claraqin / neonMicrobe

Processing NEON soil microbe marker gene sequence data into ASV tables.
GNU Lesser General Public License v3.0
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Batch structure #43

Closed claraqin closed 3 years ago

claraqin commented 3 years ago

This pull request includes a massive restructuring effort in order to align the repo with the expected R package structure. The structure of the R package does not have to be the structure used for data analysis!

New processing batch structure makes parameters easier to manage. Parameters are incorporated into the “batch environment,” rather than crowding into the global environment.

By default, parameters take precedence over the arguments that are passed to functions, but users can define as many parameters as they want. However, validation for parameters (i.e. checking to make sure users enter valid parameters that are actually incorporated into the functions) is not yet completed.