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Fix geometric_mean positive method #154

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merged 6 commits into from
Nov 12, 2024
Merged

Fix geometric_mean positive method #154

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97bd35a
Fix geometric_mean positive method
juan-umana Nov 8, 2024
39d3e31
Lint fix
juan-umana Nov 8, 2024
fc1c5e1
Update during styling
juan-umana Nov 11, 2024
2f1873a
Fix misleading stopifnot in geometric_mean
juan-umana Nov 11, 2024
e51086a
Delete not expected errors
juan-umana Nov 11, 2024
901b2af
Fix logical aggregation
juan-umana Nov 12, 2024
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6 changes: 4 additions & 2 deletions R/demographics.R
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Original file line number Diff line number Diff line change
Expand Up @@ -261,8 +261,10 @@ population_pyramid_plot <- function(pop_pyramid, sex = TRUE) {
#' )
#' @export
age_risk <- function(age, population_pyramid, sex = NULL, plot = FALSE) {
stopifnot("`age` must be a numeric vector with values greater than 0" =
((all(age > 0)) & (is.numeric(age))))
stopifnot(
"`age` must be a numeric vector with values greater than 0" =
((all(age > 0)) & (is.numeric(age)))
)
if (inherits(population_pyramid, what = "list")) {
population_pyramid <- population_pyramid$data
}
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34 changes: 20 additions & 14 deletions R/utils.R
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Expand Up @@ -183,11 +183,12 @@ incidence_rate <- function(incidence_object, level, scale = 100000) {
#' geometric_mean(x, method = "optimized")
#'
#' @export
geometric_mean <- function(x, method = c(
"positive", "shifted",
"optimized", "weighted"
),
shift = 1, epsilon = 1e-3) {
geometric_mean <- function(
x, method = c(
"positive", "shifted",
"optimized", "weighted"
),
shift = 1, epsilon = 1e-3) {
stopifnot(
"`x`must be numeric" = (is.numeric(x)),
"`shift` must be numeric" = (is.numeric(shift)),
Expand All @@ -196,10 +197,14 @@ geometric_mean <- function(x, method = c(
method <- match.arg(method)

if (method == "positive") {
stopifnot("`x` includes zero or negative values,
check the geom_mean methods" = all(x > 0))

gm <- exp(mean(log(x)))
if (any(x) <= 0) {
message(
sum(x <= 0),
" zeros or negative values where ignored in the estimation"
)
}
x_positive <- x[x > 0]
gm <- exp(mean(log(x_positive)))
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Since we previously errored if there were any negative or zero value, I believe we are guaranteed to have strictly positive values at this stage, aren't we?

If that's not the case, could you add a test case that fails on main but passes on this branch please?

} else if (method == "shifted") {
x_shifted <- x + shift
stopifnot("shifted `x` still includes zero or negative values,
Expand Down Expand Up @@ -295,11 +300,12 @@ geometric_mean <- function(x, method = c(
#' geometric_sd(x, method = "optimized")
#'
#' @export
geometric_sd <- function(x, method = c(
"positive", "shifted",
"optimized", "weighted"
),
shift = 1, delta = 1e-3) {
geometric_sd <- function(
x, method = c(
"positive", "shifted",
"optimized", "weighted"
),
shift = 1, delta = 1e-3) {
stopifnot(
"`x`must be numeric" = (is.numeric(x)),
"`shift` must be numeric" = (is.numeric(shift)),
Expand Down
4 changes: 1 addition & 3 deletions tests/testthat/test-utils.R
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Expand Up @@ -85,14 +85,12 @@ test_that("Incidence rate calculate rates", {
test_that("Geometric mean throws errors", {
expect_error(geometric_mean(c(45, 20, 1000, "a")))
expect_error(geometric_mean(c(45, 20, 1000, 100), method = "test"))
expect_error(geometric_mean(c(45, 20, 1000, 100),
expect_error(geometric_mean(c(45, 20, 1000, -3),
method = "shifted",
shift = "2"
))
expect_error(geometric_mean(c(45, 20, 1000, 100), epsilon = "test"))
expect_error(geometric_mean(c(45, 20, 1000, -100), method = "shifted"))
expect_error(geometric_mean(c(45, 20, 1000, -100), epsilon = "positive"))
expect_error(geometric_mean(c(45, 20, 1000, -100), method = "positive"))
})

test_that("Geometric mean works as expected", {
Expand Down
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