Title: Tidy Epidemiological Rates
Version: 0.0.1
Description: Compute age-adjusted rates by direct and indirect methods and other epidemiological indicators in a tidy way, wrapping functions from the 'epitools' package.
License: MIT + file LICENSE
Suggests: knitr, rmarkdown, testthat (≥ 3.0.0)
Config/testthat/edition: 3
Encoding: UTF-8
RoxygenNote: 7.3.1
Imports: checkmate, dplyr, epitools, forcats, magrittr, purrr, rlang, tibble, tidyr
Depends: R (≥ 2.10)
LazyData: true
VignetteBuilder: knitr
URL: https://rfsaldanha.github.io/tidyrates/
NeedsCompilation: no
Packaged: 2024-03-18 16:30:52 UTC; raphael
Author: Raphael Saldanha ORCID iD [aut, cre]
Maintainer: Raphael Saldanha <raphael.de-freitas-saldanha@inria.fr>
Repository: CRAN
Date/Publication: 2024-03-19 20:20:02 UTC

Pipe operator

Description

See magrittr::%>% for details.

Usage

lhs %>% rhs

Arguments

lhs

A value or the magrittr placeholder.

rhs

A function call using the magrittr semantics.

Value

The result of calling rhs(lhs).


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.