-
-
Notifications
You must be signed in to change notification settings - Fork 21
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge branch 'main' into 1301-feature-request-add-confidence-interval…
…s-for-quantiles-in-surv_time
- Loading branch information
Showing
29 changed files
with
980 additions
and
388 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,135 @@ | ||
| #' Helper functions for incidence rate | ||
| #' | ||
| #' @description `r lifecycle::badge("stable")` | ||
| #' | ||
| #' @param control (`list`)\cr parameters for estimation details, specified by using | ||
| #' the helper function [control_incidence_rate()]. Possible parameter options are: | ||
| #' * `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. | ||
| #' * `input_time_unit`: (`string`)\cr `day`, `week`, `month`, or `year` (default) | ||
| #' indicating time unit for data input. | ||
| #' * `num_pt_year`: (`numeric`)\cr time unit for desired output (in person-years). | ||
| #' @param person_years (`numeric(1)`)\cr total person-years at risk. | ||
| #' @param alpha (`numeric(1)`)\cr two-sided alpha-level for confidence interval. | ||
| #' @param n_events (`integer(1)`)\cr number of events observed. | ||
| #' | ||
| #' @return Estimated incidence rate, `rate`, and associated confidence interval, `rate_ci`. | ||
| #' | ||
| #' @seealso [incidence_rate] | ||
| #' | ||
| #' @name h_incidence_rate | ||
| NULL | ||
|
|
||
| #' @describeIn h_incidence_rate Helper function to estimate the incidence rate and | ||
| #' associated confidence interval. | ||
| #' | ||
| #' @keywords internal | ||
| h_incidence_rate <- function(person_years, | ||
| n_events, | ||
| control = control_incidence_rate()) { | ||
| alpha <- 1 - control$conf_level | ||
| est <- switch(control$conf_type, | ||
| normal = h_incidence_rate_normal(person_years, n_events, alpha), | ||
| normal_log = h_incidence_rate_normal_log(person_years, n_events, alpha), | ||
| exact = h_incidence_rate_exact(person_years, n_events, alpha), | ||
| byar = h_incidence_rate_byar(person_years, n_events, alpha) | ||
| ) | ||
|
|
||
| num_pt_year <- control$num_pt_year | ||
| list( | ||
| rate = est$rate * num_pt_year, | ||
| rate_ci = est$rate_ci * num_pt_year | ||
| ) | ||
| } | ||
|
|
||
| #' @describeIn h_incidence_rate Helper function to estimate the incidence rate and | ||
| #' associated confidence interval based on the normal approximation for the | ||
| #' incidence rate. Unit is one person-year. | ||
| #' | ||
| #' @examples | ||
| #' h_incidence_rate_normal(200, 2) | ||
| #' | ||
| #' @export | ||
| h_incidence_rate_normal <- function(person_years, | ||
| n_events, | ||
| alpha = 0.05) { | ||
| checkmate::assert_number(person_years) | ||
| checkmate::assert_number(n_events) | ||
| assert_proportion_value(alpha) | ||
|
|
||
| est <- n_events / person_years | ||
| se <- sqrt(est / person_years) | ||
| ci <- est + c(-1, 1) * stats::qnorm(1 - alpha / 2) * se | ||
|
|
||
| list(rate = est, rate_ci = ci) | ||
| } | ||
|
|
||
| #' @describeIn h_incidence_rate Helper function to estimate the incidence rate and | ||
| #' associated confidence interval based on the normal approximation for the | ||
| #' logarithm of the incidence rate. Unit is one person-year. | ||
| #' | ||
| #' @examples | ||
| #' h_incidence_rate_normal_log(200, 2) | ||
| #' | ||
| #' @export | ||
| h_incidence_rate_normal_log <- function(person_years, | ||
| n_events, | ||
| alpha = 0.05) { | ||
| checkmate::assert_number(person_years) | ||
| checkmate::assert_number(n_events) | ||
| assert_proportion_value(alpha) | ||
|
|
||
| rate_est <- n_events / person_years | ||
| rate_se <- sqrt(rate_est / person_years) | ||
| lrate_est <- log(rate_est) | ||
| lrate_se <- rate_se / rate_est | ||
| ci <- exp(lrate_est + c(-1, 1) * stats::qnorm(1 - alpha / 2) * lrate_se) | ||
|
|
||
| list(rate = rate_est, rate_ci = ci) | ||
| } | ||
|
|
||
| #' @describeIn h_incidence_rate Helper function to estimate the incidence rate and | ||
| #' associated exact confidence interval. Unit is one person-year. | ||
| #' | ||
| #' @examples | ||
| #' h_incidence_rate_exact(200, 2) | ||
| #' | ||
| #' @export | ||
| h_incidence_rate_exact <- function(person_years, | ||
| n_events, | ||
| alpha = 0.05) { | ||
| checkmate::assert_number(person_years) | ||
| checkmate::assert_number(n_events) | ||
| assert_proportion_value(alpha) | ||
|
|
||
| est <- n_events / person_years | ||
| lcl <- stats::qchisq(p = (alpha) / 2, df = 2 * n_events) / (2 * person_years) | ||
| ucl <- stats::qchisq(p = 1 - (alpha) / 2, df = 2 * n_events + 2) / (2 * person_years) | ||
|
|
||
| list(rate = est, rate_ci = c(lcl, ucl)) | ||
| } | ||
|
|
||
| #' @describeIn h_incidence_rate Helper function to estimate the incidence rate and | ||
| #' associated Byar's confidence interval. Unit is one person-year. | ||
| #' | ||
| #' @examples | ||
| #' h_incidence_rate_byar(200, 2) | ||
| #' | ||
| #' @export | ||
| h_incidence_rate_byar <- function(person_years, | ||
| n_events, | ||
| alpha = 0.05) { | ||
| checkmate::assert_number(person_years) | ||
| checkmate::assert_number(n_events) | ||
| assert_proportion_value(alpha) | ||
|
|
||
| est <- n_events / person_years | ||
| seg_1 <- n_events + 0.5 | ||
| seg_2 <- 1 - 1 / (9 * (n_events + 0.5)) | ||
| seg_3 <- stats::qnorm(1 - alpha / 2) * sqrt(1 / (n_events + 0.5)) / 3 | ||
| lcl <- seg_1 * ((seg_2 - seg_3)^3) / person_years | ||
| ucl <- seg_1 * ((seg_2 + seg_3)^3) / person_years | ||
|
|
||
| list(rate = est, rate_ci = c(lcl, ucl)) | ||
| } |
Oops, something went wrong.