State FluSight 2019-2020

State FluSight: Seasonal Influenza Forecasting for US States

When and where flu increases will occur, how large the impact of the flu season will be, and when the flu season will peak varies from season to season, making the preparation for and response to the influenza seasons difficult. Flu forecasting can change that by offering the possibility to look into the future and better plan ahead, potentially reducing the impact of flu.

To help support the development of the science of flu forecasting and its application for public health, CDC, through the Epidemic Prediction Initiative (EPI), has organized FluSight challenges to forecast the timing, intensity, and short-term activity of the influenza season since the 2013-14 season. These challenges have provided the scientific and public health community experience in real-time forecasting, the ability to evaluate forecast accuracy, and experience in communicating and applying these forecasts in real-world settings. For example, forecasts are currently used to inform CDC’s activity summaries provided to public health officials and CDC leadership and public messaging regarding the timing of the influenza season and how the public can protect themselves and their family.

As part of the forecasting initiative, CDC has developed, through EPI, the “FluSight” flu forecasting website, which facilitates the real-time sharing and visualization of weekly flu forecasts. Visitors to this site can view current and past forecasts throughout the flu season for the peak week, peak intensity, and the near-term activity at the state level. ILINet data are generally updated every Friday, and forecasts are generally available by Tuesday. During the 2019–20 season, CDC expects forecasting teams to provide over 15 state-level forecasts each week.

Interested in participating in the challenge? Please email flucontest@cdc.gov for more information.

Use the interactive tool below to explore submitted forecasts for the 2019–2020 influenza season. Click throughout the season to examine forecasts received during a given week. To see the most recent forecasts, click the forecast week immediately preceeding the dotted "Today" line.

Peak week and intensity predictions are visualized by the stand-alone dots with confidence intervals, and week-ahead forecasts are visualized as the connected dots with confidence bands. States or jurisdictions can be selected using the dropdown menu on # Submitted forecasts the right side of the graph. Please note that forecasts will not display on Internet Explorer.

Florida does not share its ILINet data through CDC's FluView Interactive. Therefore, forecasts for Florida are unavailable. To view a summary of Florida’s ILINet data (along with viewing other available data on flu and ILI), please visit www.floridahealth.gov/floridaflu or reach out to the Florida Department of Health directly at (850) 245-4444.

Forecasts for the 2019-2020 influenza season will be available in late fall 2019.

Forecast Targets

For each week during the season, participants will be asked to provide state-level probabilistic forecasts for the entire influenza season (seasonal targets) and for the next four weeks (four-week ahead targets). The seasonal targets are the peak week and the peak intensity of the 2019-2020 influenza season for each state being forecast. The four-week ahead targets are the percent of outpatient visits experiencing influenza-like illness (ILI) one week, two weeks, three weeks, and four weeks ahead from date of the forecast.

Seasonal Peak Week

Definition The peak week will be defined as the MMWR surveillance week that the weighted ILINet percentage is the highest in a given state for the 2019-2020 influenza season.

Motivation Accurate and timely forecasts for the peak week can be useful for planning and promoting activities to increase influenza vaccination prior to the bulk of influenza illness. For healthcare, pharmacy, and public health authorities, a forecast for the peak week can guide efficient staff and resource allocation.

Seasonal Peak Intensity

Definition The intensity will be defined as the highest numeric value, rounded to one decimal place, that the weighted ILINet percentage reaches during the 2019-2020 influenza season.

Motivation Accurate and timely forecasts for the peak week and intensity of the influenza season can be useful for influenza prevention and control, including the planning and promotion of activities to increase influenza vaccination prior to the bulk of influenza illness. For healthcare, pharmacy, and public health authorities, a forecast for the peak week and intensity can help with appropriate staff and resource allocation since a surge of patients with influenza illness can be expected to seek care and receive treatment in the weeks surrounding the peak.

Short Term Forecasts

Definition One- to four-week ahead forecasts will be defined as the weighted ILINet percentage for the target week, rounded to one decimal place.

Motivation Forecasts capable of providing reliable estimates of influenza activity over the next month are critical because they allow healthcare and public health officials to prepare for and respond to near-term changes in influenza activity and bridge the gap between reported incidence data and long-term seasonal forecasts.

