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Outbreak and surveillance summary table

Source: R/epi_table.R
epi_table.Rd

Build a publication-ready epidemiology table from either individual line-list records or aggregate numerator/denominator data. Unlike summary_table(), this function always makes the event and denominator explicit and always reports a confidence interval.

Usage

epi_table(
  data,
  outcomes = NULL,
  by = NULL,
  event = NULL,
  numerator = NULL,
  denominator = NULL,
  label = NULL,
  person_time = NULL,
  measure = c("proportion", "prevalence", "attack_rate", "incidence_rate"),
  multiplier = NULL,
  ci_method = c("wilson", "exact"),
  conf.level = 0.95,
  p_value = FALSE,
  p_adjust = c("none", "holm", "bonferroni", "BH", "fdr"),
  effects = "none",
  layout = c("auto", "wide", "long"),
  digits = 1,
  format = c("table", "tibble")
)

Arguments

data

A data frame.

outcomes

Line-list outcome variables selected with tidyselect syntax.

by

Optional grouping variable.

event

Event level to count. Supply one value for all outcomes or a named vector, for example c(infected = "Yes", admitted = "Yes").

numerator, denominator

Aggregate count and denominator columns. For an incidence rate, denominator is accumulated person-time.

label

Optional aggregate outcome-label column or a single text label.

person_time

Optional line-list person-time column. Required when measure = "incidence_rate".

measure

One of "proportion", "prevalence", "attack_rate", or "incidence_rate".

multiplier

Scale used for estimates. Defaults to 100 for proportions, prevalence and attack rates, and 1,000 for incidence rates.

ci_method

Binomial interval method: "wilson" or "exact". Incidence rates always use an exact Poisson interval.

conf.level

Confidence level.

p_value

Add an association/rate-comparison p-value when by is used.

p_adjust

Optional multiplicity adjustment passed to stats::p.adjust().

effects

Optional two-group effect measures. Use "none" (default), "all", or any of "rr", "rd", and "or". Incidence-rate tables support "irr".

layout

"auto", "wide", or "long". Auto uses wide output for four or fewer groups and long output otherwise.

digits

Number of decimal places.

format

"table" (default) or "tibble".

Value

A gt_epi_table object containing $summary, $table, $denominators, $p_values, $effects, $inputs, and $notes.

Examples

epi_table(
  birthwt, outcomes = low, by = smoke,
  event = "Low birth weight", measure = "prevalence"
)

aggregate_data <- data.frame(
  ward = c("A", "B"), cases = c(12, 7), population = c(80, 65)
)
epi_table(
  aggregate_data, numerator = cases, denominator = population,
  by = ward, label = "Influenza", measure = "attack_rate"
)