DENDROCHRONOLOGY WORKSHOP

GEOS, ANTH, or WSM 497C/597C (two units)


Spring 2017
Mondays, 4:00 — 5:45
Tree-Ring Building 110 (ground-floor classroom)


The patch is in.
(Click to see larger image)

Instructor: Paul Sheppard (407 BBTRB, 621-6474, sheppard @ ltrr.arizona.edu)

Prerequisite

It is generally assumed that students of Dendrochronology Workshop have either taken the Fall Introduction to Dendrochronology course and/or are otherwise actively pursuing dendrochronology in graduate or independent studies. Students who have no prior experience or interest in dendrochronology have not found this course to be helpful or pertinent to their degree program.

General objectives of this course

Primary: To actively engage in and learn basic analytical steps of dendrochronology, primarily measurement and data checking as well as chronology building and interpretation using a real collection of tree-ring samples.

Secondary: Establishing and/or improving computer and quantitative literacy will be an inevitable side effect, if not a secondary objective of this course.

Optional: To finish (or make substantial progress on) a personal project in any application of dendrochronology (requires registration for one extra unit).

Workshop meetings

The nature of this course is quite different from the fall Introduction to Dendrochronology course. The Workshop course is activity based, where students do much of what dendrochronologists worldwide do to analyze a tree-ring collection for its environmental information. These activities are mostly computer based, and each student can have an account on the server resource of the Laboratory of Tree-Ring Research. It is also possible to do the activities on a computer at home, completely apart from LTRR.

For the two units of this course, we will meet two hours a week to review the previous week's assigned activity and prepare for the current activity. Fulfilling each activity as assigned will require time outside of class, and particular computational assignments might require individual tutoring.

Grading for 497C/597C

Each assigned activity will include things to do and/or computer output to annotate and turn in. Short (one page typed) reports are required along with the annotated outputs. Requirements will be clearly specified for each activity as we do them. These activities will be graded based on how well and how completely they are done.

Upon completion of analysis of the tree-ring collection, a research report detailing the analysis of the collection will be required. This report will be mostly on the methods, results, and discussion of the project; a literature review about the site is not expected. Articles that should be cited will be those that we study along the way throughout the semester. This research report, which should be up to 10 pages of double-spaced text plus figures and appendices as necessary, is due on the Wednesday of finals week.

Examinations are NOT planned for this workshop course. Thus, final grades, for both undergraduates and graduates, will be determined as follows:

All activities: 70% of grade
Research report: 30% of grade
Final grade % of all points:
A: >90
B: 80-89
C: 65-79

Optional individual student project

Students, either undergraduate or graduate, are encouraged to undertake an individual project of some facet of quantitative dendrochronology. This may include finishing a project already in progress or starting a new one and making substantial progress on it. Projects should include analysis of actual wood, i.e., not a library research report. If you'd like to do such a project but don't have a particular idea in mind, we can help with ideas. For example, various faculty, staff, and students of the Tree-Ring Lab have tree-ring collections that need processing, analysis, and interpretation, and such collections may be useful for student projects. Important: Individual projects should apply concepts of the Workshop, e.g., data and chronology development and interpretation.

Class time at the end of the semester will be reserved for individual oral presentations. Any student wishing to take advantage of this opportunity and do a project must register for an extra unit of 497C/597C (for a total of three units). The project must be approved before it is started, and progress throughout the semester will be checked prior to presentations. In addition to an oral presentation, which should be short (about 15 minutes, as for a conference talk), a final paper (~10 pages double-spaced text, plus tables, figures, and reference list as necessary) describing the project is required and is due on the Wednesday of finals week.

Office hours, readings, and computers

Paul's office hours are essentially all the time. I'm generally around the Tree-Ring Lab most of the daytime, so your chances are good for randomly finding me for help on assigned activities. You could also e-mail questions and I'll reply as soon as possible. Furthermore, if you do your computer work at the TRL, then other TRL faculty, staff, and students will probably be hanging around and can also help. If you have problems or questions that need a specific meeting, then call or e-mail ahead and schedule.

An additional resource for help is each other. You are, of course, required to do your own work, especially all written assignments that you turn in. However, it is perfectly acceptable for you to help each other on operational details, e.g., getting through computer glitches, etc., especially if no one else is around to help.

Manuals and other readings will be provided to help understand and/or complete the assigned activities. It would behoove you to use that material, both as you do the activities and when you do your research report.

