Introduction

Package medfate is designed to assist forest scientists to simulate forest functioning and dynamics, using cohort-based description of forest stands. The package provides functions to simulate the following processes:

  • Soil water balance (De Cáceres et al. 2015)
  • Plant hydraulics, transpiration and photosynthesis (De Cáceres et al. 2021)
  • Plant growth (in preparation)
  • Forest dynamics (in preparation)

The models are parameterized for species of the Mediterranean region (particularly for Catalonia, NE Spain), but forests with different composition could be modelled with different parameter sets.

Package installation

Package medfate can be found at CRAN, where it is updated every few months. Users can also download and install the latest stable versions GitHub as follows (required package devtools should be installed/updated first):

devtools::install_github("emf-creaf/medfate")

Additionally, users can have help to run package functions directly as package vignettes, by forcing their inclusion in installation:

devtools::install_github("emf-creaf/medfate", 
                         build_opts = c("--no-resave-data", "--no-manual"),
                         build_vignettes = TRUE)

Documentation

  • The package includes a number of vignettes that illustrate how to run simulation models in medfate.

  • Additional articles can be found at the package website.

  • Complete documentation of the models included in the package can be found in medfate’s reference book.

Companion R packages

During the development of medfate some functions have been originally placed there and then moved to more specialized packages which no evolve together with medfate:

  • Package meteoland allows generating daily weather input for simulation models in medfate.
  • Package medfateland extends medfate by allowing simulations to be performed in a spatially explicit context.
  • Package medfateutils provides functions to help initializing vegetation, soil and species parameter inputs for medfate simulation functions.

References

  • De Cáceres M, Martínez-Vilalta J, Coll L, Llorens P, Casals P, Poyatos R, Pausas JG, Brotons L. (2015) Coupling a water balance model with forest inventory data to predict drought stress: the role of forest structural changes vs. climate changes. Agricultural and Forest Meteorology 213: 77-90 (https://doi.org/10.1016/j.agrformet.2015.06.012).

  • De Cáceres M, Mencuccini M, Martin-StPaul N, Limousin JM, Coll L, Poyatos R, Cabon A, Granda V, Forner A, Valladares F, Martínez-Vilalta J (2021) Unravelling the effect of species mixing on water use and drought stress in holm oak forests: a modelling approach. Agricultural and Forest Meteorology 296 (https://doi.org/10.1016/j.agrformet.2020.108233).