R: Epidemiological Tools for Outbreak Investigation and Analysis

# Epidemiological Tools for Outbreak Investigation and Analysis

## Documentation for package ‘OutbreakR’ version 0.1.0

- DESCRIPTION file

## Help Pages

A B C E H I M N O P R S V

## -- A --

attack_rate | Calculate Attack Rate
attributable_fraction_exposed | Calculate Attributable Fraction Among the Exposed
attributable_risk | Calculate Attributable Risk (Risk Difference)

## -- B --

basic_reproduction_number | Estimate the Basic Reproduction Number (R0)

## -- C --

case_fatality_rate | Calculate Case Fatality Rate

## -- E --

effective_reproduction_number | Estimate the Effective Reproduction Number (Re or Rt)

## -- H --

herd_immunity_threshold | Estimate the Herd Immunity Threshold

## -- I --

incidence_proportion | Calculate Incidence Proportion
incidence_rate | Calculate Incidence Rate

## -- M --

mortality_rate | Calculate Mortality Rate

## -- N --

number_needed_to_harm | Number Needed to Harm (NNH)
number_needed_to_treat | Calculate Number Needed to Treat

## -- O --

odds_ratio | Calculate Odds Ratio
outbreak_table | Create Publication-Ready Epidemiological Contingency Tables

## -- P --

population_attributable_fraction | Calculate Population Attributable Fraction
prevalence | Calculate Prevalence
print.outbreak_attack_rate | Print Attack Rate Results
print.outbreak_attack_rate_grouped | Print Grouped Attack Rate Results
print.outbreak_attributable_fraction_exposed | Print Attributable Fraction Among the Exposed Results
print.outbreak_attributable_fraction_exposed_grouped | Print Grouped Attributable Fraction Among the Exposed Results
print.outbreak_attributable_risk | Print Attributable Risk Results
print.outbreak_attributable_risk_grouped | Print Grouped Attributable Risk Results
print.outbreak_basic_reproduction_number | Print Basic Reproduction Number Analysis
print.outbreak_case_fatality_rate | Print Case Fatality Rate Results
print.outbreak_case_fatality_rate_grouped | Print Grouped Case Fatality Rate Results
print.outbreak_effective_reproduction_number | Print Effective Reproduction Number Analysis
print.outbreak_incidence_proportion | Print Incidence Proportion Analysis
print.outbreak_incidence_rate | Print Incidence Rate Results
print.outbreak_incidence_rate_grouped | Print Grouped Incidence Rate Results
print.outbreak_mortality_rate | Print Mortality Rate Results
print.outbreak_mortality_rate_grouped | Print Grouped Mortality Results
print.outbreak_number_needed_to_harm | Print Number Needed to Harm Analysis
print.outbreak_number_needed_to_harm_grouped | Print Grouped Number Needed to Harm Analysis
print.outbreak_number_needed_to_treat | Print Number Needed to Treat Analysis
print.outbreak_number_needed_to_treat_grouped | Print Grouped Number Needed to Treat Analysis
print.outbreak_odds_ratio | Print Odds Ratio Results
print.outbreak_odds_ratio_grouped | Print Grouped Odds Ratio Results
print.outbreak_population_attributable_fraction | Print Population Attributable Fraction
print.outbreak_population_attributable_fraction_grouped | Print Grouped Population Attributable Fraction
print.outbreak_prevalence | Print Prevalence Results
print.outbreak_prevalence_grouped | Print Grouped Prevalence Results
print.outbreak_rate_ratio | Print an OutbreakR Rate Ratio
print.outbreak_risk_ratio | Print Risk Ratio Results
print.outbreak_risk_ratio_grouped | Print Grouped Risk Ratio Results
print.outbreak_secondary_attack_rate | Print Secondary Attack Rate Results
print.outbreak_secondary_attack_rate_grouped | Print Grouped Secondary Attack Rate Results
print.outbreak_table | Print Contingency Table Results
print.outbreak_table_grouped | Print Grouped Contingency Table Results
print.outbreak_vaccine_effectiveness | Print Vaccine Effectiveness Results
print.outbreak_vaccine_effectiveness_grouped | Print Grouped Vaccine Effectiveness Results
print.outbreak_validation | Print an Outbreak Validation Result
print.summary.outbreak_attributable_fraction_exposed | Print Summary of Attributable Fraction Among the Exposed
print.summary.outbreak_attributable_fraction_exposed_grouped | Print Summary of Grouped Attributable Fraction Among the Exposed
print.summary.outbreak_attributable_risk | Print Summary of Attributable Risk
print.summary.outbreak_attributable_risk_grouped | Print Summary of Grouped Attributable Risk
print.summary.outbreak_basic_reproduction_number | Print Summary of Basic Reproduction Number Analysis
print.summary.outbreak_case_fatality_rate | Print Summary of Case Fatality Rate
print.summary.outbreak_case_fatality_rate_grouped | Print Summary of Grouped Case Fatality Rates
print.summary.outbreak_effective_reproduction_number | Print Summary of Effective Reproduction Number Analysis
print.summary.outbreak_incidence_proportion | Print Summary of Incidence Proportion Analysis
print.summary.outbreak_incidence_rate | Print Summary of Incidence Rate Analysis
print.summary.outbreak_incidence_rate_grouped | Print Summary of Grouped Incidence Rate Analysis
print.summary.outbreak_mortality_rate | Print Summary of Mortality Analysis
print.summary.outbreak_mortality_rate_grouped | Print Summary of Grouped Mortality Analysis
print.summary.outbreak_number_needed_to_harm | Print Summary of Number Needed to Harm
print.summary.outbreak_number_needed_to_harm_grouped | Print Summary of Grouped Number Needed to Harm
print.summary.outbreak_number_needed_to_treat | Print Summary of Number Needed to Treat
print.summary.outbreak_number_needed_to_treat_grouped | Print Summary of Grouped Number Needed to Treat
print.summary.outbreak_odds_ratio | Print Summary of Odds Ratio Analysis
print.summary.outbreak_odds_ratio_grouped | Print Summary of Grouped Odds Ratio Analysis
print.summary.outbreak_population_attributable_fraction | Print Summary of Population Attributable Fraction
print.summary.outbreak_population_attributable_fraction_grouped | Print Summary of Grouped Population Attributable Fraction
print.summary.outbreak_prevalence | Print Summary of Prevalence Analysis
print.summary.outbreak_prevalence_grouped | Print Summary of Grouped Prevalence Analysis
print.summary.outbreak_risk_ratio | Print Summary of Risk Ratio Analysis
print.summary.outbreak_risk_ratio_grouped | Print Summary of Grouped Risk Ratio Analysis
print.summary.outbreak_table | Print Summary of Contingency Table Analysis
print.summary.outbreak_table_grouped | Print Grouped Contingency Table Summary
print.summary.outbreak_vaccine_effectiveness | Print Summary of Vaccine Effectiveness
print.summary.outbreak_vaccine_effectiveness_grouped | Print Summary of Grouped Vaccine Effectiveness
print.summary_outbreak_rate_ratio | Print Summary of an OutbreakR Rate Ratio Analysis

