The goal of hubExamples is to provide example data for forecasting and scenario modeling hubs in the hubverse format.
This package is part of the hubverse ecosystem, which aims to provide a set of tools for infectious disease modeling hubs to share and collaborate on their work.
Installation
Latest
You can install the latest version of hubExamples from the R-universe:
install.packages("hubExamples", 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 hubExamples from GitHub with:
# install.packages("remotes")
remotes::install_github("hubverse-org/hubExamples")Example forecast hub data
The package provides three data sets that contain example model output and target data for an example forecast hub: forecast_outputs, forecast_target_ts, and forecast_target_observations. Please see the package documentation for further information about these data objects.
library(hubExamples)
head(forecast_outputs)
#> model_id reference_date target horizon location
#> 1 Flusight-baseline 2022-11-19 wk inc flu hosp 0 25
#> 2 Flusight-baseline 2022-11-19 wk inc flu hosp 0 25
#> 3 Flusight-baseline 2022-11-19 wk inc flu hosp 0 25
#> 4 Flusight-baseline 2022-11-19 wk inc flu hosp 0 25
#> 5 Flusight-baseline 2022-11-19 wk inc flu hosp 0 25
#> 6 Flusight-baseline 2022-11-19 wk inc flu hosp 0 25
#> target_end_date output_type output_type_id value
#> 1 2022-11-19 quantile 0.05 22
#> 2 2022-11-19 quantile 0.1 31
#> 3 2022-11-19 quantile 0.25 45
#> 4 2022-11-19 quantile 0.5 51
#> 5 2022-11-19 quantile 0.75 57
#> 6 2022-11-19 quantile 0.9 71
head(forecast_target_ts)
#> date location observation
#> 1 2020-01-11 01 0
#> 2 2020-01-11 15 0
#> 3 2020-01-11 18 0
#> 4 2020-01-11 27 0
#> 5 2020-01-11 30 0
#> 6 2020-01-11 37 0
head(forecast_target_observations)
#> location target_end_date target output_type output_type_id
#> 1 US 2022-10-22 wk inc flu hosp quantile <NA>
#> 2 01 2022-10-22 wk inc flu hosp quantile <NA>
#> 3 02 2022-10-22 wk inc flu hosp quantile <NA>
#> 4 04 2022-10-22 wk inc flu hosp quantile <NA>
#> 5 05 2022-10-22 wk inc flu hosp quantile <NA>
#> 6 06 2022-10-22 wk inc flu hosp quantile <NA>
#> observation
#> 1 2380
#> 2 141
#> 3 3
#> 4 22
#> 5 50
#> 6 124Example scenario hub data
The package provides two data sets that contain example model output and target data for an example scenario hub: scenario_outputs and scenario_target_ts. Please see the package documentation for further information about these data objects.
head(scenario_outputs)
#> model_id origin_date scenario_id location target horizon
#> 1 HUBuni-simexamp 2021-03-07 A-2021-03-05 US inc case 1
#> 2 HUBuni-simexamp 2021-03-07 A-2021-03-05 US inc case 1
#> 3 HUBuni-simexamp 2021-03-07 A-2021-03-05 US inc case 1
#> 4 HUBuni-simexamp 2021-03-07 A-2021-03-05 US inc case 1
#> 5 HUBuni-simexamp 2021-03-07 A-2021-03-05 US inc case 1
#> 6 HUBuni-simexamp 2021-03-07 A-2021-03-05 US inc case 1
#> output_type output_type_id value
#> 1 quantile 0.010 292495.9
#> 2 quantile 0.025 308584.4
#> 3 quantile 0.050 312990.6
#> 4 quantile 0.100 327375.0
#> 5 quantile 0.150 337199.4
#> 6 quantile 0.200 345255.6
head(scenario_target_ts)
#> location date observation target
#> 1 US 2020-10-03 300678 inc case
#> 2 US 2020-10-10 334493 inc case
#> 3 US 2020-10-17 388282 inc case
#> 4 US 2020-10-24 484422 inc case
#> 5 US 2020-10-31 571389 inc case
#> 6 US 2020-11-07 776479 inc caseCode of Conduct
Please note that the hubExamples 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 hubExamples package.