Exploration Tooling

This repo is for exploring forecasting methods and tools for both COVID and Flu. The repo is structured as a targets project, which means that it is easy to run things in parallel and to cache results. The repo is also structured as an R package, which means that it is easy to share code between different targets.

Usage

Define run parameters in your .Renviron file:

EPIDATR_USE_CACHE=true
# Choose a cache timeout for yourself. We want a long cache time, since we work with historical data.
EPIDATR_CACHE_MAX_AGE_DAYS=42
DEBUG_MODE=false
USE_SHINY=false
TAR_PROJECT=covid_hosp_explore
EXTERNAL_SCORES_PATH=legacy-exploration-scorecards.qs
AWS_S3_PREFIX=exploration

• EPIDATR_USE_CACHE controls whether epidatr functions use the cache.
• DEBUG_MODE controls whether targets::tar_make is run with the callr_function=NULL, which allows for debugging. This only works if parallelization has been turned off in scripts/targets-common.R by setting the default controller to serial on line 51.
• USE_SHINY controls whether we start a Shiny server after producing the targets.
• TAR_PROJECT controls which targets project is run by run.R. Likely either covid_hosp_explore or flu_hosp_explore
• EXTERNAL_SCORES_PATH controls where external scores are loaded from. If not set, external scores are not used.
• AWS_S3_PREFIX controls the prefix to use in the AWS S3 bucket (a prefix is a pseudo-directory in a bucket).

Run the pipeline using:

# Install renv and R dependencies
make install

# Pull pre-scored forecasts from the AWS bucket
make pull
# or
make download

# Run only the dashboard, to display results run on other machines
make dashboard

# Run the pipeline using the helper script `run.R`
make run
# or in the background
make run-nohup

# Push complete or partial results to the AWS bucket
make push
# or
make upload

Development

Directory Layout

• run.R and Makefile: the main entrypoint for all pipelines
• R/: R package code to be reused
• scripts/: plotting, code, and misc.
• tests/: package tests
• covid_hosp_explore/ and scripts/covid_hosp_explore.R: a targets project for exploring covid hospitalization forecasters
• flu_hosp_explore/ and scripts/flu_hosp_explore.R: a targets project for exploring flu hospitalization forecasters
• covid_hosp_prod/ and scripts/covid_hosp_prod.R: a targets project for predicting covid hospitalizations
• flu_hosp_prod/ and scripts/flu_hosp_prod.R: a targets project for predicting flu hospitalizations
• forecaster_testing/ and scripts/forecaster_testing.R: a targets project for testing forecasters

Debugging

Targets in parallel mode conflccts with debugging because it ignores browser() statements. To debug a target named yourTarget:

1. set DEBUG_MODE=true in .Renviron
2. insert a browser in the relevant function
3. run an R session and call tar_make(yourTarget)

Pipeline Design

See this diagram. Double diamond objects represent "plates" (to evoke plate notation, but don't take the comparison too literally), which are used to represent multiple objects of the same type (e.g. different forecasters).

Notes on Forecaster Types

Basic

The basic forecaster takes in an epi_df, does some pre-processing, does an epipredict workflow, and then some post-processing

Ensemble

This kind of forecaster has two components: a list of existing forecasters it depends on, and a function that aggregates those forecasters.

(to be named)

Any forecaster which requires a pre-trained component. An example is a forecaster with a sophisticated imputation method. Evaluating these has some thorns around training/testing splitting. It may be foldable into the basic variety though.