If you are phobic about using computers generally, then you'll need to overcome that phobia quickly or you'll be underserved by this course. An important thing to remember is not to panic when something goes wrong while computing, because on-line and hardcopy manuals and real people are all available to help you for all of what we'll do.

Ring widths can be measured using various measuring systems in the Tree-Ring Lab. The Tree-Ring Lab server holds all of the programs we'll need to process, analyze, and interpret our data. We'll do some spreadsheet games, for which you can use your favorite one; the lab computers have Excel, and library computers Minitab, both of which I use in class. Common-use computers in BBTRB can directly access the server, but you can also download many of our programs to your own computer.

Note: For reading PDF files, you'll need Adobe Acrobat Reader, which you can get free HERE: Adobe Acrobat


Flexible Schedule of Activities (subject to change, though not much change)
Week of

Activity

1
Jan 16

(Jan 13)
1. Begin measuring ring widths using J2X
Click on Voortech for a user guide to J2X.

Required reading: Ring Markings: A guide to marking tree rings for width measurement.

Optional reading: Early measuring of ring width: A 1925 article.

Optional reading: Early measuring of ring width: Another 1925 article.

Optional reading: Measuring tree rings: A 1940 Medallion Paper by Gladwin.

Optional reading: Measuring tree rings: A 1980 Forest Service pub.

Optional reading: Modernized measuring of ring width: A 1980 article on history and advancements of measuring at LTRR.

Optional reading: A how-to on measuring ring width: A 1985 manual. This publication is a classic in dendro generally.

Optional reading: More modernized measuring of ring width: A 1987 article using photography.
2
Jan 23
2. Verifying ring widths
Click on Henri's Software web page and go to the bottom of the page to see links to measurement verification programs. Download "Verify5 for DOS" and run it with your partner's data. Also try "Verify for Windows" if you'd like.

Required reading: Grissino 1997: On ring measurement errors and verifying widths (1.1 Mb, password protected)

Right click here to download a 2003 version of Verify5, re-coded slightly to avoid various output errors.

Click here to go to David Lawrence's Verify for Windows page to download either the 32-bit or the 64-bit version.
3
Jan 30
3. Data management, Telervo
Click here for the Sheep Mountain data set to practice with.
Click here for a biggish data set to practice with.
Required reading: Brewer 2014: Tellervo: Managing data in dendroarchaeology. See also the Tellervo website.
Optional reading: Brewer et al. 2011: Tricycle: A conversion tool for converting data formats in dendrochronology. See also the Tricycle website.
Optional reading: Jansma et al. 2010: TRiDaS: A new standard for data formats in dendrochronology. See also the TRiDaS website.
Optional reading: Brewer et al. 2010: Corina: A new approach for managing data in dendrochronology.

Optional reading: LaMarche and Hirschboeck 1984: A case of being off by one year because of the BC-AD boundary issue.

Optional reading: Speaking of calendar time, check out this essay by LTRR's own Don Falk: Dating Advice: How To Overcome Your Anxiety And Enjoy The New Millennium, published in the Tucson Weekly (Dec. 30, 1999, v. 16, No. 43).
3
Jan. 30
4. Introduction to logistics of LTRR server and the Dendrochronology Program Library (DPL)
Click on the LTRR Software web page and click on links to the http transfer of program files. The files are zipped, but an unzip utility is included.

Click here for the online Bibliography of Dendrochronology.
Click on the LDEO Software web page for Mac-compatible versions.
Linux users may emulate most of these programs through the program "Wine."

Non-Debian-based Linux users: Click on Linux download.
Debian-based Linux users: Type into your terminal: sudo apt-get install wine
To run wine, type (for example): wine fmt.exe
Optional reading: Bunn 2008: DPL in the R environment.
Click on Henri's Ultimate Webpage of Dendrochronology for a source of practically everything dendro.
4
Feb 6
5. Fitting cubic smoothing splines to raw ring-width series
Required reading: Cook and Peters 1981: About use of the cubic spline in dendro studies.

Click here for ring-width data from Coddington Lake white oak.

Click here for an example input file and spline run of ARSTAN.

Optional reading: Blasing et al. 1983: About removing effects of competition from ring-width series, with comments on using the cubic spline in dendro studies.

