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erahumed

The erahumed R package provides the infrastructure for the ERAHUMED Decision Support System (DSS), that consists of:

  • Data: The DSS inputs are pre-packaged as R data.frames and seamlessly imported with erahumed.
  • Analysis. The entire simulation workflow is implemented as a set of R functions, enabling flexible and reproducible analysis.
  • Outputs. Simulation results are returned as well-structured data.frames, ready for further exploration and processing in R.
  • Interactive Interface. A Shiny-based graphical interface, with predefined visualizations for model outputs, is bundled with the package, allowing users to interactively explore the results.

More information on the ERAHUMED project can be found on the main project’s website. The full documentation of the erahumed R package is hosted at erahumed.github.io/erahumed.

Installation

You can install the latest release of erahumed from Github, by running the following command in your local R session:

install.packages("remotes")  # If necessary
remotes::install_github("erahumed/erahumed", ref = remotes::github_release())

If you want the development version (notice: this may be unstable), simply omit the reference:

remotes::install_github("erahumed/erahumed")  # development version

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

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(
  date_start = "2020-01-01",
  date_end = "2020-12-31",
  variety_prop = c(J.Sendra = 0.7, Bomba = 0.15, Clearfield = 0.15)
)

where the parameters of the simulation are set through the arguments of erahumed_simulation() (see ?erahumed_simulation or this article for a full list of parameters.

Results can be inspected through:

get_results(simulation, 
            component = "exposure",  # either "hydrology", "exposure", or "risk"  
            element = "lake"         # either "lake", "ditch", or "cluster"
            ) |>
  head()
#>         date    chemical mf_kg mw_kg ms_kg cw_kg_m3 cw_outflow_kg_m3 cs_kg_m3
#> 1 2020-01-01 Acetamiprid     0     0     0       NA                0        0
#> 2 2020-01-02 Acetamiprid     0     0     0        0                0        0
#> 3 2020-01-03 Acetamiprid     0     0     0        0                0        0
#> 4 2020-01-04 Acetamiprid     0     0     0        0                0        0
#> 5 2020-01-05 Acetamiprid     0     0     0        0                0        0
#> 6 2020-01-06 Acetamiprid     0     0     0        0                0        0
#>   cs_g_kg volume_m3 element_id
#> 1       0        NA       lake
#> 2       0  27344422       lake
#> 3       0  27397000       lake
#> 4       0  27456150       lake
#> 5       0  27479153       lake
#> 6       0  27397000       lake

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.

An internal documentation, aimed at potential contributors to this project, is available at Github Wiki.