Epidemiological Tools for Outbreak Investigation and Analysis

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Documentation for package ‘OutbreakR’ version 0.1.0

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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