filtering 20 2 E Event type Fire events r js Simulations 500 5 2 Seed number 30 188 E 10 zZ Resampling Without replacement Jee we Threshold Number of fires gt 2 0 10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 E Number of series resampled Segmentation 2 Process subset or segments of dataset Plot Mean Ly of segment 1711 1910 with asymptote type r gt lueginiAuto porulatea N Tj Seg Start segEnd Mean Median C195 C199 Weibull Mean Weibull Median E N Start End Length 155 1511 1710 9 000 9 000 0 000 0 000 8 846 8 898 1 1511 1710 200 155 1611 1810 22 000 22 000 0 000 0 000 21 624 21 749 2 1611 1810 200 2 A i H 4 A P 1916 00 155 1711 1910 32 000 32 000 0 000 0 000 31 453 31 636 4 1800 1999 200 155 1800 1999 20 500 20 500 0 000 0 000 20 149 20 267 154 1511 17
54. e functions within a particular library he simply needs to supply the details of this library without having to worry about the other libraries that this new library is in turn dependent on Maven also manages versions efficiently If a library is dependent on a particular version of another library this is specified within the Maven build mechanism This means it is much easier to keep dependencies up to date without having to worry about the cascading issues that upgrades often have In short Maven is intended to save developers from JAR hell For the record FHAES currently depends upon the libraries listed in table 9 1 The table also specifies the licenses that these libraries are made available under Developing FHAES 43 Library License Apache commons lang Apache 2 0 TridasJLib Apache 2 0 JFreeChart LGPL JMapViewer GPL Log4J Apache 2 0 iText GAPL DendroFilelO Apache 2 0 Java Simple MVC MIT SLF4J MIT MigLayout BSD SwingX LGPL Table 9 1 FHAES primary and major first order dependencies along with the licenses under which they are used Library License Apache commons lang Apache 2 0 Launch4J BSD MIT NSIS zlib libpng Ant Apache 2 0 Eclipse Eclipse Public License v1 0 M2Eclipse Eclipse Public License v1 0 Subversive Eclipse Public License v1 0 Table 9 2 Additional tools libraries typically used in the development of FHAES 9 4 Multimedia resources FHAES includes infrastructure for multimedia r
55. e 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 12 FHAES Fire History Analysis and Exploration System 3 14 Summary tab The File summary tab contains a report summarising the contents of the file currently selected in the file list 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 3 1 5 Map tab The Map tab contains an interactive map displaying the location of the sites described by the latitude and longitude of currently loaded files 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 a wide variety of formats FHAES will do its best to parse these fields to ascertain the coordinates however this may fail in which case you will be warned Please also note that in addition to lat long fields FHX format files also contain location information in UTM and township range fields Because there is no field in FHX files for recording the UTM zone which is essential for the eastings and northings to make sense UTM information is disregarded by FHAES Due to the huge potential variability of to
56. e the option of specifying ZIP or XLSX format the former will give you a ZIP file containing each table as a CSV text file the latter will give you a single Microsoft Excel workbook with each table as a separate worksheet 3 2 Tools FHAES includes a number of tools for manipulating and processing your fire history data These are available from the buttons on the toolbar or from the Tools menu on the main screen Because of their complexity the Sample Size Analysis Superposed Epoch Analysis and Chart tools are described in their own chapters chapters 6 7 and 8 respectively Descriptions and instructions for all other tools are provided below 3 2 1 Merge selected files gt 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 Getting started 13 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 2 2 Create composite file The create composite file tool is similar to the merge tool with the exception that all samp
57. ecorder summary tab summarises the information recorded in a data file on a year by year basis m Of Events Of Samples Figure 4 4 The FHRecorder graph tab illustrates similar information to that provided in the summary table see figure 4 3 but in a graphical form 22 FHAES Fire History Analysis and Exploration System Additional limitations in FHX2 that are not present in FHAES include 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 4 7 Limitations of the FHX format Even though the field and data length restrictions of FHX2 outlined in section 4 6 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 gt No standardisation of metadata The metadata fields that are present in FHX files are all free text with no restrictions on how informat
58. er of fires one for the number of trees and a third for the percentage of trees that were scarred 5 4 Binary comparison matrices 5 5 Similarity and dissimilarity matrices The general form for a probability corrected similarity index is P z Ple Pe 5 8 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 0 1 d 0 0 Analyses 27 This method can be illustrated with Cohen s index Scon in which both 1 1 and 0 0 cases a and d are considered agreement P a 42 where N a b c d P e is computed as the joint probability of sites i and j having a 1 hence a b P li gt 5 9 Paj 2 5 10 P e P 1i x P 1j 5 11 Consider a comparison between a pair of sampling units with the following outcome Outcomes 1 0 Site i 1 8 1 Hence a 8 b 4 c 5 d 83 and N 100 Then 8189 100 8 4 0 920 5 P e 0 12 x 0 13 0 016 0 920 0 016 on 0 91 se T0016 en Note that similarity in this case is dominated by the d 0 0 case This represents a common outcome for rare events where d gt gt 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
