Function reference • kwb.qmra

Import data

Import pre-defined CSV configuration files used as input data for QMRA

config_read(): Config: read configuration

Perform QMRA

Functions for performing QMRA

simulate_risk(): Simulate: risk

simulate_inflow(): Simulate: inflow

simulate_treatment(): Simulate: treatment

simulate_exposure(): Simulate: exposure

Web-apps

Functions for developing web-apps with OpenCPU

opencpu_config_read(): OpenCPU wrapper: import config from CSV and convert to JSON

opencpu_simulate_risk(): OpenCPU wrapper: run risk calculation and convert results to JSON format

Visualise results

Functions for plotting QMRA results

plot_doseresponse(): plot reduction

plot_effluent(): plot effluent

plot_event_dalys(): plot dalys_per_event

plot_event_dose(): plot dose per event

plot_event_exposure(): plot exposure per event

plot_event_illnessProb(): plot illness probability

plot_event_infectionProb(): plot infection probability

plot_event_volume(): plot volume per event

plot_inflow(): plot inflow

plot_reduction(): plot reduction

plot_total_dalys(): plot total DALYs

plot_total_illnessProb(): plot total illness probability

plot_total_infectionProb(): plot total infection probability

Datasets

Datasets within R package

config_dummy_json: config_dummy_json: dummy configuration for kwb.qmra::opencpu_simulate_risk() in JSON format

config_default_json: config_default_json: default configuration developed by Christoph Sprenger for kwb.qmra::opencpu_simulate_risk() in JSON format

risk_dummy_json: risk_dummy_json: example risk_json object returned by kwb.qmra::opencpu_simulate_risk()

Export data

Functions for exporting data

config_write(): Config: create configuration

report_workflow(): Create report (not working for "shiny" reports)

Helper functions

Helper functions for performing QMRA

backcalc_infectionRisk_perDay(): Backcalculate risk: infection (using optimise() function)

calc_health_risk(): Risk calculation: health

calc_infection_risk(): Risk calculation: infection

config_write_dummy(): Config: create dummy configuration

create_random_distribution(): Create random distribution

default_max(): Default Max

default_min(): Default Min

generate_random_values(): Create random distribution based on configuration file

get_percentile(): Helper function: get percentile

distribution_repeater(): Helper function: distributon repeater

dr.betapoisson(): Dose-response model: beta-poisson

dr.db_download(): Download dose-response model database from QMRAwiki

dr.db_model(): Generate table with different doses for dr.db_download()

dr.expo(): Dose-response model: exponential

poisson_dose(): Helper function: poisson distribution based on exposure per event

run_app(): Run shiny app

who_getTreatment(): Treatment: get WHO reductions