Tree-Ring Matlab Toolbox

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Description


Matlab is a commercial software package for numeric computation, graphics, visualization, and high-level programming. Matlab is available from The MathWorks, Inc. The basic Matlab package has many functions generally useful for tree-ring studies. Matlab "toolboxes" with specialized functions can also purchased from The MathWorks, Inc. Toolboxes are available for signal processing, mapping, image processing, neural networks, statistics, and many other topics.

The "Tree-Ring Toolbox" is not a commercially available Matlab toolbox, but is a collection of Matlab functions I have written to do various tasks in tree-ring analysis. For example, the function crn2vec2 reads an ITRDB-formatted ".crn" file and returns the site chronology, years, and sample size as matlab vectors.
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Requirements


To use the Tree-Ring Toolbox, you must have Matlab installed on your computer or network. I use the University of Arizona Matlab site license, which has the most recent Matlab release. The functions may not work on older versions. Depending on which functions you intend to use, you may also need to have one or more "Matlab toolboxes" (e.g., statistics) installed. The comment section of each function lists which toolboxes are required. Some functions requre statistics, signal processing or spline toolboxes.

To use the Tree-Ring Toolbox, you must its functions in a directory on your Matlab path. My functions usually call on other utility functions I wrote. The best method to be sure you don't call an "unknown" function is to download the whole set of Tree-Ring Toolbox functions. I have zipped these into a file File_pooled.zip, which you should unzip into a directory on your Matlab path. I recommend keeping those functions by themselves in a dedicated folder. Put that folder first on your Matlab path, so that no other functions you might have by the same name, or not obsolete versions of the same function, are used. Alternatively, move your data to the dedicated folder and run programs with that folder as the current working directory.

I distribute these function freely. I require no acknowledgement of the source. Go ahead and modify them as you wish. I welcome any comments on the functions in the function list. But due to time constraints, I cannot promise anything more than grudging cooperation in updating or correcting functions when I'm in the mood.

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Notation

To find out what's in the Tree-Ring Matlab Toolbox, check out the function list, , which give a brief description of what the function does. I suggest you read the comment section at the beginning of any function before using the function. My opening comments are organized as follows:

  1. function name with 1-line description
  2. syntax of the function call
  3. date of most recent revision
  4. extended description of what the function does
  5. Input requirements
  6. Output
  7. References
  8. UW Functions Called (other functions I wrote)
  9. Matlab toolboxes required (e.g., signal processing)
Among other things, the comment secti0ons defines the input and output arguments. I use a shorthand code for such data. The best way of describing this code is by way of example:
(1x1)r  real number, scalar
(3x2)r  matrix (3 x 2) of real numbers 
(3x1)i  column vector (3 elements) of integers
(1x8)s  character string of length 8
(1x1)L  logical scalar

Matlab also has data types called "cells" and "structures", which are best found out about by reading the Matlab documentation. My code for cells uses braces. For example, the code below indicates a 1 x 3 "cell" variable containing a 2x2 integer matrix, a 1x5 character string and a 1x10 row vector of real numbers.
{1x3}
  (2 x 2)i
  (1 x 5)s
  (1 x 10)r  

Among the files included is seascorr, which has been published in Computers & Geosciences. A pdf of the paper and a zip of sample data are included for seascorr. Sample data are also included for function skelcrn.
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List of Functions