Background

• Covid-19 Pandemic required quickly implementing forecasting systems.

• Basic processing—outlier detection, reporting issues, geographic granularity—implemented in parallel / error prone

• Data revisions complicate evaluation

• Simple models often outperformed complicated ones

• Custom software not easily adapted / improved by other groups

• Hard for public health actors to borrow / customize community techniques

{epiprocess}

Basic processing operations and data structures

• General EDA for “panel data”
• Calculate rolling statistics
• Fill / impute gaps
• Examine correlations
• Store revision history smartly
• Inspect revision patterns
• Find / correct outliers

{epiprocess} Data Structures

epi_df: snapshot of a data set

• a tibble with a couple of required columns, geo_value and time_value.
• arbitrary additional columns containing “measured” values, called “signals”
• additional “keys” that index subsets (age_group, ethnicity, etc.)

{epiprocess} Data Structures

epi_archive: collection of epi_dfs

• full version history of a data set
• acts like a bunch of epi_dfs
• but stored “compactly”
• Allows you to do things you would do on an epi_df but based on the data that “would have been available at the time”

Revision patterns

Simple sliding computations

dav14 <- jhu_csse_daily_subset %>%
  group_by(geo_value) %>%
  epi_slide(cases_14dav = mean(cases), n = 14)

{epipredict}

+ Framework for customizing from modular components.

1. Preprocessor: do things to the data before model training
2. Trainer: train a model on data, resulting in an object
3. Predictor: make predictions, using a fitted model object
4. Postprocessor: do things to the predictions before returning

Making dumb (but useful!) forecasts in epidemiology

• Suppose we want to predict new hospitalizations \(y\), \(h\) days ahead, at many locations \(j\).

• We’re going to make a new forecast each week.

{epipredict}

A forecasting framework

• Flatline forecaster
• AR-type models
• Backtest using the versioned data
• Easily create features
• Quickly pivot to new tasks
• Highly customizable for advanced users

{epipredict}

Canned forecasters that work out of the box.

You can do a limited amount of customization.

We currently provide:

• Baseline flat-line forecaster
• Autoregressive-type forecaster
• Autoregressive-type classifier

Basic autoregressive forecaster

• Predict death_rate, 1 week ahead, with 0,7,14 day lags of cases and deaths.
• Use lm for estimation. Also create “intervals”.

library(epipredict)
jhu <- case_death_rate_subset # grab some built-in data
canned <- arx_forecaster(
  epi_data = jhu, 
  outcome = "death_rate", 
  predictors = c("case_rate", "death_rate")
)

The output is a model object that could be reused in the future, along with the predictions for 7 days from now.

Adjust lots of built-in options

rf <- arx_forecaster(
  epi_data = jhu, 
  outcome = "death_rate", 
  predictors = c("case_rate", "death_rate", "fb-survey"),
  trainer = parsnip::rand_forest(mode = "regression"), # use ranger
  args_list = arx_args_list(
    ahead = 14, # 2-week horizon
    lags = list(c(0:4, 7, 14), c(0, 7, 14), c(0:7, 14)), # bunch of lags
    levels = c(0.01, 0.025, 1:19/20, 0.975, 0.99), # 23 ForecastHub quantiles
    quantile_by_key = "geo_value" # vary q-forecasts by location
  )
)

Do (almost) anything manually

# A preprocessing "recipe" that turns raw data into features / response
r <- epi_recipe(jhu) %>%
  step_epi_lag(case_rate, lag = c(0, 1, 2, 3, 7, 14)) %>%
  step_epi_lag(death_rate, lag = c(0, 7, 14)) %>%
  step_epi_ahead(death_rate, ahead = 14) %>%
  step_epi_naomit()

# A postprocessing routine describing what to do to the predictions
f <- frosting() %>%
  layer_predict() %>%
  layer_threshold(.pred, lower = 0) %>% # predictions/intervals should be non-negative
  layer_add_target_date(target_date = max(jhu$time_value) + 14) %>%
  layer_add_forecast_date(forecast_date = max(jhu$time_value))

# Bundle up the preprocessor, training engine, and postprocessor
# We use quantile regression
ewf <- epi_workflow(r, quantile_reg(tau = c(.1, .5, .9)), f)

# Fit it to data (we could fit this to ANY data that has the same format)
trained_ewf <- ewf %>% fit(jhu)

# examines the recipe to determine what we need to make the prediction
latest <- get_test_data(r, jhu)

# we could make predictions using the same model on ANY test data
preds <- trained_ewf %>% predict(new_data = latest)