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More intuitive parameter names in control_incidence_rate #975

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merged 7 commits into from
Jun 20, 2023
Merged

More intuitive parameter names in control_incidence_rate #975

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2736c00
Update parameter names in control_incidence_rate
edelarua Jun 19, 2023
90894c6
Define deprecated params
edelarua Jun 19, 2023
1831de9
Rename n_pt_years_rate to num_pt_year
edelarua Jun 19, 2023
4b0df9e
Update default value
edelarua Jun 20, 2023
24e76f7
Merge branch 'main' into 973_incidence_ctrl_params@main
Melkiades Jun 20, 2023
c6e0bf9
Update version
edelarua Jun 20, 2023
f3cda52
Merge branch 'main' into 973_incidence_ctrl_params@main
edelarua Jun 20, 2023
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3 changes: 2 additions & 1 deletion NEWS.md
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Expand Up @@ -15,7 +15,8 @@

### Miscellaneous
* Updated README to include installation instructions for CRAN.
* Began deprecation of `indent_mod` argument and replace it with the `.indent_mods` argument in `summarize_num_patients` and `analyze_num_patients`.
* Began deprecation of `indent_mod` argument and replaced it with the `.indent_mods` argument in `summarize_num_patients` and `analyze_num_patients`.
* Began deprecation of `time_unit_input` and `time_unit_output` arguments and replaced them with the `input_time_unit` and `n_pt_years_rate`, respectively, in `control_incidence_rate`.

# tern 0.8.2

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35 changes: 26 additions & 9 deletions R/control_incidence_rate.R
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Expand Up @@ -6,11 +6,13 @@
#' internally to specify details in `s_incidence_rate()`.
#'
#' @inheritParams argument_convention
#' @param time_unit_input (`string`)\cr `day`, `month`, or `year` (default)
#' indicating time unit for data input.
#' @param time_unit_output (`numeric`)\cr time unit for desired output (in person-years).
#' @param conf_type (`string`)\cr `normal` (default), `normal_log`, `exact`, or `byar`
#' for confidence interval type.
#' @param input_time_unit (`string`)\cr `day`, `week`, `month`, or `year` (default)
#' indicating time unit for data input.
#' @param n_pt_years_rate (`numeric`)\cr number of patient-years to use when calculating AE rate.
#' @param time_unit_input `r lifecycle::badge("deprecated")` Please use the `input_time_unit` argument instead.
#' @param time_unit_output `r lifecycle::badge("deprecated")` Please use the `n_pt_years_rate` argument instead.
#'
#' @return A list of components with the same names as the arguments.
#'
Expand All @@ -22,17 +24,32 @@
#' @export
control_incidence_rate <- function(conf_level = 0.95,
conf_type = c("normal", "normal_log", "exact", "byar"),
time_unit_input = c("year", "day", "week", "month"),
time_unit_output = 1) {
input_time_unit = c("year", "day", "week", "month"),
n_pt_years_rate = 1,
time_unit_input = lifecycle::deprecated(),
time_unit_output = lifecycle::deprecated()) {
if (lifecycle::is_present(time_unit_input)) {
lifecycle::deprecate_warn(
"0.8.3", "control_incidence_rate(time_unit_input)", "control_incidence_rate(input_time_unit)"
)
input_time_unit <- time_unit_input
}
if (lifecycle::is_present(time_unit_output)) {
lifecycle::deprecate_warn(
"0.8.3", "control_incidence_rate(time_unit_output)", "control_incidence_rate(n_pt_years_rate)"
)
n_pt_years_rate <- time_unit_output
}

conf_type <- match.arg(conf_type)
time_unit_input <- match.arg(time_unit_input)
checkmate::assert_number(time_unit_output)
input_time_unit <- match.arg(input_time_unit)
checkmate::assert_number(n_pt_years_rate)
assert_proportion_value(conf_level)