Congratulations to Dr. Ed Cook, Lamont-Doherty Tree-Ring Lab, for receiving the Harold C. Fritts Award for Lifetime Achievement, acknowledging significant influence on the field of dendrochronology, emphasizing innovative research that has advanced the field, and distinguishing it amongst peer sciences, presented at the 9th International Conference on Dendrochronology, Melbourne, Australia, January, 2014.
5
Feb 13
6. AR modeling raw ring-width series
Required reading: Hoff 1983: Basics of Box-Jenkins time-series analysis (4.1 Mb, password protected)

Recommended reading: Bailey 1970: One reason tree-ring width can be auto-correlated

Recommended reading: Monserud 1986: About ARMA modeling in dendrochronology (3.0 Mb, password)

Recommended reading: Yamaguchi 1986: Comment about cross-correlation with auto-correlated series

Optional reading: Brown 1995: An example of applying Yamaguchi's paper

Minitab help: A short help file to start Minitab at the Library

A cartoon: Making fun of time series prediction.
6
Feb 20
7. Log transformations of raw ring-width and index series
More Minitab help: A short help file to turn on skewness in Minitab at the Library
Optional reading: Leptokurtophobia: You might never log transform data again after reading this.
I need your measurement data by now. Please email me one *.rwl file with your dated, measured cores. Use your name in place of the *. In all cases, use Tucson decadal format.
7
Feb 27
8. COFECHA I: input options
Required Reading: Grissino-Mayer 2001: Essentially a user's manual to running and interpreting COFECHA.
Click here for an Excel file showing the power of missing rings.
Click here for an Excel file showing the difference between Pearson and Spearman correlations.
Click here for an Excel file showing an effect of first-differencing tree-ring data.
7
Feb 27
9. COFECHA II: output results. We will mark up the output in class, so you'll be done with this week's homework by the time class is over.
Please come to class with a COEFCHA output for the class data set. Run this file as a dated data set, and just hit enter (nothing) for the undated file. You're welcome to snoop around the input options to see what's available, but for the class output, use all default options. If successful, COFECHA will result in an output file with the extension *.out. To print correctly, open output file in Word, set all margins at 0.5" and use landscape, courier, and font size 8. Note: This works in Word, but not in Notepad. Print double-sided with long edge as the binder. It is typical to staple this output as if it were a book, i.e., three staples up the long edge. Click here for an example of what printed DPL outputs should look like.
Dataset to be provided: Right click here to download (Save Link As) the Sunset Crater Visitor Center Update data set.
Required Reading: Grissino-Mayer 2001: Essentially a user's manual to running and interpreting COFECHA.
8
Mar 6
10. COFECHA III: ITRDB and other chronologies
Click here to go directly to the search page of the ITRDB.
Click here to go to the NOAA open page of the ITRDB.
Required reading: Grissino-Mayer and Fritts 1997: About the ITRDB as a research tool.

Right click here to download data from ponderosa pine growing at Sunset Crater, near Flagstaff, Arizona, if you don't have data of your own to practice with.
Congratulations to Mr. Bruce Bauer, representing the International Tree-Ring Data Bank (ITRDB), for receiving the Richard L. Holmes Award for Service to Dendrochronology, acknowledging the development and maintenance of the ITRDB, a data archiving effort providing public access to tree-ring data and derived products, presented at the 9th International Conference on Dendrochronology, Melbourne, Australia, January, 2014.
Late April, 2014: Congratulations also to the ITRDB generally, which was formed 40 years ago this month at the International Dendroclimatology Workshop of April, 1974, held in Tucson, Arizona, and led by Hal Fritts.
8
Mar 6
11. COFECHA IV: special uses
Mar 13-17 Spring Break, no classes
9
Mar 20
12. COFECHA V: by spreadsheet
Optional Readings:
Baillie and Pilcher 1973: An early program (588 Kb, password)
Monserud 1986: About ARMA modeling in dendrochronology (3.0 Mb, password)
Monserud and Yamaguchi 1989: Comments about cross-correlation (537 Kb, password)
Yamaguchi and Allen 1992: Yet another program (1.1 Mb, password)
Yamaguchi 1994: Yet more comment (486 Kb, password)
Holmes 1983: About COFECHA (1.0 Mb, password)
9
Mar 20
13. ARSTAN I: detrending options
Required reading: Cook et al. 1990: On rationales for choosing detrending strategies.
Optional reading: Fang et al. 2010: removing biological trends from tree-ring series: testing modified Hugershoff curves.
Optional reading: Helama et al. 2004: A comparison of tree-ring standardization methods.
Optional reading: Cook et al. 1995: The 'segment length curse' in long tree-ring chronology development for paleoclimatic studies.
Optional reading: Salzer et al. 2009: Recent unprecedented tree-ring growth in bristlecone pine at the highest elevations and possible causes (a case of analyzing unstandardized ring widths).
Optional reading: Barber et al. 2000: Reduced growth of Alaskan white spruce in the twentieth century from temperature-induced drought stress (another case of analyzing unstandardized ring widths).
Click here to see detrending with the Hugershoff function.
Click here to see detrending with the mean.
10
Mar 27
14. ARSTAN II: Standardization: modified negative exponential by spreadsheet
Required reading: Fritts et al. 1969: How to perform the modified negative exponential (720 kb, password protected), please bring to class
Right click here to download an Excel97 file that has formulas all set up. You'll have to enter your personal data, recalculate the starting b value, and copy formulas down for all columns. Then iterate away and find the modified negative exponential curve.
Paul's first modified negative exponential
11
Apr 3
15. PAGEPLOT raw data
Click here for a new PAGEPLOT application.
Click here to download a Minitab macro that plots out lots of times series, fast.
11
Apr 3
16. PAGEPLOT of index series, alternative standardization strategies
Optional reading: Cook and Peters 1997: About a potential bias in calculating indices.
Click here for an Excel demo of the potential end effect.
12
Apr 10
17. ARSTAN III: Mean sensitivity and standard deviation
Required reading: Douglass 1920: The original mention of mean sensitivity in dendrochronology (in the first ever issue of Ecology).

