obis2index
This repo is a home for materials related to calculating biodiversity health indicies from DwC Archive data (pulled from OBIS and|or GBIF). The code here is more like notes than it is a library or demo.
☣️ This repo is being used as a jumping-off point for the BioDiversity Indicator Dev Group at the 2022 NOAA IOOS Code Sprint. For more info please see the code sprint topic page.
📣 If you are new here please jump over to the "Discussions" tab and introduce yourself!
quicklinks
Usage
easy-access mybinder jupyter notebooks
Use the button below to open example .ipynb files in the /notebooks/ directory:
This may take some time to start up but it is a very easy way to get started with this repo.
Scripted
Use calculate_indicators.sh to calculate all indicators and output updated csv files to ./indicies/.
technical details
Scripts for fetching obis data and calculating indicators are in obis2index/indicies.
Scripts for exploratory data visualizations are in obis2index/explore.
All scripts should be run from the root directory of this project.
Data will get downloaded into the ./data subdirectory and the final indecies output will be put in ./indicies.
other data visualizations included
# see most frequent measurement or facts in mof .csv
python3 -m obis2index.explore.top_column_values data/FKNMS-black_grouper-mof.csv measurementType
# see most frequent values in samplingEffort column
python3 -m obis2index.explore.top_column_values data/FKNMS-everything-ocr.csv samplingEffort
python3 -m obis2index.explore.top_column_values data/FKNMS-everything-ocr.csv yearadditional links
Some output from this project can be found on slides 6 & 7 in this g presentation.
These were generated using the indicators_from_obis project on Axiom's ResearchWorkspace.
A link to this project (currently defunct) is here.