Phd scripts book
Overview
This book compiles the scripts developed as part of the PhD project “Evaluation of above-ground carbon dynamics in Sustainable Forest Management in the Amazon: providing support to Brazil’s climate commitments”, carried out by Gustavo Bediaga within the Graduate Program in Ecology at the University of Brasília.
The project is supervised by Dr. Mercedes Bustamante and conducted in partnership with CIRAD, with the collaboration of Drs. Plinio Sist, Sylvain Schmidt, and Géraldine Derroire.
The scripts were developed during a research mobility at CIRAD, from October 2025 to January 2026, with support from the PEPR FORESTT program. During this period, the following activities were carried out:
Learning Quarto:
Acquired proficiency in Quarto to ensure that all data processing and analyses performed during the PhD are reproducible and transparent.
Data harmonization and standardization:
All datasets were prepared and translated into Quarto, with a full step-by-step description. Permanent plots data were standardized (1 Preparation of Permament Plots data) and harmonized (2 Harmonizing Permanent Plots data) following the methodology of the BioForest project. Commercial forest inventories were also prepared (3 Merging IF100 + logbook data) and merged with logbook datasets.
Data exploration:
Performed exploratory (4 Exploring data) and comparative analyses (5 Comparing wood density databases) to understand patterns and behavior in the data.
Data processing and analyses:
Developed a workflow (6 Workflow to extract tree height from Lidar CHM to retrieve total tree height from Canopy Height Models (CHMs) derived from LiDAR (7 Workflow to extract tree height from Lidar CHM).
Estimated tree biomass using multiple approaches (8 Estimate biomass with different total height estimations).
Initiated tree height modeling with various datasets from the same study site (9 Modelling DBH x Height).
During the mobility, we established contact with researcher Fabian Fischer, author of Fischer et al. (2024), who processed the CHMs for the entire study area using his published methodology and made the data available for this PhD project.
We also discussed the project methodology with CIRAD partners and delivered a presentation on Brazilian Forest Concessions at the Unit of Forêts et Sociétés at CIRAD.
Overall, this mobility was highly beneficial, providing valuable skills, methodological insights for the PhD project, and strengthening collaboration with CIRAD.
All scripts were written in RStudio 2025.09.2+418 as Quarto files and were subsequently rendered into the HTML documents made available here.