CharAnalysis is a program for analyzing sediment-charcoal records, when the goal is peak detection to reconstruct "local" fire history. Diagnostic tools help determine if peak detection is warranted, and if so, what parameters are most reasonable. Analytical tools help summarize results statistically and graphically. The entire code is distributed and well commented. Users are encouraged to "look under the hood", understand what's going on, and modify the program to suit individual needs.

(c) 2004-2012

Philip Higuera, Assistant Professor, College of Natural Resources, University of Idaho, http://webpages.uidaho.edu/phiguera/

Using this site

Downloads

Downloads are found in the Downloads tab. Be sure to select "current downloads" to obtain the most up-to-date version of each file. To view older versions, modify the selection in the "Search" pull-down menu.

Updates and Comments

Updates are described in the Wiki tab, with the title including "CharAnalysisUpdate".

You may also leave comments on the Wiki page, provided you have a gmail log in. See below ("Issues") for information on using the generic CharAnalysis.users login.

Issues

If you are having problems running CharAnalysis, please use the "Issues" tab to (1) look for other users who may have had the same issue or (2) register your issue. To look for old, resolved issues, be sure to select the "all issues" category in the search pull-down menu. If your problem is not listed, then please register your problem by selecting "new issue" in the upper left of the page. To register a new issue, you must have a gmail account. If you do not have a gmail account, please log is as CharAnalysis.user, and use the password "charanalysis.user". Check this web site for updates to your issue and/or provide an e-mail address for correspondence.

Understanding and citing the program

The following citations provide the most thorough background for the analyses employed in CharAnalysis, including the assumptions inherent in charcoal peak identification using a local threshold. These may be downloaded from the author's web site, linked to above.

• Kelly, R.F., P.E. Higuera, C.M. Barrett, and F.S. Hu. 2011. A signal-to-noise index to quantify the potential for peak detection in sediment-charcoal records. Quaternary Research 75: 11-17.

• Higuera, P.E., D.G. Gavin, P.J. Bartlein and D.J. Hallett. 2010. Peak detection in sediment-charcoal records: impacts of alternative data analysis methods on fire-history interpretations. International Journal of Wildland Fire 19: 996-1014.

Please use the following citation (also available via the author's web site) if you use the CharAnalysis program in a publication, and please note that it is freely available via the web site http://sites.google.com/site/charanalysis/

• Higuera, P.E., L.B. Brubaker, P.M. Anderson, F.S. Hu, T.A. Brown. 2009. Vegetation mediated the impacts of postglacial climatic change on fire regimes in the south-central Brooks Range, Alaska. Ecological Monographs 79: 201-219.

Other studies using CharAnalysis (incomplete list)

• Marlon, J.R., P.J. Bartlein, D.G. Gavin, C.J. Long, R.S. Anderson, C.E. Briles, K.J. Brown, D. Colombaroli, D.J. Hallett, M.J. Power, E.A. Scharf, and M.K. Walsh. 2012. Long-term perspective on wildfires in the western USA. Proceedings of the National Academy of Sciences doi:10.1073/pnas.1112839109

• Higuera, P.E., M.L. Chipman, J.L. Barnes, J.L., M.A. Urban, and F.S. Hu. 2011. Variability of tundra fire regimes in Arctic Alaska: millennial scale patterns and ecological implications. Ecological Applications 21: 3211-3226.

• Briles, C.E., C. Whitlock, C.N. Skinner, and J. Mohr. 2011. Postglacial forest development on different substrates in the Klamath mountains, northern California, USA. Ecology 92: 590-601.

• Whitlock, C., C.E. Briles, M.C. Fernandez, J. Gage. 2011. Holocene vegetation, fire, and climate history of the Sawtooth Range, central Idaho, U.S.A. Quaternary Research 75: 114-124.

• Higuera, P.E., C. Whitlock, and J. Gage. 2011. Linking tree-ring and sediment-charcoal records to reconstruct fire occurrence and area burned in subalpine forests of Yellowstone National Park, U.S.A. The Holocene 21: 327-341.

