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

extract_diagnostics(): Extract diagnostic metrics from model fit and data

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

low_case_count_diagnostic(): Calculate low case count diagnostic flag

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

process_samples() process_quantiles(): Process posterior samples from a Stan fit object (raw draws).

write_model_outputs(): Write model outputs to specified directories

write_output_dir_structure(): Create output directory structure for a given job and task.