Package index • nowcastNHSN

Data Sources

Factory functions for creating data source objects

delphi_epidata_source(): Create a data source object for the Delphi Epidata API
hub_data_source(): Create a data source object for a forecast hub S3 bucket

Data Fetching

Functions for fetching NHSN reporting data

fetch_nhsn_data(): Fetch NHSN hospital admissions data
fetch_reporting_data(): Fetch reporting data from a source object
fetch_reporting_data(<delphi_epidata_source>): Fetch reporting data from Delphi Epidata
fetch_reporting_data(<hub_data_source>): Fetch reporting data from a forecast hub S3 bucket
fetch_reporting_data_epidatr(): Fetch NHSN data formatted for reporting triangle construction

Nowcasting

Functions for running nowcasts and configuring pipeline

nowcast_config(): Create a nowcast configuration object
nowcast_config_test(): Create a test configuration for quick pipeline validation
print(<nowcast_config>): Print method for nowcast_config
run_state_nowcasts(): Run nowcasts for multiple states/locations
run_single_nowcast(): Run nowcast for a single location
get_uncertainty_fns(): Get uncertainty model and sampler functions by name

Output

Functions for summarizing and storing nowcast results

summarize_nowcast(): Summarize nowcast draws into quantiles
write_nowcast_parquet(): Write nowcast results to partitioned parquet files
read_nowcast_parquet(): Read nowcast results from partitioned parquet

Date Utilities

Utilities for working with epidemiological weeks and Saturday conventions

saturdays_to_epirange(): Convert Saturday dates to epidatr::epirange with MMWR epiweeks

Probabilistic Methods

Fitting and sampling methods for uncertainty quantification

fit_normal(): Fit a normal distribution with fixed mean to estimate variance
fit_skellam(): Fit a Skellam distribution with fixed mean to estimate variance
sample_normal(): Sample from a normal distribution given predictions and variance
sample_skellam(): Sample from a Skellam distribution given predictions and variance

Data Processing

Data transformation utilities

cumulative_to_incremental(): Convert cumulative counts to incremental counts