59. erms 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 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
60. es 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 References Brewer P Murphy D Jansma E 2011 TRiCYCLE a universal conversion tool for digital tree ring data Tree Ring Research 67 135 144 Falk D A 2004 Scaling rules for fire regimes Ph D thesis University of Arizona Tucson Arizona Grissino Mayer H 2001
61. esources such as icons and images within the Maven resource folder src main resources of the FHUtil module The icons are accessed via the static Builder class This has various accessor functions which take the filename and return the icon itself or a URI of the icon from within the Jar 9 5 Logging Logging in FHAES is handled by the SLF4J and Log4J packages Rather than write debug notes directly to System out Log4J handles logging in a more intelligent way First of all each log message is assigned a log level which are in order of severity fatal error warn info debug and trace Through a log4j xml configuration file contained within the FHUtil resources folder we can control the level at which messages are displayed For instance while we develop we would likely show all messages up to and including trace but when we deploy we might only want to show messages up to and including warn Log4J also enables us to log to several places known as appenders e g console log file or a component within our application It is also possible to change the level of logging depending on the log type so minimal messages can be sent to the console but verbose messages to the log file FHAES has the following appenders configured Standard log file fhaes log that rolls over up to 2mb of messages Console standard messages to the console when launched from command line Help console simple console component available
62. f 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 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 wor
63. 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 P a P ex Sp 5 12 1 P ex Pe Where P a the probability of the a case given a fire in either site P 1 db P 1x amp and P ex P 1x x P 1x the probability of joint 1s occurring by chance in an event year In the example given L a b c 8 4 5 17 8 Pla 0471 8 4 Pia eo 17 28 FHAES Fire History Analysis and Exploration System 8 5 P e 0 706 x 0 765 0 540 0 471 0 540 A This index reflects only the distribution of the event cases a b and c The outcome is negative if b c gt a and positive if a gt 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 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 remnant 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
64. here this site is located Forest Name of forest where this site is located Ranger district The Ranger district that covers this site 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 Data entry 19 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
65. hether the event is a fire or other 20 FHAES Fire History Analysis and Exploration System 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 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 has been determined that trees record fires regardless of whether they have already sustained an injury or not clarification and citation required In some samples there may be periods whe
66. ifferent characters for the last year of the series indicating whether the sample still had bark or if it had bare wood that could potentially have eroded The position of a fire scar or other indicator in an annual ring relative to its earlywood or latewood can be recorded This provides evidence of wildfire season A complete list of the characters used for recording all these conditions 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 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
67. imers 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 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 Termination of your rights under this section does not terminate the licenses of parties who have rece
68. in native apps will fail to load under default security settings and the OS reports the file as damaged because the JavaApplicationStub used has an existing signature and the contents of the package has changed This signature must be removed or replaced with another before the application can be launched If a self signed or third party certificate is used then the GateKeeper will block the application saying that it isn t from a trusted developer It is possible for users to go to the System Properties gt Security and Privacy and set the application security level to any developer but this is long and involved for novice users and results in a lot of warnings Please note that all signing of Mac application must be done on a recent Mac There are no cross platform tools currently available The best way to fix the issue is to sign the application using an Apple certified Developer ID certificate and GateKeeper will allow the application to launch with the default security settings Obtaining this certificate is a fairly involved process and requires an annual subscription to Apple Developer Connection Note that your certificate must begin with Developer ID to work Other Apple provided certificates are used for distributing your application through the Mac App store and will not work Once you have your Developer ID certificate installed on your Mac you can sign your application using the command Z codesign f s Developer ID FH
