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Kathy's project files for the NES-LTER project with EDI for 2019 Summer
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NES-LTER Transect Analysis Workflow Diagram.png
README.md
environment.yml

README.md

EDI-NES-LTER-2019

Overview

Kathy's project files for the NES-LTER project with EDI for 2019 Summer. This includes Python and R scripts for data analysis and publication. The purpose of this program is to run analyses on IFCB data for manual and automatic classifications, drawing data from the IFCB dashboard and NES-LTER rest API.

This workflow is intended to be reproducible to other IFCB transect cruise data. Additionally, the data produced will be packaged and submitted to several online repositories such as Environmental Data Initiative (EDI), NASA SeaBASS, BCO-DMO.

For additional information, visit https://nes-lter.whoi.edu/

Project members and collaboraters

Stace Beaulieu, Joe Futrelle, Heidi Sosik, Katherine Qi (klqi@ucsd.edu)

Base Requiremeents

R, Python 3.6+, Anaconda, jupyter notebook, bash

Installation

Clone this repository into your current working directory:

git clone https://github.com/klqi/EDI-NES-LTER-2019.git

Create a conda enviornment from EDI-NES-LTER repo:

conda env create -f environment.yml

Or use an existing, activated Python3 conda environment:

conda env update -f environment.yml

Workflow

See current workflow diagram

Status

As of August 9, this complete version (Cruise EN608) was developed over Summer 2019 as an EDI fellowship project. Further capabilities are developed to allow this workflow to become more reproducible.

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