erahumed

The {erahumed} R package implements the ERAHUMED Decision Support System, a modelling framework for assessing hydrology, pesticide exposure, and ecological risk in the Albufera Natural Park (València, Spain). It integrates models that simulate water flows, contaminant transport, and biological effects across the park’s interconnected water bodies.

With {erahumed}, users can:

• Configure simulations – Define landscape, chemical, and management parameters, or use built-in presets for rapid setup.

• Run the model – Execute hydrology, exposure, and risk assessment modules in a reproducible R workflow.

• Analyse outputs – Retrieve results as tidy data.frames, ready for statistical analysis or visualization.

• Explore interactively – Launch a bundled Shiny application with predefined plots, maps, and tables for model inputs and results.

The package is designed for both research and practical decision-making, enabling transparent scenario analysis and reproducible environmental assessments.

Comprehensive resources are available to support users at different levels:

• The package documentation covers the R functions, datasets, and Shiny interface bundled with {erahumed}.

• The user manual provides an in-depth description of the underlying models, algorithms, and assumptions.

Further background on the ERAHUMED project can be found on the main project website.

Installation

You can install the latest release of {erahumed} from GitHub, by running the following command in R:

install.packages("remotes")  # If necessary
remotes::install_github("erahumed/erahumed")

Version compatibility

Versions of {erahumed} follow standard semantic versioning. If you encounter issues running code written for an earlier version of {erahumed} with your current installation, you may consider installing the specific version the code was developed with.

To install a particular version of {erahumed}, use:

remotes::install_github("erahumed/erahumed", ref = "vX.Y.Z")

where "vX.Y.Z" should be replaced with the desired version number.

Usage

Example 1: Using the interactive dashboard

The graphical interface to the ERAHUMED DSS can be accessed through the following R command:

erahumed::launch_dss()

This will open the DSS dashboard in your default browser, from where you can explore simulation outputs in a user-friendly manner.

Example 2: Command-line interface to simulations

library(erahumed)

The following example illustrates the workflow for manually running the ERAHUMED simulation chain, and extracting the outputs of the various simulation layers. For more detailed information, see the main package vignette.

Simulations are run via:

simulation <- erahumed_simulation()
#> Initializing inputs
#> Computing hydrology: lake
#> Computing hydrology: clusters
#> Computing hydrology: ditches
#> Computing exposure: clusters
#> Computing exposure: ditches
#> Computing exposure: lake
#> Computing risk: clusters
#> Computing risk: ditches
#> Computing risk: lake

where simulation inputs can be customized through the arguments of erahumed_simulation(). Results can be inspected through:

get_results(simulation, 
            component = "exposure",  # either "hydrology", "exposure", or "risk"  
            element = "lake"         # either "lake", "ditch", or "cluster"
            ) |>
  head()
#>   element_id       date mf_kg mw_kg ms_kg mw_outflow_kg cw_kg_m3 cs_kg_m3
#> 1       lake 2023-01-01     0     0     0             0       NA        0
#> 2       lake 2023-01-02     0     0     0             0        0        0
#> 3       lake 2023-01-03     0     0     0             0        0        0
#> 4       lake 2023-01-04     0     0     0             0        0        0
#> 5       lake 2023-01-05     0     0     0             0        0        0
#> 6       lake 2023-01-06     0     0     0             0        0        0
#>   cs_g_kg cw_outflow_kg_m3 volume_m3 outflow_m3    chemical
#> 1       0                0        NA     406452 Acetamiprid
#> 2       0                0  27170258     743304 Acetamiprid
#> 3       0                0  27081533     738990 Acetamiprid
#> 4       0                0  26992808     587238 Acetamiprid
#> 5       0                0  26966519     724464 Acetamiprid
#> 6       0                0  26928729     390420 Acetamiprid

Getting help

The full documentation of the {erahumed} R package is hosted at erahumed.github.io/erahumed.

If you have issues running {erahumed} or want to suggest an improvement, please file an issue on GitHub.