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hubVis

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The goal of hubVis is to provide plotting methods for hub model outputs, following the hubverse format. The hubverse is a collection of open-source software and data tools, developed by the Consortium of Infectious Disease Modeling Hubs. For more information, please consult the hubDocs website

Installation

Latest

You can install the latest version of hubVis from the R-universe:

install.packages("hubVis", repos = c("https://hubverse-org.r-universe.dev", "https://cloud.r-project.org"))

Development

If you want to test out new features that have not yet been released, you can install the development version of hubVis from GitHub with:

remotes::install_github("hubverse-org/hubVis")

Usage

The R package contains currently one function plot_step_ahead_model_output() plotting 50%, 80%, and 95% quantiles intervals, with a specific color per “model_id”.

The function can output 2 types of plots:

  • interactive (Plotly object)
  • static (ggplot2 object)
library(hubExamples)
head(scenario_outputs)
head(scenario_target_ts)
projection_data <- dplyr::mutate(scenario_outputs,
     target_date = as.Date(origin_date) + (horizon * 7) - 1)

target_data_us <- dplyr::filter(scenario_target_ts, location == "US",
                                date < min(projection_data$target_date) + 21,
                                date > "2020-10-01")
projection_data_us <- dplyr::filter(projection_data,
                                    scenario_id == "A-2021-03-05",
                                    location == "US")
plot_step_ahead_model_output(projection_data_us, target_data_us)

Faceted plots can be created for multiple scenarios, locations, targets, models, etc.

projection_data_us <- dplyr::filter(projection_data,
                                    location == "US")
plot_step_ahead_model_output(projection_data_us, target_data_us, 
                             use_median_as_point = TRUE,
                             facet = "scenario_id", facet_scales = "free_x", 
                             facet_nrow = 2, facet_title = "bottom left")

Code of Conduct

Please note that the hubVis package is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

Contributing

Interested in contributing back to the open-source Hubverse project? Learn more about how to get involved in the Hubverse Community or how to contribute to the hubVis package.