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README.Rmd
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README.Rmd
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---
output: github_document
---
<!-- Edit the README.Rmd only!!! The README.md is generated automatically. -->
```{r echo=FALSE}
knitr::opts_chunk$set(
comment = '#>',
collapse = TRUE,
warning = FALSE,
message = FALSE,
eval = FALSE,
cache = FALSE
)
```
fuse: an R package implementing the Framework for Understanding Structural Errors
=================================================================================
[](https://zenodo.org/badge/latestdoi/67341718) [](http://joss.theoj.org/papers/392a55daada04a86f95eaa8da134a28d)
[](https://travis-ci.org/cvitolo/fuse.svg?branch=master) [](https://ci.appveyor.com/project/cvitolo/fuse) [](https://codecov.io/github/cvitolo/fuse?branch=master)
The Framework for Understanding Structural Errors (FUSE) was developed by Clark et al. (2008) and is a state-of-the-art modelling toolbox. It includes 1248 hydrological model structures, amongst which some well established models for rainfall-runoff simulations (i.e. PRMS, SACRAMENTO, TOPMODEL and ARNO/VIC, also defined as parent models). Each model is characterised by a different architecture of the upper and lower soil layers and parameterisation of processes such as: evaporation, vertical percolation, interflow, base flow and surface runoff.
Fuse takes as input rainfall and potential evapotranspiration time series (areal averages over the river catchment area) and returns a simulated time series of river discharges. It can be used to understand the variability of expected hydrological responses based on model structures.
This package is a re-implementation of the framework described in Clark et al. (2008) and based on the Fortran code provided by M. Clark in 2011. The package consists of two modules: Soil Moisture Accounting module (fusesma.sim) and Gamma routing module (fuserouting.sim). It also contains default parameter ranges (fusesma.ranges and fuserouting.ranges) and three data objects: fuse\_hydrological\_timeseries (sample input dataset), parameters (sample parameters) and modlist (list of FUSE model structures).
### Dependencies
The fuse package, as well as the examples in the vignette, depend on a number of CRAN packages. Check for missing dependencies and install them:
```{r}
packs <- c("dplyr", "zoo", "tgp", "stats", "utils", "BH", "Rcpp", "testthat",
"qualV", "devtools")
new.packages <- packs[!(packs %in% installed.packages()[, "Package"])]
if(length(new.packages)) install.packages(new.packages)
```
### Installation
You can install this package from Github with [devtools](https://github.com/hadley/devtools):
```{r}
devtools::install_github("cvitolo/fuse")
```
Load the package:
```{r}
library("fuse")
```
### Usage
The simplest way to test `fuse` is to use the dummy data provided with this package, sample the parameter range using the built-in function `generateParameters()` and run the model with 1 model structure (e.g. TOPMODEL):
```{r}
# Load the dummy data
data(fuse_hydrological_timeseries)
# Sample the parameter range
parameters <- generateParameters(1)
# Run fuse
streamflow <- fuse(DATA = fuse_hydrological_timeseries,
mid = 60, # Model structure = TOPMODEL
deltim = 1, # Daily time step
ParameterSet = parameters)
plot(streamflow, xlab = "", ylab = "Streamflow [mm/day]")
```
For details and more complex examples (e.g. multi-model ensemble), please refer to the [vignette](https://cvitolo.github.io/fuse/articles/fuse_vignette.html).
Fortran users are advised to refer to the latest version of fuse available [here](https://github.com/naddor/fuse).
### Meta
- Code contributions are welcome! Please note that this project is released with a [Contributor Code of Conduct](CONDUCT.md). By participating in this project you agree to abide by its terms.
- Please [report any issues or bugs](https://github.com/cvitolo/fuse/issues).
- License: [GPL-3](https://opensource.org/licenses/GPL-3.0)
- Get citation information for the `fuse` package in R doing `citation(package = 'fuse')`
- This package was reviewed by [Maëlle Salmon](https://github.com/masalmon) for the Journal of Open Source Software, see review [here](https://github.com/openjournals/joss-reviews/issues/52).