Optional reading: Strackee and Jansma 1992: A detailed look at mean sensitivity, etc., as used in dendrochronology.

Optional reading: Biondi and Qeadan 2008: More on mean sensitivity.

Optional reading: Bunn et al. 2013: Yet more detail on mean sensitivity.

Click here to see a demo of mean sensitivity versus standard deviation for a particular, interesting tree-ring series.
12
Apr 10
18. ARSTAN IV: input options
Click here for the clean Sunset Visitor Center data set.
Required reading: Cook and Holmes 1986. A manual on ARSTAN. Some of this is outdated, but timeless background theory is given, including the rationale for double detrending. Click here for an unmarked version. Click here for a marked version.
Optional reading: Fritts 1963: Early computer programs.
Optional reading: Graybill 1979: Revised computer programs.
Click here to download an Excel spreadsheet demo of the variance stabilization process of ARSTAN.
Click here to see an issue with making tree averages in ARSTAN.

Click here to see a nice summary explanation of ARSTAN input options (from Eddie Bevilacqua, Syracuse ESF).
13
Apr 17
19. ARSTAN V: output results
Click here for the clean Sunset Visitor Center data set.
Optional reading: Cook and Holmes 1986. A manual on ARSTAN. Some of this is outdated, but timeless background theory is given, including the rationale for double detrending. Click here for an unmarked version. Click here for a marked version.
Optional reading: Wigley et al. 1984. On the average value of correlated time series, with applications in dendroclimatology and hydrometeorology. Click here for an unmarked version. Click here for a marked version.
14
Apr 24
20. ARSTAN VI: Biweight robust mean estimation
Required reading: Cook dissertation section: on the biweight robust mean estimation (337 kb, password protected)
Right click here to download an Excel spreadsheet to do this activity.
14
Apr 24
21. ARSTAN VII: more tidbits
Required reading: Briffa and Jones 1990: on SNR as an indicator of chronology signal strength.
Click here for prototype presentation of a dendrochronology.
15
May 1
22. Preliminary Climate and tree-growth modeling
Map of NCDC-NOAA Climate Divisions
NCDC-NOAA Divisional Climate Data

Click here to download Arizona Division 02 climate data.
Optional reading: Blasing et al. 1981: On the use of divisional climate data for dendroclimatic modeling. (password protected)
Optional reading: Blasing et al. 1984: A comparison between response-function and correlation function analyses. (password protected)
Optional reading: Fritts and Wu 1986: A comparison between response-function analysis and other regression techniques. (password protected)
Optional reading: Biondi and Waikul 2004: DENDROCLIM2002: A C++ program for statistical calibration of climate signals in tree-ring chronologies. (password protected)
Optional reading: Meko et al. 2011: Seascorr: A Matlab program for identifying the seasonal climate signal in an annual tree-ring time series. (password protected)
15
May 1
See how to submit data to ITRDB
Extra-unit student presentations
Final course summary: Sheppard, P.R. 2010. Dendroclimatology: extracting climate from trees. Wiley Interdisciplinary Reviews: Climate Change.
Student course evaluation
May 10 Final reports due

Laboratory of Tree-Ring Research, University of Arizona
Tucson, Arizona 85721 USA
Main Office: (520) 621-1608, Fax: (520) 621-8229
Comments to Paul Sheppard: sheppard @ ltrr.arizona.edu