Overview
This application combines existing pipelines and data sources. Some additional components and connections are integrated.PH1 calculations require monthly aggregated plankton lifeform data and are analysed in lifeform pairs.
flowchart LR
A[PLET] --> B[Harvest PLET library]
B --> C[PLET Export - Stored on EDITO]
E[OSPAR Regions] --> B
C --> F[PH1 App - using code from PH1 Rmd]
I[Select online dataset] --> F
L[any private pipeline] --> G
G[Upload custom datasets] --> F
F --> H[PH1 analytical plots]
J[EDITO data lake] --> K
K[custom export script] --> I
PLET
Plankton Lifeform Extraction Tool (PLET) is a central repository for lifeform abundances. Users can submit their species-level data together with trait descriptions. The description is added to the master list: Plankton lifeform traits master list, and lifeform classification is based on this master list.It is advised that all dataset managers contribute their data to PLET. It is a central repository for this information and an important node in pelagic habitat assessment.
From a user perspective, it provides several functionalities such as spatial and temporal aggregation of abundances. PLET allows users to manually download data. There is no API available, but there is a basic Python endpoint.
Harvest PLET library
A Python library built around the PLET endpoint. It offers additional functionality to request data aggregated according to the OSPAR Common Procedure Assessment Units.- Make programmatic requests to the PLET database for individual datasets.
- Request all datasets aggregated according to the Common Procedure Assessment Units.
Custom pipelines
An example of data extraction from the EDITO data lake can be found on GitHub.This shows:
- How to access data on EDITO using R.
- How to perform custom monthly lifeform aggregation.
PH1 script
This is the primary open-source analytical tool for PH1 analysis. It is provided as an R Markdown script.
Credits:
Holland, M. M., & McQuatters-Gollop, A. (2022).
PH1_PLET_tool (Version 2.0) [Computer software].
https://github.com/hollam2/PH1_PLET_tool