69. ion number of Java however it can only be guaranteed when run on exactly the same system Sample Size Analysis 31 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 way 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 will skew the analysis Include series with no events this option enables the user to choose whether to include or exclude series which don t include events By excluding series with no events the user should 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 series are included then the asymptote is indicative of the number of trees required to characterise the regime of the study region regardless of whether the trees have any visible signs of fire damage This could be useful for instance if you are studying insect oubreaks where trees are sampled without any visible damage 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 el
70. ion 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 gt Single data point per sample per year The format only allows for a single data point to be recorded for each sample in each 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 included Perhaps more importantly it means that fire scars and other injuries cannot be coded in the same years which provides significant problems for those attempting to do analysis comparing say fire and insect outbreaks in the same stand gt 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 although the user can list the species in the header there is no mechanism for defining which species applies to which series There is a similar issue with coordinates as it s routine now to record each tree location with a GPS rather than more general co
71. 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 60 FHAES Fire History Analysis and Exploration System 10 11 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 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 discla
72. ived 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 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 Relicensing Massive Multiauthor Collaboration Site or MMC Site means any World Wide Web server that publishes copyrightable works and also provides prominent faciliti
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74. les from a file are combined into a single series in the output The output file therefore contains the same number of series as input files Like the merge tool a dialog will open asking whether the output file should be restricted to specified years or whether all years should be included However you will also be asked to specify how the composite should be calculated When creating a composite it is often desirable to ignore events that are not widely represented in your datasets The composite filter enables you to specify a threshold of absolute number of events or to specify a percentage of series which must share the event for it to be included Note that events in composite files are always recorded as having an unknown seasonality because FHX files cannot represent events without multiple seasons within a single year 3 2 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 3 2 4 Spatial join on selected files O The spatial join tool provides a method for creating event composite and merge files based on location I
75. mentation 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 B 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 lt 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 recommen
76. ments FHAES will run on any relatively modern operating system the only requirement being that Java 6 or later is installed We do however highly recommend using Java 7 for FHAES and for any other Java application because Java 6 has passed its end of life and security updates are no longer released Only use Java 6 if you have a compelling reason to do so for example you are running an older versions of OSX that does not readily support Java 7 As with all aspects of FHAES if you run up against any specific problems installing and running FHAES then please get in touch with the developers for assistance 2 2 How to install FHAES Installation packages for the FHAES are available for Windows MacOSX and Linux For users of other operating systems FHAES can be run from an executable JAR file To install FHAES download the installation file for your operating system from gt http download fhaes org The website should provide you with a link to the installer for your current operating system Windows Run the setup exe and follow the instructions If you do not have Java installed the installer will direct you to the Java website where you can get the latest version Once installed FHAES can be launched via the Start menu Although FHAES should run on all version of Windows back to Windows 98 testing has been focused on Windows 7 and 8 amp Mac OSX To install FHAES download then open the zip file and drag the FHAES app into you
77. n are scar positions being compared to the first season 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 with a value of 1 then all fire events will be used The percentage of fires value is continuous and ranges from 1 to 99 The larger the filter the more that extensive events in the record are emphasized The analysis options dialog will open automatically each time you load FHX files If you want to repeat analyses without being asked to confirm options each time you can choose to use the same choices without being asked to confirm for the rest of the session The next time you load FHAES although it will remember you preferred analysis options 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 Getting started 11 pr e FHAES Fire History Analysis and Exploration System Y Y Y File Edit Tools Help 5 3 wh ag 2 dA OTH B_ Fatal error reading file Second start indicator found in sample 13 column 13 The error occurred at line number 153 of the input file us101001 fhx
