README

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hubEvals

The goal of hubEvals is to provide tools for evaluating infectious disease model outputs. This package is part of the Hubverse project, which aims to provide a suite of tools for infectious disease modeling hubs.

Installation

Latest

install.packages("hubEvals", 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 hubEvals from GitHub with:

# install.packages("remotes")
remotes::install_github("hubverse-org/hubEvals")

Example

Predictions can be evaluated directly using the scoring function in hubEvals, which assumes a hubverse format for the model outputs and target data:

library(hubEvals)

# compute default metrics (in this case, absolute error) for
# median forecasts, summarized by the mean score for each model
median_scores <- score_model_out(
  model_out_tbl = hubExamples::forecast_outputs |>
    dplyr::filter(output_type == "median"), # only one output type allowed
  oracle_output = hubExamples::forecast_oracle_output,
  by = "model_id"
)
median_scores
#>             model_id ae_point
#>               <char>    <num>
#> 1: Flusight-baseline  401.875
#> 2:   MOBS-GLEAM_FLUH  416.375
#> 3:          PSI-DICE  277.000

# compute WIS and interval coverage rates at 80% and 90% levels based on
# quantile forecasts, summarized by the mean score for each model
quantile_scores <- score_model_out(
  model_out_tbl = hubExamples::forecast_outputs |>
    dplyr::filter(output_type == "quantile"), # only one output type allowed
  oracle_output = hubExamples::forecast_oracle_output,
  metrics = c("wis", "interval_coverage_80", "interval_coverage_90"),
  relative_metrics = "wis",
  by = "model_id"
)
quantile_scores
#> Key: <model_id>
#>             model_id      wis interval_coverage_80 interval_coverage_90 wis_relative_skill
#>               <char>    <num>                <num>                <num>              <num>
#> 1: Flusight-baseline 329.4545                  0.0               0.1250          1.1473659
#> 2:   MOBS-GLEAM_FLUH 315.2393                  0.5               0.5625          1.0978597
#> 3:          PSI-DICE 227.9527                  0.5               0.5000          0.7938733

# compute log scores based on pmf predictions for categorical targets,
# summarized by the mean score for each combination of model and location.
# Note: if the model_out_tbl had forecasts for multiple targets using a
# pmf output_type with different bins, it would be necessary to score the
# predictions for those targets separately.
pmf_scores <- score_model_out(
  model_out_tbl = hubExamples::forecast_outputs |>
    dplyr::filter(output_type == "pmf"), # only one output type allowed
  oracle_output = hubExamples::forecast_oracle_output,
  metrics = c("log_score", "rps"),
  by = c("model_id", "location", "horizon"),
  output_type_id_order = c("low", "moderate", "high", "very high")
)
head(pmf_scores)
#>             model_id location horizon   log_score          rps
#>               <char>   <char>   <int>       <num>        <num>
#> 1: Flusight-baseline       25       0  0.02107606 0.0008531043
#> 2: Flusight-baseline       25       1  6.69652380 0.5029240066
#> 3: Flusight-baseline       25       2 17.73313203 1.0057355863
#> 4: Flusight-baseline       25       3         Inf 1.8665126816
#> 5: Flusight-baseline       48       0  2.18418007 0.4873966597
#> 6: Flusight-baseline       48       1  7.49960792 0.9659026096

Sample forecasts can be scored marginally (each modeling task scored independently) or jointly using compound scoring:

# marginal sample scoring with CRPS
sample_scores <- hubExamples::forecast_outputs |>
  dplyr::filter(output_type == "sample") |>
  score_model_out(
    oracle_output = hubExamples::forecast_oracle_output,
    metrics = "crps",
    by = "model_id"
  )
sample_scores
#>             model_id     crps
#>               <char>    <num>
#> 1: Flusight-baseline 351.5887
#> 2:   MOBS-GLEAM_FLUH 347.1502
#> 3:          PSI-DICE 247.3640

Compound scoring uses the energy score to evaluate the joint distribution across task dimensions that vary within a sample draw. The compound_taskid_set specifies which task IDs stay constant within a sample group and can be found by referencing the hub’s tasks.json configuration file. Here, each draw spans all horizons for a given reference date and location (i.e., a trajectory over time).

compound_scores <- hubExamples::forecast_outputs |>
  dplyr::filter(output_type == "sample") |>
  score_model_out(
    oracle_output = hubExamples::forecast_oracle_output,
    compound_taskid_set = c("reference_date", "location"),
    by = "model_id"
  )
compound_scores
#>             model_id energy_score variogram_score
#>               <char>        <num>           <num>
#> 1: Flusight-baseline     772.7608        1524.474
#> 2:   MOBS-GLEAM_FLUH     811.4625        1695.037
#> 3:          PSI-DICE     571.0879        1264.238

Or, users may transform predictions into a forecast object that can be used as an input to scoringutils functions and use their tooling directly.

median_forecast <- transform_point_model_out(
  model_out_tbl = hubExamples::forecast_outputs |>
    dplyr::filter(output_type == "median"),
  oracle_output = hubExamples::forecast_oracle_output,
  output_type = "median"
)
median_forecast

quantile_forecast <- transform_quantile_model_out(
  model_out_tbl = hubExamples::forecast_outputs |>
    dplyr::filter(output_type == "quantile"),
  oracle_output = hubExamples::forecast_oracle_output
)
quantile_forecast

pmf_forecasts <- transform_pmf_model_out(
  model_out_tbl = hubExamples::forecast_outputs |>
    dplyr::filter(output_type == "pmf"),
  oracle_output = hubExamples::forecast_oracle_output,
  output_type_id_order = c("low", "moderate", "high", "very high")
)
pmf_forecasts

sample_forecast <- hubExamples::forecast_outputs |>
  dplyr::filter(output_type == "sample") |>
  transform_sample_model_out(
    oracle_output = hubExamples::forecast_oracle_output
  )
sample_forecast

Code of Conduct

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

Contributing

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.