| 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 
[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 |
.value_var |
Variable containing values. Defaults to |
.age_group_var |
Variable name of age groups. Defaults to |
.age_group_pop_var |
Variable name of population size on |
.events_label |
Label used for events at the |
.population_label |
Label used for population at the |
.progress |
Whether to show a progress bar. Defaults to |
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 |
.value_var |
Variable containing values. Defaults to |
.age_group_var |
Variable name of age groups. Defaults to |
.age_group_pop_var |
Variable name of population size on |
.events_label |
Label used for events at the |
.population_label |
Label used for population at the |
.progress |
Whether to show a progress bar. Defaults to |
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.