medfateland

Functions to simulate hydrology, forest functioning and dynamics over landscapes

https://github.com/emf-creaf/medfateland

Repository

Functions to simulate hydrology, forest functioning and dynamics over landscapes

README.Rmd

---
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 landscape simulation 

  [![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/medfateland)](https://cran.r-project.org/package=medfateland)
  [![](https://cranlogs.r-pkg.org/badges/medfateland)](https://cran.rstudio.com/web/packages/medfateland/index.html)
 [![R-CMD-check](https://github.com/emf-creaf/medfateland/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/emf-creaf/medfateland/actions)

## Introduction

The R package **medfateland** has been designed to extend the capabilities of package [**medfate**](https://emf-creaf.github.io/medfate/) to a spatially-explicit context. It allows running the stand-level models available in medfate on points and cells within landscape or region, including the possibility of parallelization. Additionally, medfateland allows considering seed dispersal and lateral water transfer processes in forested watersheds. Hence, medfateland can be used as a tool for eco-hydrological applications.   


## Package installation

Since both packages evolve together, installing **medfateland** normally requires an up-to-date version of [**medfate**](https://emf-creaf.github.io/medfate/). 

Package **medfateland** can be found at [CRAN](https://CRAN.R-project.org/package=medfateland), where it is updated every few months. Installation from CRAN can be done via:

```{r installation cran, eval = FALSE}
install.packages("medfateland")
```

Users can also download and install the latest stable versions GitHub as follows (required package `remotes` should be installed/updated first):

```{r installation, eval = FALSE}
remotes::install_github("emf-creaf/medfateland")
```


## Documentation and training

+ A number of *vignettes* illustrate how to initialize inputs and run simulation models in **medfateland**. These can be found [here](https://emf-creaf.github.io/medfateland/articles/). The user is also advised to read the articles about package **medfate** included [here](https://emf-creaf.github.io/medfate/articles/).

+ A complete documentation of both packages, including a *reference book*, can be found at https://emf-creaf.github.io/medfatebook/index.html. 

+ Presentation slides for a course devoted to process-based forest modelling using packages **medfate** and **medfateland** can be found [here](https://emf.creaf.cat/training/medfate_course/).

## Companion R packages

The modelling tools included in **medfate** and **medfateland** are closely developed with another package:

  + Package [**traits4models**](https://emf-creaf.github.io/traits4models) provides functions to help creating species parameter inputs for process-based models such as those in for **medfate** and **medfateland** functions.

Two other R 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 **medfateland** 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='60%', fig.align="center", echo=FALSE}
knitr::include_graphics("man/figures/institution_logos.png")
```

## Funding

+ **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.

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