## -- R --

rate_ratio | Calculate Incidence Rate Ratio
risk_ratio | Calculate Risk Ratio (Relative Risk)

## -- S --

secondary_attack_rate | Calculate Secondary Attack Rate
summary.outbreak_attributable_fraction_exposed | Summary of Attributable Fraction Among the Exposed Analysis
summary.outbreak_attributable_fraction_exposed_grouped | Summary of Grouped Attributable Fraction Among the Exposed
summary.outbreak_attributable_risk | Summary of Attributable Risk Analysis
summary.outbreak_attributable_risk_grouped | Summary of Grouped Attributable Risk Analysis
summary.outbreak_basic_reproduction_number | Summary of Basic Reproduction Number Analysis
summary.outbreak_case_fatality_rate | Summary of Case Fatality Rate
summary.outbreak_case_fatality_rate_grouped | Summary of Grouped Case Fatality Rates
summary.outbreak_effective_reproduction_number | Summary of Effective Reproduction Number Analysis
summary.outbreak_incidence_proportion | Summary of Incidence Proportion Analysis
summary.outbreak_incidence_rate | Summary of Incidence Rate Analysis
summary.outbreak_incidence_rate_grouped | Summary of Grouped Incidence Rate Analysis
summary.outbreak_mortality_rate | Summary of Mortality Analysis
summary.outbreak_mortality_rate_grouped | Summary of Grouped Mortality Analysis
summary.outbreak_number_needed_to_harm | Summary of Number Needed to Harm Analysis
summary.outbreak_number_needed_to_harm_grouped | Summary of Grouped Number Needed to Harm Analysis
summary.outbreak_number_needed_to_treat | Summary of Number Needed to Treat Analysis
summary.outbreak_number_needed_to_treat_grouped | Summary of Grouped Number Needed to Treat
summary.outbreak_odds_ratio | Summary of Odds Ratio Analysis
summary.outbreak_odds_ratio_grouped | Summary of Grouped Odds Ratio Analysis
summary.outbreak_population_attributable_fraction | Summary of Population Attributable Fraction Analysis
summary.outbreak_population_attributable_fraction_grouped | Summary of Grouped Population Attributable Fraction
summary.outbreak_prevalence | Summary of Prevalence Analysis
summary.outbreak_prevalence_grouped | Summary of Grouped Prevalence Analysis
summary.outbreak_rate_ratio | Summarize an OutbreakR Rate Ratio Analysis
summary.outbreak_risk_ratio | Summary of Risk Ratio Analysis
summary.outbreak_risk_ratio_grouped | Summary of Grouped Risk Ratio Analysis
summary.outbreak_table | Summary of Contingency Table Analysis
summary.outbreak_table_grouped | Summary of Grouped Contingency Table Analysis
summary.outbreak_vaccine_effectiveness | Summary of Vaccine Effectiveness Analysis
summary.outbreak_vaccine_effectiveness_grouped | Summary of Grouped Vaccine Effectiveness Analysis

## -- V --

vaccine_effectiveness | Calculate Vaccine Effectiveness
validate_linelist | Validate an Outbreak Line List