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README.Rmd
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README.Rmd
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---
title: "medfate - Mediterranean Forest Simulation"
output: github_document
---
```{r setup, echo = FALSE}
knitr::opts_chunk$set(collapse = TRUE, comment = "#>", fig.path = "README-")
knitr::opts_chunk$set(fig.path = "man/figures/")
```
[](https://cran.r-project.org/package=medfate)
[](https://cran.rstudio.com/web/packages/medfate/index.html)
[](https://github.com/emf-creaf/medfate/actions)
## 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, Ruffault et al. 2022)
+ Carbon balance, plant growth, senescence and mortality (De Cáceres et al. 2023)
+ Forest dynamics, including recruitment and management (De Cáceres et al. 2023)
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 & documentation
Package **medfate** can be found at [CRAN](https://CRAN.R-project.org/package=medfate), where it is updated every few months. Installation from CRAN can be done via:
```{r installation cran, eval = FALSE}
install.packages("medfate")
```
Users can also download and install the latest stable versions GitHub as follows (required package `remotes` should be installed/updated first):
```{r installation github, eval = FALSE}
remotes::install_github("emf-creaf/medfate")
```
A number of *vignettes* illustrate how to run simulation models in **medfate**. These, and additional articles regarding parameter estimation and model evaluation can be found at the package [website](https://emf-creaf.github.io/medfate/).
A complete documentation of the models included in the package can be found in [medfate's reference book](https://emf-creaf.github.io/medfatebook/index.html).
## Companion R packages
During the development of **medfate** some functions have been originally placed there and then moved to more specialized packages which evolve together with **medfate**:
+ Package [**meteoland**](https://github.com/emf-creaf/meteoland) allows generating daily weather input for simulation models in **medfate**.
+ Package [**medfateland**](https://github.com/emf-creaf/medfateland) extends **medfate** by allowing simulations to be performed in a spatially explicit context.
+ Package [**medfateutils**](https://github.com/emf-creaf/medfateutils) provides functions to help initializing vegetation, soil and species parameter inputs for **medfate** simulation functions.
## Authorship
The set of R packages are developed and maintained by the [*Ecosystem Modelling Facility*](https://emf.creaf.cat) unit at [*CREAF*](https://www.creaf.cat/) (in Spain), in close collaboration with researchers from [*URFM-INRAE*](https://www6.paca.inrae.fr/ecologie_des_forets_mediterraneennes/) (in France) and [*CTFC*](https://www.ctfc.cat/) (in Spain).
```{r, out.width='60%', fig.align="center", echo=FALSE}
knitr::include_graphics("man/figures/logos.png")
```
## 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).
+ Ruffault J, Pimont F, Cochard H, Dupuy JL, Martin-StPaul N (2022) SurEau-Ecos v2.0: a trait-based plant hydraulics model for simulations of plant water status and drought-induced mortality at the ecosystem level. Geoscientific Model Development 15, 5593-5626 (https://doi.org/10.5194/gmd-15-5593-2022).
+ De Cáceres M, Molowny-Horas R, Cabon A, Martínez-Vilalta J, Mencuccini M, García-Valdés R, Nadal-Sala D, Sabaté S, Martin-StPaul N, Morin X, D'Adamo F, Batllori E, Améztegui A (2023) MEDFATE 2.9.3: A trait-enabled model to simulate Mediterranean forest function and dynamics at regional scales. Geoscientific Model Development 16, 3165–3201 (https://doi.org/10.5194/gmd-16-3165-2023).