These documents and scripts support the processing of trait and
allometry data bases. The script is intended to work particularly the TRY data base, but it
provides a framework to incorporate data from additional sources.
- TidyTraitAllomDB.Rmd. This
(mostly) R Markdown script takes data downloaded from the TRY data base
(plus additional sources) and apply tidy
data standards. In a tidy data set, each row represents one
observation, each column represents a variable, and each cell represents
a value. In addition, categorical traits are also harmonised into
consistent categories and species taxonomy is standardised to the best
extent possible (likely with some user input).
- TraitTradeOffs.Rmd. This R
Markdown script takes the tidy data produced by TidyTraitAllomDB.Rmd, and performs
multiple analyses to identify trait trade-offs. It also runs a cluster
analysis on mixed data to define plant functional types, and creates a
series of plots to explore the traits.
- AllomModelFit.Rmd. This R Markdown
script takes the tidy data with PFT classification produced by TraitTradeOffs.Rmd, and fits multiple
allometric models relating diameter at breast height (DBH), tree height
(\(H_t\)) and weight-related scales
(wood density and specific leaf area) with biomass, crown size, bark
thickness and rooting depth (in addition to relationships between DBH
and \(H_t\)). .
In the future, additional utilities for analysing trait and allometry
will be incorporated to this workflow.
Important
- Make sure to download the directory “RUtils” available on GitHub, and set
variable
util_path accordingly for scripts that have this
variable.
- For plotting Brazilian states in trait abundance maps (generated by
TraitTradeOffs.Rmd), download
directory “BrazilianStatesMap” available on GitHub, and set
variable
br_state_shp accordingly for scripts that have
this variable.
- Some data were not included in the repository because they are
available through different servers or because the files are too large
to be maintained on GitHub.