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README.Rmd
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README.Rmd
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---
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/")
```
# Mediterranean forest simulation <a href="https://emf-creaf.github.io/medfate/"><img src="man/figures/logo.png" align="right" height="139" alt="medfate website" /></a>
[](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 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 were originally placed there but then moved to more specialized packages which evolve together with **medfate**:
+ Package [**medfateland**](https://emf-creaf.github.io/medfateland) extends **medfate** by allowing simulations to be performed in a spatially explicit context.
+ Package [**traits4models**](https://emf-creaf.github.io/traits4models) provides functions to help creating species parameter inputs for **medfate** and **medfateland** simulation functions.
Two other packages complete the simulation framework, but can be used for many other purposes beyond forest modelling:
+ Package [**meteoland**](https://emf-creaf.github.io/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**](https://emf-creaf.github.io/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.
```{r, out.width='80%', fig.align="center", echo=FALSE}
knitr::include_graphics("man/figures/packages.png")
```
## Authorship
Package **medfate** is 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='50%', fig.align="center", echo=FALSE}
knitr::include_graphics("man/figures/institution_logos.png")
```
## Funding
+ **Fellowship**: *Ramon y Cajal* research fellowship to M. De Cáceres. **Financial Entity**: Ministerio de Economía y Competitividad ( RYC-2012-11109). **Duration from**: 01/01/2013 **to**: 31/12/2018.
+ **Research project**: Forecasting of ecosystem services on forests: impacts and adaptation to extreme climate events (FORESTCAST). **Financial Entity**: Ministerio de Economia y Competitividad (CGL2014-59742-C2-2-R). **Duration from**: 01/01/2015 **to**: 31/12/2017. **PI**: Lluís Brotons/Miquel De Cáceres.
+ **Research project**: Modeling plant water use and drought resistance strategies across scales (DRESS). **Financial Entity**: Ministerio de Economia y Competitividad (CGL2017-89149-C2-2-R). **Duration from**: 01/01/2018 **to**: 31/12/2021. **PI**: Miquel De Cáceres.
+ **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.
## 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).