TESS-Laboratory/Akhabue_PFT_Classification

Created as part of Enimhien Akhabue's research to support the systematic classification of Plant Functional Types (PFTs) based on species occurring in Africa, using trait data from the TRY database. The goal is to improve the representation of vegetation diversity in land surface models and ecological studies with a focus on African ecosystems. # Critical Classification Parameters Linking Species to Plant Functional Type in African Ecosystems --- This was created by Enimhien (efa206@exeter.ac.uk), Andrew Cunliffe, Karina Bett-Williams, Anna B. Harper, Petra Holden, and Tom Powell as part of Enimhien’s Doctoral research within the Oppenheimer Programme in African Landscape Systems (OPALS) (opals-exeter.org). --- The permanent version of this code is available on Repository for species classification into different PFT classes in JULES. The species data is from the TRY data base. - The JULES_pub_count.R script: This script uses the europepmc R package to search for publications related to the JULES land surface model in the Europe PubMed Central database. Keywords were used to retrieve relevant literature for background research and citation tracking. - Mapped_PFT_Harmonized.csv contains the final output of the plant functional type (PFT) mapping and taxonomic harmonization process. Each record includes the mapped PFT, and harmonized species names. This is the final output product. - TRYdata_analysis.R contains the initial steps for accessing and extracting trait data from the TRY Plant Trait Database using R. The script makes use of methods and examples adapted from the rtry package, which provides a standardized interface to interact with TRY data. This script was used to retrieve plant trait and species records for subsequent PFT mapping and analysis. Note: Access to TRY data requires an approved data request and login credentials. - Taxonomic_Harmonization_LCVP.R contains an alternative approach for taxonomic harmonization using the Leipzig Catalogue of Vascular Plants (LCVP) via the lcvplants R package. Although this method was tested during the workflow, it was not used in the final analysis. The script is retained here as a reference for future comparisons or alternative workflows. - Taxonomic_Harmonization_WFO.R contains the script used for taxonomic harmonization of species names us …