DENDROCHRONOLOGY WORKSHOPGEOS, ANTH, or WSM 497C/597C (two units)Spring 2008:
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Instructor: Paul Sheppard (W. Stadium 105-C1, 621-6474,
sheppard @ ltrr.arizona.edu)
General objectives of this course
Primary: To actively engage in and learn the 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 that must be done and/or computer output that must be annotated and turned 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 that site will be required. This report will be mostly on the methods, results, and discussion of the project; a literature review per se is not expected, but any 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 double-spaced typed 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 devlopment 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, or PC computers specifically, then you'll need to overcome that phobia quickly or you'll be underserved by this course. The most 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 will be measured in the Tree-Ring Lab measuring room, now in the new Tree-Ring West annex. 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 Minitab, which I'll use in class. We have a few machines in room West Stadium 104 that 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,
at least 4.0, which you can get free HERE: 
| Flexible Schedule of Activities (subject to change, though not much change) | |
|---|---|
| Week of |
Activity |
| 0 Jan. 16 |
Organizational meeting: January 10 @ 1:00 in new LTRR classroom, to choose meeting time. Bring your class schedules. If you cannot attend, email me your schedule ahead of time. |
| 1 Jan. 21 |
Begin measuring ring widths using J2X. Click on Voortech for a user guide to J2X. |
| 2 Jan. 28 |
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. |
| 3 Feb. 4 |
Converting measurement formats Click on Henri's Software web page and go to the bottom of the page to see links to his measurement file convert program. Download "Convert5 for DOS" and run it with your partner's data. 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 |
| 3 Feb. 4 |
Introduction to logistics of LTRR server and the
Dendrochronology Program Library 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. |
| 4 Feb. 11 |
Fitting cubic smoothing splines to raw ring-width series Required reading: Cook and Peters 1981: About use of cubic spline in dendro studies (0.7 Mb, password protected) |
| 5 Feb. 18 |
AR modeling raw ring-width series Required reading: Hoff 1983: Basics of Box-Jenkins time-series analysis (4.1 Mb, password protected) Optional reading: Yamaguchi 1986: Comment about cross-correlation with auro-correlated series (724 Kb, password) |
| 6 Feb. 25 |
Log transformations of raw ring-width and index series I need your measurement data by now. Please email me one *.rwl file with your dated cores and one *.und file with your undated core. Use your name in place of the *. In all cases, use Tucson decadal format. |
| 7 Mar. 3 |
Dataset to be provided: Right click here
to download (Save Link As) the Sunset Crater Visitor Center dated data set (7 Kb,
Tucson decadal) Please come to class with a COEFCHA output for the class data set. You're welcome to snoop around the input options to see what's available, but use all default options. To print correctly, 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. It is typical to staple this output as if it were a book, i.e., three staples up the lefthand side. COFECHA I: input options. Required Reading: Grissino 2001: Essentially a user's manual to running and interpreting COFECHA (2.1 Mb, password protected) |
| 7 Mar. 3 |
COFECHA I: 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. |
| 8 Mar. 10 |
ITRDB and other chronologies Click here to go directly to the search page of the ITRDB. Required reading: Grissino-Mayer and Fritts 1997: About the ITRDB as a research tool. (727 Kb,password) |
| 8 Mar. 10 |
COFECHA III: special uses |
| Mar. 17 | Spring Break, no classes. |
| 9 Mar. 24 |
COFECHA 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. 24 |
ARSTAN I: detrending options Required reading: Cook et al. 1990: On rationales for choosing detrending strategies. 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. |
| 10 Mar. 31 |
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. |
| 11 Apr. 7 |
PAGEPLOT: Click
here to download a Minitab macro that plots out lots of times
series, fast. Click here to download a final data set of the stupid trees project. Click here to download a final data set of the stupid trees project, this time with average growth values added. |
| 11 Apr. 7 |
PAGEPLOT of index series, alternative standardization
strategies Optional reading: Cook and Peters 1997: About a potential bias in calculating indices (1.7 Mb, password protected). |
| 12 Apr. 14 |
ARSTAN: Mean senstivity and standard deviation Optional reading: Strackee and Jansma 1992 : A detailed look at mean sensitivity, etc., as used in dendrochronology (549 kb, password protected). Click here for my Sunset Crater Visitor Center data set. |
| 12 Apr. 14 |
ARSTAN: input options Click here to download an Excel spreadsheet demo of the variance stabilization process of ARSTAN. |
| 13 Apr. 21 |
ARSTAN: output results |
| 14 Apr. 28 |
ARSTAN: 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. 28 |
ARSTAN: more tidbits |
| 15 May 5 |
Student course evaluation Preliminary Climate and tree-growth modeling NCDC-NOAA Divisional Climate Data Right click here to download Arizona Division 2 climate data. Optional reading: Blasing et al. 1984: A comparison between response-function and correlation function analyses. (1.0-Mb pdf file, password protected) Optional reading: Fritts and Wu 1986: A comparison between response-function analysis and other regression techniques. (1.9-Mb pdf file, password protected) Optional reading: Blasing et al. 1981: On the use of divisional climate data for dendroclimatic modeling. (532-kb pdf file, password protected) |
| 15 May 5 |
Submit class data to ITRDB Final course summary |
| May 14 | Final reports due |