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Software by INBO: packages for environmentalists and ecologists!

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At the Research Institute for Nature and Forest (INBO), we are eager to sustain, promote and develop open-source software that is relevant to biodiversity researchers! This page lists R and Python packages which INBO developed or made a significant contribution to. Several of these packages continue being developed.

Please, feel free to try out packages! If you encounter a problem or if you have a suggestion, we encourage you to post an issue on the package’s code repository. You can also directly contribute improvements with a pull request.

The package links below refer to the package’s documentation website, if available. When there is no documentation website, often one or more vignettes are available within the package, describing the package’s purpose and demonstrating its use.

The following table gives a quick overview:

Research stage Related INBO packages
Study design grts, protocolhelper
Retrieve data: general frictionless, inbodb, inbospatial
Retrieve data: environmental pydov, wateRinfo, watina, inbolims
Retrieve data: biological bioRad, camtrapdp, etn, forrescalc, gulltracking, n2khab, pyinaturalist, rgbif
Store data frictionless, git2rdata
Validate data pywhip
Analyze data: geoprocessing qgisprocess, inbospatial
Analyze data: graphs inboggvegan
Analyze data: models dhcurve, effectclass, gwloggeR, inlatools, multimput, niche_vlaanderen
Analyze data: indices LSVI
Publish INBOmd, INBOtheme, checklist
Miscellaneous (mixed content) inborutils, checklist

Study design

  • R package grts: draw a sample from a sampling frame with the Generalized Random Tessellation Stratified (GRTS) sampling strategy.
  • R package protocolhelper: provides templates for protocols and helper functions to start developing a new protocol or move an existing protocol to the INBO protocols repository

Retrieve data

General

  • R package frictionless: read and write Frictionless Data Packages. A Data Package is a simple container format and standard to describe and package a collection of (tabular) data. It is typically used to publish FAIR and open datasets.
  • R package inbodb: connect to and retrieve data from databases on the INBO server, with dedicated functions to query some of these databases.
  • R package inbospatial: provides functions to retrieve data from web feature, web mapping and web coverage services.

Environmental data

  • Python package pydov: to query and download data from Databank Ondergrond Vlaanderen (DOV). DOV aggregates data about soil, subsoil and groundwater of Flanders and makes them publicly available. Interactive and human-readable extraction and querying of the data is provided by a web application, whereas the focus of this package is to support machine-based extraction and conversion of the data.
  • R package wateRinfo: facilitates access to waterinfo.be, a website managed by the Flanders Environment Agency (VMM) and Flanders Hydraulics Research. The website provides access to real-time water and weather related environmental variables for Flanders (Belgium), such as rainfall, air pressure, discharge, and water level. The package provides functions to search for stations and variables, and download time series.
  • R package watina: provides functions to query and process data from the Watina database (mainly groundwater data).
  • R package inbolims: provides functions to query and process data from the INBO Laboratory Information Management System (LIMS), e.g. soil physical and chemical analyses.

Biological data

  • R package bioRad: extract, visualize and summarize aerial movements of birds and insects from weather radar data.
  • R package camtrapdp: aims to experiment and test visualization functionalities for camera trap data formatted following the Camera Trap Data Package standard.
  • R package etn: provides functionality to access and process data from the European Tracking Network (ETN) database hosted by the Flanders Marine Institute (VLIZ) as part of the Flemish contribution to LifeWatch.
  • R package forrescalc: provides aggregated values on dendrometry, regeneration and vegetation of the Flemish forest reserve monitoring network, and functions to derive these data starting from individual tree measurements in Fieldmap.
  • R package gulltracking: provides functionality to annotate GPS tracking data of gulls stored in Movebank. These data are collected by the LifeWatch GPS tracking network for large birds.
  • R package n2khab: provides preprocessed reference data (including checklists, spatial habitat distribution, administrative & environmental layers, GRTSmaster_habitats) and preprocessing functions, supporting reproducible and transparent analyses on Flemish Natura 2000 (n2k) habitats (hab) and regionally important biotopes (RIBs).
  • Python package pyinaturalist: Python client for the iNaturalist APIs.
  • R package rgbif: provides an R interface to the Global Biodiversity Information Facility API.

Store data

  • R package frictionless: read and write Frictionless Data Packages. A Data Package is a simple container format and standard to describe and package a collection of (tabular) data. It is typically used to publish FAIR and open datasets.
  • R package git2rdata: an R package for writing and reading dataframes as plain text files. Important information is stored in a metadata file, which allows to maintain the classes of variables. git2rdata is ideal for storing R dataframes as plain text files under version control, as it strives to minimize row based diffs between two consecutive commits. The package is intended to facilitate a reproducible and traceable workflow.

Validate data

  • Python package pywhip: a package to validate data against whip specifications, a human and machine-readable syntax to express specifications for data.

Analyze data

Geoprocessing

  • R package qgisprocess: R interface to the geoprocessing algorithms of QGIS and other providers that can interface with QGIS (e.g. GDAL, GRASS GIS, SAGA and WhiteboxTools).
  • R package inbospatial: provides a collection of useful R functions for spatial data retrieval and analysis

Make graphs

  • R package inboggvegan: provides R functions for multivariate plots. More specifically, extended biplot and screeplot functionality is offered for the vegan package.

Fit models and make model predictions

  • R package dhcurve: an R package to predict tree height for a given girth, based on a model and data on tree height, tree girth, tree species and location (in Dutch).
  • R package effectclass: an R package to classify and visualize modelled effects by comparing their confidence interval with thresholds.
  • R package gwloggeR: an R package to detect anomalous observations in timeseries of groundwater loggerdata (water pressure and air pressure). Additive outliers, temporal changes and level shifts are detected.
  • R package inlatools: provides a set of functions which can be useful to diagnose INLA models: calculating Pearson residuals, simulation based checks for over- or underdispersion, simulation based checks for the distribution, visualising the effect of the variance or precision on random effects (random intercept, first order random walk, second order random walk). The functions can be useful to choose sensible priors and diagnose the fitted model.
  • R package multimput: an R package that assists with analysing datasets with missing values using multiple imputation.
  • Python package niche_vlaanderen: Python package to run the NICHE Vlaanderen model. Based on calculated abiotic properties of the location, NICHE Vlaanderen determines whether certain vegetation types can develop. An additional flooding module allows the user to test whether the predicted vegetations are compatible with a particular flooding regime. The package is a redevelopment of an existing ArcGIS plugin in Python, without external non-open source dependencies.

Calculate indices

  • R package LSVI: bundles a number of functions to support researchers in determining the local conservation status (‘LSVI’) of Natura 2000 habitats in Flanders. Several functions retrieve the criteria and/or associated species lists for determining the LSVI. A specific function allows to calculate the LSVI. The package is written in Dutch.

Publish your workflow and discuss your results

  • R package INBOmd: provides several styles for rmarkdown files and several templates to generate reports, presentations and posters. The styles are based on the corporate identity of INBO and the Flemish government. All templates are based on bookdown, which is an extension of rmarkdown. bookdown is taylored towards writing books and technical documentation.
  • R package INBOtheme: contains ggplot2 themes for INBO, the Flemish government and Elsevier journals. The documentation website includes a set of example figures for each available theme.
  • R package checklist: provides an elaborate and strict set of checks for R packages and R code, which includes setting up GitHub actions to publish to Zenodo.

Last but not least: miscellaneous!

  • R package inborutils: provides a collection of useful R utilities and snippets that we consider recyclable for multiple projects. The functions are either out of scope or just not mature enough to include as extensions to existing packages.
  • R package checklist: provides an elaborate and strict set of checks for R packages and R code.