Package 'tidyrates'

Title: Tidy Epidemiological Rates
Description: Compute age-adjusted rates by direct and indirect methods and other epidemiological indicators in a tidy way, wrapping functions from the 'epitools' package.
Authors: Raphael Saldanha [aut, cre]
Maintainer: Raphael Saldanha <[email protected]>
License: MIT + file LICENSE
Version: 0.0.1
Built: 2025-02-13 02:56:28 UTC
Source: https://github.com/rfsaldanha/tidyrates

Help Index

Fleiss data

Description

Fleiss dataset from epitools package examples, with event counts and population per age group in tidy format.

Usage

fleiss_data

Format

An object of class tbl_df (inherits from tbl, data.frame) with 60 rows and 4 columns.

Compute direct adjusted rates with tibbles

Description

Computes direct adjusted rates and confidence intervals.

Usage

rate_adj_direct(
  .data,
  .std,
  .keys = NULL,
  .name_var = "name",
  .value_var = "value",
  .age_group_var = "age_group",
  .age_group_pop_var = "population",
  .events_label = "events",
  .population_label = "population",
  .progress = TRUE
)

Arguments

.data

A tibble containing events counts and population per groups (e.g. age groups)
.std

A vector with standard population values for each group
.keys

Optional. A character vector with grouping variables, like year and region code.
.name_var

Variable containing variable names. Defaults to name.
.value_var

Variable containing values. Defaults to value.
.age_group_var

Variable name of age groups. Defaults to age_group.
.age_group_pop_var

Variable name of population size on .std. Defaults to population.
.events_label

Label used for events at the name_var variable. Defaults to events.
.population_label

Label used for population at the name_var variable. Defautls to population.
.progress

Whether to show a progress bar. Defaults to TRUE.

Details

This functions wraps the epitools ageadjust.direct function to compute direct adjusted rates and "exact" confidence intervals using tibble objects with multiple grouping keys.

A tibble (.data) must be informed containing key variables like year and region code, and population and and events count (e.g. cases) per age group. Check the fleiss_data for an example.

A tibble (.std) must be also supplied containing the age groups and population size. By default, this tibble has two variables, named age_group and pop.

Value

A tibble with crude and adjusted rate, lower and upper confidence intervals.

Examples

standard_pop <- tibble::tibble(
   age_group = c("Under 20", "20-24", "25-29", "30-34", "35-39", "40 and over"),
   population = c(63986.6, 186263.6, 157302.2, 97647.0, 47572.6, 12262.6)
 )
rate_adj_direct(fleiss_data, .std = standard_pop)

Compute direct adjusted rates with tibbles

Description

Computes indirect adjusted rates and confidence intervals.

Usage

rate_adj_indirect(
  .data,
  .std,
  .keys = NULL,
  .name_var = "name",
  .value_var = "value",
  .age_group_var = "age_group",
  .age_group_pop_var = "population",
  .events_label = "events",
  .population_label = "population",
  .progress = TRUE
)

Arguments

.data

A tibble containing events counts and population per groups (e.g. age groups)
.std

A vector with standard population values for each group
.keys

Optional. A character vector with grouping variables, like year and region code.
.name_var

Variable containing variable names. Defaults to name.
.value_var

Variable containing values. Defaults to value.
.age_group_var

Variable name of age groups. Defaults to age_group.
.age_group_pop_var

Variable name of population size on .std. Defaults to population.
.events_label

Label used for events at the name_var variable. Defaults to events.
.population_label

Label used for population at the name_var variable. Defautls to population.
.progress

Whether to show a progress bar. Defaults to TRUE.

Details

This functions wraps the epitools ageadjust.indirect function to compute indirect adjusted rates and "exact" confidence intervals using tibble objects with multiple grouping keys.

A tibble (.data) must be informed containing key variables like year and region code, and population and and events count (e.g. cases) per age group. Check the fleiss_data for an example.

A tibble (.std) must be also supplied containing the age groups, events and population size. By default, this tibble has three variables, named age_group, name and value. Check the selvin_data_1940 for an example.

Value

A tibble with crude and adjusted rate, lower and upper confidence intervals.

Examples

rate_adj_indirect(.data = selvin_data_1960, .std = selvin_data_1940)

Standard population reference table

Description

This table present standard population reference for age groups from SEER*Stat WHO adjusted proportions.

Usage

seer_std_pop

Format

An object of class tbl_df (inherits from tbl, data.frame) with 21 rows and 2 columns.

Selvin data, 1940

Description

Selvin dataset from epitools package examples for 1940, with event counts and population per age group in tidy format.

Usage

selvin_data_1940

Format

An object of class tbl_df (inherits from tbl, data.frame) with 22 rows and 3 columns.

Selvin data, 1960

Description

Selvin dataset from epitools package examples for 1960, with event counts and population per age group in tidy format.

Usage

selvin_data_1960

Format

An object of class tbl_df (inherits from tbl, data.frame) with 22 rows and 3 columns.

Standard population reference table

Description

This table present standard population reference for age groups from the World Health Organization (WHO).

Usage

who_std_pop

Format

An object of class tbl_df (inherits from tbl, data.frame) with 21 rows and 2 columns.