Medfate R package

Introduction: The R package medfate has been designed to study the characteristics and simulate dynamics of Mediterranean forests. Fire and drought impacts are the main drivers covered by the package. Representation of vegetation is not spatially-explicit (i.e. trees or shrubs do not have explicit coordinates within plots). This simplified representation is chosen so that package functions can be easily applied to plot data from national forest inventories. Since the package intends to facilitate predictions of both structure and composition, the taxonomic identity of plants is stored, and parameter values need to be provided for each taxonomic entity (but the package could be used with functional groups). Although landscape-level processes will eventually included, the package currently offers simulation of local processes only.

Package functionality:

  • Drought stress is a key factor to understand the dynamics of most terrestrial ecosystems worldwide. Being able to anticipate where, when and which plant species will be impacted by cumulative drought or extreme drought events requires developing tools capable of generating drought stress predictions using the projections of climatic models. Package medfate implements a soil water balance model that aims to predict temporal variations in soil water content and assess drought stress for plant cohorts in a forest stand. The model is suited to be applied to forest inventory plots and calculates water balance on a daily basis. Soil is represented using two layers – topsoil and subsoil – and the model keeps track of the proportion of moisture relative to field capacity for each layer. Soil water holding capacity includes the effects of rock fragment content. Vegetation is represented as a set of plant cohorts having different height, root distribution, species identity and leaf area index (LAI).
  • The package implements functions that allow calculating fuel characteristics and potential fire behaviour for forest inventory plots. Calculations were adapted from the Fuel Characteristics Classification System (FCCS; Prichard et al. 2013). In FCCS, fuelbed is divided into six strata, including canopy, shrub, herbaceous vegetation, dead woody materials, leaf litter and ground fuels. All except ground fuels are considered here, although in a simplified way. The intensity of burning depends on several factors, including topography, wind conditions, fuel structure and its moisture content, which is determined from antecedent and current meteorological conditions. A modi cation of the Rothermel’s (1972) model is used to calculate the intensity of surface reaction and the rate of spread of surface assuming a steady-state. Both quantities are dependent on fuel characteristics, windspeed and direction, and topography. The model returns the following results: (1) Fuel characteristics by stratum; (2) Surface behavior (i.e. reaction intensity, rate of spread, fi reline intensity and flame length);(3) Crown re behavior; (4) Fire potential ratings of surface behavior and crown behavior.

Authors: Miquel De Cáceres

Availability: Download medfate from CRAN.

Package dependencies: meteoland, Rcpp, sp, spdep

Requirements (for compilation): Rtools (Windows), Command Line tools for Xcode (Mac)