Package index • CFAEpiNow2Pipeline

All functions

apply_exclusions(): Convert case counts in matching rows to NA

download_from_azure_blob(): Download specified blobs from Blob Storage and save them in a local dir

fetch_blob_container(): Load Azure Blob endpoint using credentials in environment variables

fetch_credential_from_env_var(): Fetch Azure credential from environment variable

fit_model(): Fit an EpiNow2 model

gostic_gt_pmf: Generation interval corresponding to the sample gostic_toy_rt dataset

gostic_toy_rt: Synthetic dataset of stochastic SIR system with known Rt

format_generation_interval() format_delay_interval() format_right_truncation(): Format PMFs for EpiNow2

read_data(): Read in the dataset of incident case counts

read_disease_parameters(): Read in disease process parameters from an external file or files

read_exclusions(): Read exclusions from an external file

read_interval_pmf(): Read parameter PMF into memory