State ILI and laboratory data

Data on the weekly proportion of people seeing their health-care provider for influenza-like illness (ILI) is reported through the ILINet System for the United States as a whole, for each HHS health region, and for most individual US States. These data can be accessed directly from CDC. Alternatively, the R package cdcfluview (available from CRAN or GitHub) can be used to access the data as shown in the following example

# Option 1: Install from CRAN
install.packages("cdcfluview")

# Option 2: Install from GitHub (most up-to-date version)
devtools::install_github("hrbrmstr/cdcfluview")

library(cdcfluview)

# National ILINet data for 1997/98 - 2019/29 seasons
usflu <- get_flu_data(region = "national", data_source = "ilinet", years = 1997:2019)

# HHS Regional ILINet data for 1997/98 - 2019/20 seasons
regionflu <- get_flu_data(region = "HHS", sub_region = 1:10, data_source = "ilinet", years = 1997:2019)

# State ILINet data for 1997/98 - 2019/20 seasons  --  only available via GitHub version
stateflu <- get_flu_data(region = "state", sub_region = "all", data_source = "ilinet", years = 1997:2019)

Please note that while cdcfluview accesses publically available CDC data, it is not produced, maintained, or endorsed by the CDC.

For those states that have not publically released their data, participating teams can access state-level reports of influenza like illness as well as clinical and public health laboratory data through the "State ILI data" tab at left. This tab is only accessible to participating teams - if you would like to participate please email flucontest@cdc.gov for more information!

Additional Data

Teams are welcome to use data sources for model development beyond the provided data - possible additional data sources include but are not limited to:

Forecast Evaluation

All forecasts will be evaluated using the weighted observations pulled from the ILINet system in week 28, and the logarithmic score will be used to measure the accuracy of the probability distribution of a forecast. Logarithmic scores will be averaged across different time periods, the seasonal targets, the four-week ahead targets, and locations to provide both specific and generalized measures of model accuracy. Official rankings of teams by forecast accuracy will only be based on the log score. Nonetheless, forecasters are requested to continue to submit point predictions, which should aim to minimize the absolute error (AE). CDC may report on the accuracy of point predictions in manuscripts and analyses.

Logarithmic Score

If ;;\mathbf{p};; is the set of probabilities for a given forecast, and ;;\mathbf{p_i};; is the probability assigned to the observed outcome ;;i;;, the logarithmic score is:

$$S(\mathbf{p},i) = \text{ln}(p_i)$$

For each forecast of each target, ;;\mathbf{p_i};; will be set to the probability assigned to the single bin containing the observed outcome (based on the rounded weighted ILINet value). For the peak week target, in the case of multiple peak weeks, the probability assigned to the bins containing each peak week will be summed.

Undefined natural logs (which occur when the probability assigned to the observed outcome was 0) will be assigned a value of -10. Forecasts which are not submitted (e.g. if a week is missed) or that are incomplete (e.g. sum of probabilities greater than 1.1) will also be assigned a value of -10.

In addition to the final scores, CDC may provide interim score reports to participants on a semi-regular basis during the season. Interim scores will not impact final team standings.

Example: A forecast predicts, for a given state, there is a probability of 0.3 (i.e., a 30% chance) that peak week is on week 6, with the remaining 0.7 probability distributed across the other weeks. Once the flu season has started, the prediction can be evaluated, and the ILINet data show that the peak week for this given state was on week 6. The probability assigned to week 6, 0.3, would be derived, and the forecast would receive a score of log(0.3) = -1.20. If the peak occurred on another week, the score would be calculated on the probability assigned to that week.

References

FluSight Package

The FluSight R package contains functions to help create and format forecasts, read and verify forecast CSVs, and score forecasts. These are the functions that will be used at CDC to verify and score submitted forecasts. Teams are welcome to use these tools to ensure their forecasts fit the required template and score their forecasts prior to receiving official scores from CDC

The package can be downloaded from GitHub.

Install and load package
devtools::install_github("jarad/FluSight")
library(FluSight)
Read in state forecast entry CSV
entry <- read_entry("your_csv.csv", challenge = "state_ili")
Verify entry
verify_entry(entry, challenge = "state_ili")
verify_entry_file("your_csv.csv", challenge = "state_ili")
Create file of observed truth
truth <- create_truth(fluview = T, year = 2018, challenge = "state_ili")
Score a weekly entry against the observed truth
exact_scores <- score_entry(entry, truth, challenge = "state_ili")
Guidance Documents

Guidelines for the 2019-20 State FluSight challenge can be found here

The submission document for the 2019-20 State FluSight challenge can be found here

The intructions for registering your model(s) and submitting forecasts can be found here.

Model Questionnaire

Each team must submit a copy of this form to CDC (flucontest@cdc.gov) by November 15, 2019. The completed form should contain a seperate entry for each model your team submits. If your team implements changes to a model during the challenge, please submit an updated form.