Being able to anticipate the impact of global change on forest ecosystems is one of the major environmental challenges in contemporary societies. However, uncertainties in how forests function and practical constraints in how to integrate available information prevent the development of robust and reliable predictive models. Despite the amount of knowledge accumulated about the functioning and dynamics of Mediterranean forests, scientists should make coordinate their efforts to address the challenge of integrating the different global change drivers in a modelling framework useful for research and applications.
The R package
medfate has been designed to study the
characteristics and simulate the functioning and structural dynamics of
forest ecosystems. Climatic conditions are the main environmental
drivers, with a particular focus on drought and fire impacts under
Mediterranean conditions. Representation of vegetation accounts for
structural and compositional variation but is not spatially-explicit
(i.e. trees or shrubs do not have explicit coordinates within forest
stands). This representation is chosen so that package functions can be
easily applied to forest plot data from national forest inventories.
Since the package intends to facilitate predictions of not only forest
functioning but also forest structural and compositional dynamics, 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
Currently, the distributed R package does not include any vignette, but the package website includes articles covering model simulation examples, sensitivity analysis, parameter specification, model evaluation and applications. In addition, complete documentation on the design and formulation of the simulation models can be found at the medfate reference book.
Three main kinds of simulations can be done in medfate, each model building on the previous ones.
Eco-hydrological processes are fundamental for the simulation models
included in the
medfate package. In particular, the package
allows the simulation of water balance of soils and plants within forest
stands. Processes affecting soil water content include rainfall, canopy
interception, infiltration and runoff, percolation and deep drainage,
soil evaporation and plant transpiration. In
soil water balance of a forest is primarily used to predict drought
stress for living plants in it. Soil/plant water balance can be studied
for a given forest stand using function
spwb() can be run using a different level of complexity.
The basic approach focuses on soil water balance and strongly
simplifies processes underlying plant transpiration. In contrast, the
advanced approach is computationally more demanding but
provides an explicit simulation of processes regulating stomatal
behaviour and water transport through the plant, which also requires an
explicit energy balance.
Changes in leaf area and plant growth are key to evaluate the influence of climatic conditions on forest structure and function. Processes affecting changes leaf area and plant size are those involved in water, energy and carbon balances, as well as those directly affecting meristematic activity (e.g. phenology or other sink limitations). Carbon balance arises from the interplay between carbon assimilation via photosynthesis and the respiration costs required for the maintenance of existing cells and the formation of new tissue. Water and carbon balances are coupled through the regulation of gas exchange done by leaf stomata. Plant growth is affected by the availability of carbon (source limitation), but also by temperature and water status (sink limitation). In addition, water and carbon status of cohort plants can increase the likelihood of mortality, resulting in a decrease of the number of individuals in the cohort.
medfate allows simulating daily water/carbon
balances, growth and mortality of a set of cohorts (competing for light
and water) in a single forest stand using function
growth(), which adds carbon balance, growth and mortality
processes to those simulated by function
spwb(). As before,
growth() can be run using two levels of complexity
which match the two transpiration modes of function
Changes in forest structure and composition result from the interplay
of demographic processes (growth, mortality and recruitment) and may
include disturbances such as forest management. The package includes
fordyn(), which allows simulating these processes
at yearly time steps on a given forest stand. Function
fordyn() builds on the previous two simulation functions
and incorporates recruitment and forest management to the set of
The package includes a number of functions to examine properties of
the plants conforming the
forest object, summary functions
at the stand level or vertical profiles of several physical
plant_*: Cohort-level information (species name, id,
leaf area index, height…).
species_*: Species-level attributes (e.g. basal area,
leaf area index).
stand_*: Stand-level attributes (e.g. basal area).
vprofile_*: Vertical profiles (light, wind, fuel
density, leaf area density).
Many of the functions included in
medfate are internally
called by simulation functions. Some of them are made available to the
user to facilitate a deeper understanding the different sub-models and a
more creative use of the package, but most users can ignore them.
Sub-model functions are grouped by subject, which is included in the name of the function. The different sub-model functions are (by subject):
biophysics_*: Physical and biophysical utility
carbon_*: Carbon balance.
fire_*: Fire behavior and severity.
fuel_*: Fuel properties.
hydraulics_*: Plant hydraulics.
hydrology_*: Canopy and soil hydrology (rainfall
interception, soil evaporation, soil infiltration).
light_*: Radiation extinction and absorption.
moisture_*: Live tissue moisture.
pheno_*: Leaf phenology.
photo_*: Leaf photosynthesis.
root_*: Root distribution and conductance
soil_*: Soil hydraulics and thermodynamics.
transp_*: Stomatal regulation and resulting
wind_*: Canopy turbulence.
Simulation models produce multiple outputs and it is important to
learn how to visualize them and extract information for further
analysis. Each simulation function returns an output object whose S3
class has the same name as the simulation function
spwb() returns an object of class
are available for simulation output objects, which facilitates
displaying and summarizing information.
shinyplot() (as well as its
implementation for different output objects) allows an interactive
exploration of simulation results.
objects through function
Additional package function are meant to be used on simulation results and produce time series of additional (derived) properties:
Vegetation functioning and dynamics have strong, but complex, effects on fire hazard. On one hand, growth and death of organs and individuals changes the amount of standing live and dead fuels, as well as downed dead fuels. On the other, day-to-day changes in soil and plant water content changes the physical properties of fuel, notably fuel moisture content.
medfate provides functions to estimate fuel
properties and potential fire behaviour in forest inventory plots.
fuel_stratification() estimates the
division of live fuels in the stand between understory and canopy
fuel_FCCS() calculates fuel characteristics
forest object following an adaptation of the
protocols described for the Fuel Characteristics Classification System
(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. 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 modification of the Rothermel’s (1972) model is used in
fire_FCCS() to calculate the intensity of surface
fire reaction and the rate of fire spread of surface fires assuming a
steady-state fire. Both quantities are dependent on fuel
characteristics, windspeed and direction, and topographic slope and
During the development of medfate some functions have been originally placed there and then moved to more specialized packages which evolve together with medfate:
The set of R packages are developed and maintained by the Ecosystem Modelling Facility at CREAF (Spain).