list(
conf_level = conf_level,
conf_type = conf_type,
time_unit_input = time_unit_input,
time_unit_output = time_unit_output
input_time_unit = input_time_unit,
n_pt_years_rate = n_pt_years_rate
)
}
40 changes: 20 additions & 20 deletions R/incidence_rate.R
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Expand Up @@ -11,9 +11,9 @@
#' * `conf_level` (`proportion`)\cr confidence level for the estimated incidence rate.
#' * `conf_type` (`string`)\cr `normal` (default), `normal_log`, `exact`, or `byar`
#' for confidence interval type.
#' * `time_unit_input` (`string`)\cr `day`, `week`, `month`, or `year` (default)
#' * `input_time_unit` (`string`)\cr `day`, `week`, `month`, or `year` (default)
#' indicating time unit for data input.
#' * `time_unit_output` (`numeric`)\cr time unit for desired output (in person-years).
#' * `n_pt_years_rate` (`numeric`)\cr time unit for desired output (in person-years).
#' @param person_years (`numeric`)\cr total person-years at risk.
#' @param alpha (`numeric`)\cr two-sided alpha-level for confidence interval.
#' @param n_events (`integer`)\cr number of events observed.
Expand Down Expand Up @@ -52,8 +52,8 @@ NULL
#' .var = "AVAL",
#' n_events = "n_events",
#' control = control_incidence_rate(
#' time_unit_input = "month",
#' time_unit_output = 100
#' input_time_unit = "month",
#' n_pt_years_rate = 100
#' )
#' )
#' }
Expand Down Expand Up @@ -81,14 +81,14 @@ s_incidence_rate <- function(df,
checkmate::assert_integer(df[[n_events]], any.missing = FALSE)
}

time_unit_input <- control$time_unit_input
time_unit_output <- control$time_unit_output
input_time_unit <- control$input_time_unit
n_pt_years_rate <- control$n_pt_years_rate
conf_level <- control$conf_level
person_years <- sum(df[[.var]], na.rm = TRUE) * (
1 * (time_unit_input == "year") +
1 / 12 * (time_unit_input == "month") +
1 / 52.14 * (time_unit_input == "week") +
1 / 365.24 * (time_unit_input == "day")
1 * (input_time_unit == "year") +
1 / 12 * (input_time_unit == "month") +
1 / 52.14 * (input_time_unit == "week") +
1 / 365.24 * (input_time_unit == "day")
)
n_events <- sum(df[[n_events]], na.rm = TRUE)

Expand All @@ -100,7 +100,7 @@ s_incidence_rate <- function(df,
list(
person_years = formatters::with_label(person_years, "Total patient-years at risk"),
n_events = formatters::with_label(n_events, "Number of adverse events observed"),
rate = formatters::with_label(result$rate, paste("AE rate per", time_unit_output, "patient-years")),
rate = formatters::with_label(result$rate, paste("AE rate per", n_pt_years_rate, "patient-years")),
rate_ci = formatters::with_label(result$rate_ci, f_conf_level(conf_level))
)
}
Expand All @@ -118,7 +118,7 @@ s_incidence_rate <- function(df,
#' df,
#' .var = "AVAL",
#' n_events = "n_events",
#' control = control_incidence_rate(time_unit_input = "month", time_unit_output = 100)
#' control = control_incidence_rate(input_time_unit = "month", n_pt_years_rate = 100)
#' )
#' }
#'
Expand Down Expand Up @@ -149,8 +149,8 @@ a_incidence_rate <- make_afun(
#' vars = "AVAL",
#' n_events = "n_events",
#' control = control_incidence_rate(
#' time_unit_input = "month",
#' time_unit_output = 100
#' input_time_unit = "month",
#' n_pt_years_rate = 100
#' )
#' ) %>%
#' build_table(df)
Expand Down Expand Up @@ -192,9 +192,9 @@ estimate_incidence_rate <- function(lyt,
#' * `conf_level`: (`proportion`)\cr confidence level for the estimated incidence rate.
#' * `conf_type`: (`string`)\cr `normal` (default), `normal_log`, `exact`, or `byar`
#' for confidence interval type.
#' * `time_unit_input`: (`string`)\cr `day`, `week`, `month`, or `year` (default)
#' * `input_time_unit`: (`string`)\cr `day`, `week`, `month`, or `year` (default)
#' indicating time unit for data input.
#' * `time_unit_output`: (`numeric`)\cr time unit for desired output (in person-years).
#' * `n_pt_years_rate`: (`numeric`)\cr time unit for desired output (in person-years).
#' @param person_years (`numeric`)\cr total person-years at risk.
#' @param alpha (`numeric`)\cr two-sided alpha-level for confidence interval.
#' @param n_events (`integer`)\cr number of events observed.
Expand Down Expand Up @@ -311,7 +311,7 @@ h_incidence_rate_byar <- function(person_years,
#' control_incidence_rate(
#' conf_level = 0.9,
#' conf_type = "normal_log",
#' time_unit_output = 100
#' n_pt_years_rate = 100
#' )
#' )
#' }
Expand All @@ -328,9 +328,9 @@ h_incidence_rate <- function(person_years,
byar = h_incidence_rate_byar(person_years, n_events, alpha)
)