78. n the registry and in Linux they are stored in a hidden file within the users home folder The preferences are accessed from the static member as follows FHAESPreferences setPref PrefKey PREFKEY value where PrefKey PREFKEY is an enum containing a unique string to identify the preference and the second value is the string value to set To retrieve a preference you use a similar syntax 7 FHAESPreferences getPref PrefKey PREFKEY default value When you get a preference the second parameter contains the default value to return if no preference is found There are a number of variations on the setPref and getPref functions which ensure the data type of the preference you are saving retrieving e g setIntPref setBooleanPref etc 9 7 Build script FHAES is built using Maven and is controlled through the pom xml file stored in the base of the FHAES source code It would be possible to distribute FHAES as an executable JAR file however we we have chosen to also produce native installers for the major platforms This gives us the opportunity to tightly integrate FHAES into the users operating system making it behave more like the native applications they are used to using For instance it means that we can associate the FHX file extension in Windows with FHAES enabling users to double click on files and have them open automatically It also means the application has its own icon rather than the generic Java coffee icon In MacOSX it al
79. n the sample reverts to non recording status in the middle of the series For instance a tree that has been injured by fire and therefore considered to be in recording status may grow over and around the scar until it is completely covered At this point the tree would be considered to be in non recording status again until another cambium damaging 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 FHRecorder 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 colour bar summarising the seasonality of the events recorded The colour bar can be customised with the button at the top of the screen This enables the user to change colours as well as merge together seasons into a single colour 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
80. ns 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 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 m
81. nsparent 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
82. nt season 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 Beginning of sample s tree ring series if pith is not present End of sample s tree ring series if no bark is present Pith date of a sample not always present Bark date of a sample not always present Recorder year starts the year after the first fire event 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 I 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
83. o Populate Add Recording J X Delete Recording 072 1850 1984 073 1832 1984 Recording Start Year Recording End Year 071 1733 1984 1892 1983 a 634 1833 1985 635 1882 1985 638 1695 1985 639 1779 1985 y Sort samples Manually v el Save Close Jil Discard changes 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 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 w
84. o produce a chart simply select the file of interest in your file list on the left panel in FHAES then either click the chart button on the toolbar select View gt Fire History Chart or right click and select Fire history chart from the popup menu Figure 8 1 shows a typical chart produced by FHAES Bo usblF002 Fhx FHX Chart File Edit View Help Bluff Lake paues nnmmmmmmmmmmm 44 4 H I r O INI U O ML feomooste 1300 1350 1400 1450 1500 1550 1600 1650 1700 1750 1800 1850 1900 1950 2000 Year m 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 36 FHAES Fire History Analysis and Exploration System A Please note that in this release of FHAES the chart module only supports the plotting of standard FHX files with series that begin and end with bracket characters If you try to plot composite files or files which begin or end with an event 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
85. ode is via the web viewer on the Sourceforge website http sourceforge net p fhaes code HEAD tree trunk If you have Subversion installed you can do an anonymous checkout of the code as follows 7 svn checkout svn svn code sf net p fhaes code fhaes code An overview of the development can be seen through the FHAES Open Hub pages at https www openhub net p fhaes Open Hub provides graphics summarizing the code over time including timelines of commits by user 9 2 Development environment The IDE of choice of the main FHAES developers is Eclipse http www eclipse org There are many other IDEs around and there is no reason you can t use them instead Either way the following instructions will hopefully be of use We have successfully developed FHAES on Mac Windows and Linux computers The methods for setting up are almost identical The first step is to install Eclipse Java 6 or 7 JDK Subversion Maven RPM and NSIS These are all readily available from their respective websites On Ubuntu they can be install from the command line easily as follows 7 sudo apt get install eclipse subversion default jdk maven2 nsis rpm Tlf you do not have NSIS and or RPM installed you will get an error when packaging FHAES however all other aspects of the development environment should work fine if you comment out the NSIS and or RPM sections in the pom xml file Remember not to commit this change to the repository though 42 FHAES
