Interface

The BayesForest Toolbox operates via the Matlab command line. Function BayesForest is the main function of the Toolbox. BayesForest(input) takes the input configuration file input (string).

The input configuration file has the following syntax rules:

• whole line is a comment, if it begins with #

• one line contains one statement (usually) in the form var = value, where var is a specific variable that defines the behavior of BayesForest, whereas value is a desired value for var.

For example at the Matlab prompt:

BayesForest('input-test.txt')

runs the simulation process defined in the configuration file input-test.txt.

Below an excerpt from a sample configuration file is shown:

# This is a comment
# Target directory, the below statement is processed by the BayesForest
target_dir = ./

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Functions and tools from the BayesForest Toolbox can be used independently. In this case, it is better to consult the corresponding function's help pages using:

help import_qsm_data

or

doc import_qsm_data

The above will print help pages of the function import_qsm_data.

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Along with this Wiki the help pages of Matlab is a good source for instruction. Use help BayesForest to start with the Toolbox (follow links to other help pages at the bottom). BayesForest is exhaustively documented.

It is also advisable to consult BayesForest (open) publications:

a. Ilya Potapov, Marko Järvenpää, Markku Åkerblom, Pasi Raumonen, Mikko Kaasalainen, Bayes Forest: a data-intensive generator of morphological tree clones, GigaScience, in press.

b. Ilya Potapov, Marko Järvenpää, Markku Åkerblom, Pasi Raumonen, Mikko Kaasalainen, Data-based stochastic modeling of tree growth and structure formation, Silva Fennica, 50, 2016.