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In addition to the online applications LifeWatch is developing and maintaining, a number of open source software packages (mostly R packages) that support biodiversity data analysis. A list of these packages can be found below.

Benthos Ecosystem Quality Index (BEQI)

The Benthos Ecosystem Quality Index (BEQI) is a biological index that will be used assessing the state of the benthos of coastal and transitional waters for the Water Framework Directive. The software package is available through here.

bioRad

bioRad is an R package for analysis and visualisation of biological signals in weather radar data. The R package is available through GitHub.

BVMtool

BVMtool is a tool for marine biological valuation mapping. The software package is available through here.

etn

etn is an R package with functions to access and process data from the European Tracking Network (ETN). The R package is available through GitHub.

LifeWatch/EMODnet Biocheck

The LifeWatch/EMODnet Biocheck tool checks if IPT resources meet the OBIS guidelines. The R package is available through GitHub and RShiny.

marinespeed

marinespeed is an R package for working with the Marine SPEcies and Environmetal Data dataset. The R package is available on GitHub. More information about the R package: http://rshiny.lifewatch.be/marinespeed/.

mregions

mregions is an R package to get data from marineregions.org. Available through GitHub.

niche_vlaanderen

niche_vlaanderen is a Python package to run the NICHE Vlaanderen model. This hydro-ecological model predicts the occurrence of vegetation based on abiotic site conditions and was calibrated for Flanders. Background information of the model is only available in Dutch, documentation of the Python package in English. The Python package is available through GitHub.

pydov

pydov is a Python package to retrieve data from Databank Ondergrond Vlaanderen (DOV). The Python package is available through GitHub.

pyhydrophone

pyhydrophone is an open-source Python package that has been developed to ease the import of underwater sound data recorded with a hydrophone to python, so postprocessing and AI can be easily performed on the data afterwards. Different recorders can be added with their different way of reading metadata, so the scientists do not have to worry about he format but just about the outcome. It is still in constant development and improvement. The Python package is available through GitHub.

pyporcc

pyporcc is an open-source Python package developed to detect and classify harbor porpoise’s clicks in audio files using the PorCC algorithm and offering the possibility to create new clicks classifiers. It provides a framework to train different models such Support Vector Machines, Linear Support Vector Machines, Random Forest and K-Nearest Neighbor that classify sound clips in Noise, and Low-Quality and High-Quality Harbor Porpoises’ clicks. The algorithm from PAMGuard to detect possible clicks clips is also implemented. The Python package is available through GitHub.

pywhip

pywhip is a Python package to validate data against whip specifications. The Python package is available through GitHub.

rgbif

The rgbif package gives you access to data from GBIF, were the Research Institute for Nature and Forest (INBO) contributes their biodiversity data. A tutorial illustrates how you can use the package to search and download data from GBIF and how to create and interactive map of the downloaded data. The R package is available through GitHub.

sdmpredictors

sdmpredictors is an R package from Bio-ORACLE v2.0: Marine Data Layers for Bioclimatic Modelling. The software package is available on GitHub.

taxize

The taxize package allows users to search over many taxonomic data sources for species names (scientific and common) and download up and downstream taxonomic hierarchical information - among other things. The R package is available through GitHub.

uvabits

uvabits is an R package to download bird tracking data from UvA-BiTS. The R package is available on GitHub.

wateRinfo

The wateRinfo package provides data access to the waterinfo.be data, the data portal provided by the Flemish environmental agency (VMM). Different meteorological, flow and fysico-chemical variables are provided for set of stations.The R package is available through GitHub.

worrms

The worrms package is a R client for the World Register of Marine Species (WoRMS). The R package is available through GitHub.