trait-geo-diverse

Repository to collect data sets, notes, and prototypes of integration of phylogeny, trait, and occurrence data. The general layout is as follows:

• "raw", uncleaned data files are collected in data. Using simple, throwaway, cleaning and conversion scripts, these data are processed into tab-separated tables that go in data/sql. Subsequently, these tables are imported in a SQLite database with a to-be-developed schema. The data model (column names, relations between tables) should mirror that of Bio::Phylo.
• from the schema of the SQLite database an object-relational mapping is generated with DBIx::Class, and dumped into lib. Minor additions to these modules should result in opportunistic subclassing of Bio::Phylo functionality to make data access richer.
• the code in the script directory consists of larger scripts that filter and subset the data in the database in order to analyze these and/or export them into a file format suitable for analysis by 3rd party tools and R packages.
• the R directory will contain lightweight, re-usable library code in R to be used by some of the scripts.

The general idea is that this is not a repository for heavy development of reusable libraries, but a place for doing research and implementing computational workflows. Which are going to use a little bit of library code, as needed.