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From plant traits to model parameters

Introduction

Package traits4models is designed to facilitate creating plant species parameter tables for process-based models of forest function and/or dynamics. Specifically utility functions are provided to:

  1. Harmonize plant trait databases.
  2. Harmonize allometry databases.
  3. Populate species parameter tables from harmonized data.

At present, species parameter estimation is tailored to be used for the models included in packages medfate and medfateland, but it other functions could be added to become useful for other process-based models (see section Contributing guide).

Package installation

Since both packages evolve together, installing traits4models normally requires an up-to-date version of package medfate, which is available at CRAN.

The latest stable versions GitHub as follows (required package remotes should be installed/updated first):

remotes::install_github("emf-creaf/traits4models")

Usage

The main functions for harmonization are harmonize_taxonomy_WFO(), check_harmonized_trait() and check_harmonized_allometry(). A number of functions are provided for inspecting the set of harmonized trait/allometry data. Finally, model-specific functions are provided to populate species parameter tables from them.

Documentation

A number of vignettes illustrate how to initialize inputs and run simulation models in traits4models. These can be found at the package website.

Companion R packages

The development of traits4models is intended to complement packages medfate and medfateland.

Two other packages complete the simulation framework, but can be used for many other purposes beyond forest modelling:

  • Package meteoland allows generating daily weather input for simulation models in medfate and medfateland. Package meteoland is a dependency for medfate and medfateland, but can be used independently to obtain daily weather data.
  • Package forestables allows reading and harmonizing forest inventory data to a common data structure. Initialization workflows in medfateland can use data from forestables, but the data structures of the package can be used for many studies beyond modelling.

The relationships between the five packages are illustrated in the figure below, where black arrows indicate package dependencies and gray arrows indicate model parameter or data provision.

Authorship

The set of R packages are developed and maintained by the Ecosystem Modelling Facility unit at CREAF (in Spain), in close collaboration with researchers from URFM-INRAE (in France) and CTFC (in Spain).

Funding

  • Research project: Boosting process-based models to project forest dynamics and associated ecosystem services at stand-to-regional scales (BOMFORES). Financial Entity: Ministerio de Ciencia e Innovación (PID2021-126679OB-I00). Duration from: 01/09/2022 to: 31/08/2024. PI: Miquel De Cáceres.
  • Research project: Improving the modelling of key forest dynamic processes to forecast long-term changes in Mediterranean forests under climate change (IMPROMED). Financial Entity: Ministerio de Ciencia e Innovación (PID2023-152644NB-I00). Duration from: 01/09/2024 to: 31/08/2025. PI: Miquel De Cáceres/Josep Mª Espelta.