• Hu, F.S., P.E. Higuera, J.E. Walsh, W.L. Chapman, P.A. Duffy, L.B. Brubaker and M.L. Chipman. 2010. Tundra burning in Alaska: linkages to climatic change and sea-ice retreat. Journal of Geophysical Research - Biogeosciences 115, G04002, doi:10.1028/2009JG001270

• Higuera, P.E., L.B. Brubaker, P.M. Anderson, F.S. Hu, T.A. Brown. 2009. Vegetation mediated the impacts of postglacial climatic change on fire regimes in the south-central Brooks Range, Alaska. Ecological Monographs 79: 201-219.

• Chepstow-Lusty, A. J., M. R. Frogley, B. S. Bauer, M. J. Leng, K. P. Boessenkool, C. Carcaillet, A. A. Ali, and A. Gioda. 2009. Putting the rise of the Inca Empire within a climatic and land management context. Climate of the Past, Discussion 5:771-796.

• Marlon, J.R., P.J. Bartlein, M.K. Walsh, S.P. Harrison, K.J. Brown, M.E. Edwards, P.E. Higuera, M.J. Power, R.S. Anderson, C. Briles, A. Brunelle, C. Carcaillet, M. Daniels, F.S. Hu, M. Lavoie, C. Long, T. Minckley, P.J.H. Richard, S.L. Shafer, W. Tinner, C. Umbanhowar, and C. Whitlock. 2009. Wildfire responses to abrupt climate change in North America. PNAS 106: 2519-2524.

• Walsh, M. K., C. Whitlock, and P. J. Bartlein. 2008. A 14,300-year-long record of fire-vegetation-climate linkages at Battle Ground Lake, southwestern Washington. Quaternary Research 70:251-264.

• Huerta, M. A., C. Whitlock, and J. Yale. 2009. Holocene vegetation-fire-climate linkages in northern Yellowstone National Park, USA. Palaeogeography, Palaeoclimatology, Palaeoecology 271:170-181.

• Briles, C.E., C. Whitlock, P.J. Bartlein, and P.E. Higuera. 2008. Regional and local controls on postglacial vegetation and fire in the Siskiyou Mountains, northern California, USA. Palaeogeography Palaeoclimatology Palaeoecology. 265: 159-169.

• Higuera, P. E., L. B. Brubaker, P. M. Anderson, T. A. Brown, A. T. Kennedy, and F. S. Hu. 2008. Frequent Fires in Ancient Shrub Tundra: Implications of Paleorecords for Arctic Environmental Change. PLoS ONE 3:e0001744.

Acknowledgments

Many features in CharAnalysis are based on the programs CHAPS, by Patrick Bartlein (U of OR), and Charster, by Daniel Gavin (U of OR). The Gaussian mixture model used in CharAnalysis_was created by Charles Bouman (Purdue). CharAnalysis_was written in and compiled by Matlab 7.0 with resources from the University of Washington, Montana State University, the University of Illinois, and the University of Idaho. Development of the program has benefited greatly from discussions with and testing by members of the Whitlock Paleoecology Lab at Montana State University, Dan Gavin, and Ryan Kelly. Please see the CharAnalysis User's Guide for more details.

Disclaimer

THIS SOFTWARE PROGRAM AND DOCUMENTATION ARE PROVIDED “AS IS” AND WITHOUT WARRANTIES AS TO PERFORMANCE. THE PROGRAM CharAnalysis IS PROVIDED WITHOUT ANY EXPRESSED OR IMPLIED WARRANTIES WHATSOEVER. BECAUSE OF THE DIVERSITY OF CONDITIONS AND HARDWARE UNDER WHICH THE PROGRAM MAY BE USED, NO WARRANTY OF FITNESS FOR A PARTICULAR PURPOSE IS OFFERED. THE USER IS ADVISED TO TEST THE PROGRAM THOROUGHLY BEFORE RELYING ON IT. THE USER MUST ASSUME THE ENTIRE RISK AND RESPONSIBILITY OF USING THIS PROGRAM.

THE USE OF THE SOFTWARE DOWNLOADED FROM THIS WEBSITE IS DONE AT YOUR OWN RISK AND WITH AGREEMENT THAT YOU ARE SOLELY RESPONSIBLE FOR ANY DAMAGE TO YOUR COMPUTER SYSTEM OR LOSS OF DATA THAT RESULTS FROM SUCH ACTIVITIES.