time_unit_output <- control$time_unit_output
n_pt_years_rate <- control$n_pt_years_rate
list(
rate = est$rate * time_unit_output,
rate_ci = est$rate_ci * time_unit_output
rate = est$rate * n_pt_years_rate,
rate_ci = est$rate_ci * n_pt_years_rate
)
}
14 changes: 10 additions & 4 deletions man/control_incidence_rate.Rd
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6 changes: 3 additions & 3 deletions man/h_incidence_rate.Rd
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14 changes: 7 additions & 7 deletions man/incidence_rate.Rd
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18 changes: 9 additions & 9 deletions tests/testthat/test-estimate_incidence_rate.R
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Original file line number Diff line number Diff line change
Expand Up @@ -2,8 +2,8 @@ testthat::test_that("control_incidence_rate works with customized parameters", {
result <- control_incidence_rate(
conf_level = 0.9,
conf_type = "exact",
time_unit_input = "month",
time_unit_output = 100
input_time_unit = "month",
n_pt_years_rate = 100
)

res <- testthat::expect_silent(result)
Expand All @@ -13,8 +13,8 @@ testthat::test_that("control_incidence_rate works with customized parameters", {
testthat::test_that("control_incidence_rate fails with wrong input", {
testthat::expect_error(control_incidence_rate(conf_level = 1.1))
testthat::expect_error(control_incidence_rate(conf_type = "wald"))
testthat::expect_error(control_incidence_rate(time_unit_input = "decade"))
testthat::expect_error(control_incidence_rate(time_unit_output = "one"))
testthat::expect_error(control_incidence_rate(input_time_unit = "decade"))
testthat::expect_error(control_incidence_rate(n_pt_years_rate = "one"))
})

testthat::test_that("h_incidence_rate_normal works as expected with healthy input", {
Expand Down Expand Up @@ -49,7 +49,7 @@ testthat::test_that("h_incidence_rate works as expected with healthy input", {
result <- h_incidence_rate(
200,
2,
control_incidence_rate(conf_level = 0.9, conf_type = "normal_log", time_unit_output = 100)
control_incidence_rate(conf_level = 0.9, conf_type = "normal_log", n_pt_years_rate = 100)
)

res <- testthat::expect_silent(result)
Expand All @@ -72,8 +72,8 @@ testthat::test_that("s_incidence_rate works as expected with healthy input", {
control = control_incidence_rate(
conf_level = 0.9,
conf_type = "normal_log",
time_unit_input = "month",
time_unit_output = 100
input_time_unit = "month",
n_pt_years_rate = 100
)
)

Expand All @@ -100,8 +100,8 @@ testthat::test_that("estimate_incidence_rate works as expected with healthy inpu
control = control_incidence_rate(
conf_level = 0.9,
conf_type = "normal_log",
time_unit_input = "month",
time_unit_output = 100
input_time_unit = "month",
n_pt_years_rate = 100
)
) %>%
build_table(df)
Expand Down