Package index • CFAEpiNow2Pipeline

Azure

Functions which manage interaction with Azure blob

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

download_if_specified(): Download if specified

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

fetch_credential_from_env_var(): Fetch Azure credential from environment variable

Data

Example data included in the package

gostic_toy_rt: Synthetic dataset of stochastic SIR system with known Rt

sir_gt_pmf: Generation interval corresponding to the sample gostic_toy_rt dataset

Configuration

Manages the input of all configuration settings into the EpiNow2 model

Config(): Config Class

Data(): Data Class

Interval(): Interval Class

Parameters(): Parameters Class

read_json_into_config(): Read JSON Configuration into Config Object

Exclusions

Functions to handle exclusion of data from models

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

read_exclusions(): Read exclusions from an external file

Diagnostics

Functions to calculate diagnostics from fitted EpiNow2 model

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

low_case_count_diagnostic(): Calculate low case count diagnostic flag

low_case_count_threshold(): Determine Low Case Count Threshold Based on Pathogen

Parameter

Functions for parameter values that are input into the EpiNow2 model

check_returned_pmf(): Run validity checks on the PMF returned from the file

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

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

read_interval_pmf(): Read parameter PMF into memory

Pipeline

Functions to orchestrate running of the pipeline including fitting the EpiNow2 model

fit_model(): Fit an EpiNow2 model

format_stan_opts(): Format Stan options for input to EpiNow2

orchestrate_pipeline() execute_model_logic(): Run an Rt Estimation Model Pipeline

Read data

Functions for data that are input into the EpiNow2 model

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

Write output

Functions for post-processing and writing EpiNow2 model output

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.