86. 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 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 gt Filter Options gt Composite Axis Filters __ Recorder year po Non recorder year H Fire event HE Injury event Inner year with pith Inner year without pith 4 H Outer year with bark LA Outer year without bark Figure 8 2 Legend for fire chronology plots Each of the chart components can be displa
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88. ordinates 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 access to this data would be extremely useful especially for charting purposes 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 defined in the FHX format means that users may have difficulties in adapting 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 effort with regards 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
89. 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 58 FHAES Fire History Analysis and Exploration System 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 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 Tra
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92. r applications folder In theory FHAES should be able to run on any version of OSX that runs Java 6 however no testing has been done prior to Intel version 10 6 Snow Leopard 3 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 and similar distributions the package should add a FHAES shortcut to your applications menu Alternatively you can start FHAES from the command line by typing fhaes Redhat Linux An RPM file is available which was designed for use with Redhat but should work on any Linux Standard Base LSB distribution such as SUSE Mandriva Fedora etc Install using your favorite package management system Note that due to the variation in naming conventions for Java between these distributions the RPM does not include Java as a dependency You will however need to install Java for FHAES to work KG Other operating systems Make sure you have Java 6 or later installed then download the FHAES JAR file to your hard disk You can run FHAES from the command line by typing 7 java jar fhaes jar 8 FHAES Fire History Analysis and Exploration System 2 3 Howto 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 work for you Without this feedb
93. re T T 1 4 5 1 4 Weibull Scale Parameter Ae 0 00 5 2 5 1 5 Weibull Shape Parameter ke 0 00 5 3 5 1 6 Weibull Mean AT L a 5 4 5 1 7 Weibull Median A ln 2 5 5 5 1 8 Weibull Modal we 59 26 FHAES Fire History Analysis and Exploration System 5 1 9 Weibull Standard Deviation 5 1 10 Weibull Fire Frequency 5 1 11 Weibull Skewness T 1 3 A3 310 u ae 5 7 5 1 12 Exceedance Intervals 5 2 Seasonality 5 3 Binary summary matrices The binary summary matrices provide summaries of presence or absence of events be they fire other injuries or both If an event is recorded then the matrix includes 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 is no data for that particular year perhaps the tree ring record doesn t extend to that particular year then a value of 1 is recorded in the matrix There are three types of binary summary matrices produced by FHAES Binary site summary this provides a summary on a site by site basis therefore the matrix has one column per file Binary tree summary this provides a similar summary but divided into individual trees 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 NTP matrix the NTP matrix contains three columns per file one for the numb
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96. s optionally used depending on 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 18 FHAES Fire History Analysis and Exploration System de Fire History Recorder cadmm001b fhx x G amp Data Metadata summary Graphs Samples in the currently loaded file Data contained within the sample 666 lojio X sample Name 666 First Year 1790 O Pith Last Year 1984 Y Bark 607 1775 1985 A 727 1898 1984 Add Event JI X Delete Event I Event Type Event Season Event Year 330 1573 1984 256 1801 1984 Fire Scar Early earlywood 1892 s 807 1907 1984 Fire Scar Early earlywood 1922 816 1912 1984 Fire Scar Early earlywood 1962 815 1939 1984 329 1698 1984 095 1824 1984 112 1760 1984 v 113 1796 1984 i 468 1894 1984 gt consolidate J 2 Aut
97. same material under section 10 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 GNU General Public License 55 10 11 12 13 14 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 Corre
98. sewhere in the dataset Segmentation the segmentation parameters enable you to run the 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 click 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 asked you 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 Once you have entered your parameters you can 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 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 shaded area on the chart shows the confidence interval This chart can be exported to in both PNG and PDF formats by right clicking and it can also be copied and pasted into other applications Some basic properties of the chart can
