Skip to content

Change binom_ci error to warning when all values are NA (#105) #142

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Draft
kelliemac wants to merge 1 commit into
base: develop
Choose a base branch
from
Draft

Change binom_ci error to warning when all values are NA (#105) #142

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
26 changes: 22 additions & 4 deletions R/statistical_tests_and_estimates.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -461,14 +461,32 @@ binom_ci <- function(x,
methods = 'wilson',
...){

.check_response_input(x)
.check_numeric_input(conf.level, lower_bound = 0, upper_bound = 1 - 1E-12,
scalar = TRUE, whole_num = FALSE, allow_NA = FALSE)

x <- stats::na.omit(x)
# Check input type/length (errors for empty or wrong type)
# but handle all-NA case with warning instead of error
if (length(dim(x)) > 1) stop('"x" must be a vector (one-dimensional object)')
if (length(x) == 0) stop('"x" length must be > 0')

x_nona <- x[!is.na(x)]

if (!is.logical(x) & length(x_nona) > 0 & !all(x_nona %in% c(0, 1)))
stop('"x" must be a numeric vector containing only 0/1 values or a logical vector containing only T/F values')

if (length(x_nona) == 0) {
warning('"x" has no non-NA values. Returning NA results.')
na_result <- binom::binom.confint(x = 0, n = 0,
conf.level = conf.level,
methods = methods)
na_result$mean <- NA_real_
na_result$lower <- NA_real_
na_result$upper <- NA_real_
return(na_result)
}

npos <- sum(x);
n <- length(x);
npos <- sum(x_nona);
n <- length(x_nona);

binom::binom.confint(x = npos,
n = n,
Expand Down
10 changes: 8 additions & 2 deletions tests/testthat/test_statistical_tests_and_estimates.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -493,14 +493,20 @@ test_that("test-wilson_ci", {
test_that("test-binom_ci", {

# check x
expect_error(binom_ci(c(NA, NA, NA)), '"x" must have at least one non-NA value')
expect_error(binom_ci(c()), '"x" length must be > 0')
expect_error(binom_ci(c(NA, NA, NA)), '"x" must have at least one non-NA value')
expect_error(binom_ci(x = c("F", "T", "F", "T")),
'"x" must be a numeric vector containing only 0/1 values or a logical vector containing only T/F values')
expect_error(binom_ci(x = factor(c("F", "T", "F", "T"))),
'"x" must be a numeric vector containing only 0/1 values or a logical vector containing only T/F values')

# all-NA input should warn and return NAs (issue #105)
expect_warning(result <- binom_ci(c(NA, NA, NA)), 'no non-NA values')
expect_true(all(is.na(result$mean)))
expect_true(all(is.na(result$lower)))
expect_true(all(is.na(result$upper)))
expect_equal(result$x, 0)
expect_equal(result$n, 0)

# binom_ci() should match binom::binom.confint()
x <- c(1, 1, 1, 0, 0)
expect_equal(binom_ci(x), binom::binom.wilson(3, 5))
Expand Down
Loading