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.
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
run.R
and Makefile
: the main entrypoint for all pipelinesR/
: R package code to be reusedscripts/
: plotting, code, and misc.tests/
: package testscovid_hosp_explore/
and scripts/covid_hosp_explore.R
: a targets
project for exploring covid hospitalization forecastersflu_hosp_explore/
and scripts/flu_hosp_explore.R
: a targets
project for exploring flu hospitalization forecasterscovid_hosp_prod/
and scripts/covid_hosp_prod.R
: a targets
project for predicting covid hospitalizationsflu_hosp_prod/
and scripts/flu_hosp_prod.R
: a targets
project for predicting flu hospitalizationsforecaster_testing/
and scripts/forecaster_testing.R
: a targets
project for testing forecastersTargets in parallel mode conflicts with debugging because it ignores browser()
statements. To debug a target named yourTarget
:
DEBUG_MODE=true
in .Renviron
tar_make(yourTarget)
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).
The basic forecaster takes in an epi_df, does some pre-processing, does an epipredict workflow, and then some post-processing
This kind of forecaster has two components: a list of existing forecasters it depends on, and a function that aggregates those forecasters.
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.