99. so means the menu bar is placed at the top of the screen rather than in the window While you develop Maven should automatically build FHAES for you in the background Specific build commands are only required as you approach a release We use the standard Maven life cycle for building packaging and deploying FHAES The method for doing this in Eclipse is by right clicking on the pom xml file and selecting Run as gt Maven package etc If the option you want is not displayed you will need to create an entry in the build menu by going to Run gt Run configurations then create a new Maven Build with the required goal The main goals are as follows Developing FHAES 45 clean This deletes any previously compiled classes and packages in the target folder It should only be necessary to run this occassionally if Maven has got a bit confused If this is the case you may also need to force Eclipse to clean too by going to Project gt Clean package This compiles FHAES and builds a single executable JAR containing all dependencies thanks to the maven shade plugin along with native Windows MacOSX and Linux packages These are all placed in structured folders within target Binaries ready for deploying on the website deploy This uploads the compiled jar into the maven tridas org repository Note that you will need to either run this phase from the command line or by setting up a customer run configuration in Eclipse 9 7 1
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101. 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 interval from the final event marker until the end of the series as an interval or not during 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 Common years required Select the number of common years or overlap that must be present between two datasets before comparison matrices can be calculated First season combination Scar positions in the earlywood latewood or between growth rings are com pared 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 combinatio
102. sponding 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 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
103. t 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 54 FHAES Fire History Analysis and Exploration System 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 modificati
104. t 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 simply 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 2 5 Create site summary shapefile 2 The
105. t may differ in detail to address new problems or concerns 56 FHAES Fire History Analysis and Exploration System 15 16 IT 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 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 PARTICU
106. wnshop range data and the very limited use of these fields in FHX they are also disregarded by FHAES We strongly recommend using standardized WGS84 decimal latitude and longitude in your FHX files FHAES uses the latitude and longitude fields in all spatial analyses For further information see sections 3 2 4 and 3 2 5 3 1 6 Analysis results tab The Analysis results tab contains the results of all the analyses performed by FHAES A categorized list shows all the available results on the right while the table on the left shows the currently selected result A full description of each of the analyses is provided in chapter 5 as well as through the online help system accessed by pressing the help button To view the results of the analyses simply select the analysis type from the categorical list on the right and it 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 Certain tables may also 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 13 for more information To save all the analysis results at once you can go to File gt Save gt Save analysis results or use the save button on the toolbar You hav
107. yed or hidden by toggling them on and off using the toolbar buttons or the options in the view menu 8 2 Modifying the chart The main features of the chart can be altered through the chart properties dialog This can be access through the toolbar menu or by right click popup menu Options such as fonts colors ticks grids titles labels etc can all be altered here It is possible to restrict the temporal scope of the chart to a certain year range by clicking and dragging on the chart To return the chart to the full extent simply click the zoom to full extent button on the toolbar Fire History Charts 37 The contents of the chart i e exactly what is plotted can be altered in a couple of ways First through the use of the Edit gt Filter Options gt Select Series to be Plotted menu Here you can choose to hide one or more series from the file and you can also alter the order that they appear in the fire chronology plot The contents of the composite plot can be altered using the Edit gt Filter Options gt Composite axis filters dialog This works in a similar way as the composite filter dialogs elsewhere in FHAES whereby a threshold of number or percentage of samples recording an event can be specified 8 3 Exporting charts Once you are happy with your chart you have two options for exporting it for use in publications and reports The chart can either be saved as a PNG image or as a PDF file Both of these options can be ac
108. ysis The more simulations you run the small 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 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 resample 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 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 1This should be the case when run on different computers running the same major vers

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