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plotsdatabase

R package for managing and exploring the Central African forest plot database cafriplot network

Overview

plotsdatabase provides tools for querying a PostgreSQL database containing forest inventories data from Tropical Africa. The package offers comprehensive functions for working with individual tree measurements on which either taxa or stem level traits sensus largo measurements (or observations) can be aggregated.
The great advantage of this package is allow managing inventories, traits and observations under the same taxonomic backbone, facilitating data integration, reproductibility in data analysis and manipulation, data reusability.

Key features: - Query plot data, individual tree measurements, and ecological features - Update database tables with new measurements and observations - Resolve taxonomic synonyms - Access and aggregate species-level taxonomic traits

Installation 

# Install from GitHub
install.packages(c("tidyverse", "dbplyr", "devtools"))
devtools::install_github("gdauby/bdd_plots_central_africa")

In case of slow internet connection, the installation from github above may fail. You may try to first launch this code line in the console, it will increase the time for trying to install :

options(timeout = max(3000, getOption("timeout")))

Note: Access to the database is restricted and requires appropriate credentials.

Package Logic & Access Control

The plotsdatabase package offers tools to manipulate, export, visualize, standardize, and enrich forest inventory data.

Access Model

The package implements a two-tier access system:

  1. Plot inventories (row-level security):
    • Each user has access to their own plots, controlled by database row-level security policies
    • Policies define which specific plots each user can query and update
    • Ensures data providers maintain control over their contributed inventories
  2. Species-level traits (access across all users):
    • All users have read access to the taxa database
    • These data are grafted and aggregated to inventories

Future Development

  • Species occurrence data: Open access to occurrence records across Central Africa (not yet implemented)

This design ensures data sovereignty for plot owners while enabling the research community to benefit from shared taxonomic and trait knowledge.

Database Architecture

The package connects to two PostgreSQL databases:

  1. Main database (plots_transects): Plot, subplot, and individual tree data
  2. Taxa database (rainbio): Taxonomic information and species-level traits

Quick Start 

library(plotsdatabase)

# Connect to databases
mydb <- call.mydb()
mydb_taxa <- call.mydb.taxa()

# Query plots
plots <- query_plots(plot_ids = c(1, 2, 3))

# Query plots
plots <- query_plots(country = "GABON")

# Visualize database structure
get_database_fk(mydb)

Core Functions

Connection Management

Data Querying

Utilities

Documentation

  • Function help: Use ?function_name for detailed documentation
  • Changelog: See NEWS.md for version history and updates

Recent Updates

See NEWS.md for the latest changes, including: - Breaking changes and migration guides - New features and enhancements - Bug fixes and improvements

Package Metadata

  • Authors: Gilles Dauby, Hugo Leblanc
  • Maintainer: Gilles Dauby ()
  • License: GPL-2
  • Minimum R version: 4.0

Contributing

This package follows a git branching workflow: - All code changes are made on feature branches - Changes are documented in NEWS.md - Pull requests are reviewed before merging to master

Support

For issues, questions, or feature requests, contact the package maintainer.