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R Scripts — Bird trait analysis

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Bird trait analysis

Pipeline for avian trait data — FuSE_FuS project

01_DATA_load_and_clean — Step 1

Load AVONET BirdLife morphological traits, fetch IUCN Red List categories via API v4 (rredlist), mer

01_DATA_load_and_clean — Step 2

Build a bird megatree (from GitHub), compute phylogenetic PCoA eigenvectors, add missing species via

01_DATA_load_and_clean — Step 3

Assemble the final PhenoBird matrix: remove problematic species, filter DD/EX/EW categories, compute

01_DATA_load_and_clean — Step 4

Run PCoAGraph() separately for morphological (M), life-history/reproduction (L), diet (D), and combi

01_DATA_load_and_clean — Step 5

Load 5 BirdLife BOTW shapefiles, reconcile taxonomy with the trait dataset via ITIS synonymy lookup,

01_DATA_load_and_clean — Step 6

Compute community-level Trait Probability Densities (TPDs) for each functional dimension (M, L, D, M

01_DATA_load_and_clean — Step 7

Compute community-level FRic for all species, combine all PCA objects into a named list, export PCoA