Skip to content

Fix comma parsing in exclusion reasons for PRISMA flowdiagram data #3

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

Closed
Copilot wants to merge 2 commits into from
Closed

Fix comma parsing in exclusion reasons for PRISMA flowdiagram data #3

Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
8fe4fdf
Initial plan
Copilot Oct 21, 2025
0abbdc8
Fix comma parsing in exclusion reasons by using split_reason_n helper
Copilot Oct 21, 2025
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
195 changes: 63 additions & 132 deletions R/PRISMA_flowdiagram.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -1202,6 +1202,21 @@ PRISMA_data <- function(data) { #nolint
# Ensure data is a df, not a tibble;
# tibbles do not return vectors using df[, 1].
data <- as.data.frame(data)

# Helper function to split reason/count pairs on the LAST comma
# This allows reasons to contain commas without breaking the parsing
split_reason_n <- function(vec) {
if (length(vec) == 0 || (length(vec) == 1 && vec[1] == "")) {
return(data.frame(reason = character(0), n = character(0)))
}
# Use regex to capture everything before the last comma as reason
# and everything after as n (count)
# Pattern: ^(.*),\s*([^,]+)$
reasons <- sub("^(.*),\\s*([^,]+)$", "\\1", vec)
counts <- sub("^(.*),\\s*([^,]+)$", "\\2", vec)
return(data.frame(reason = reasons, n = counts, stringsAsFactors = FALSE))
}

#Set parameters
previous_studies <- scales::comma(
as.numeric(
Expand Down Expand Up @@ -1243,75 +1258,33 @@ PRISMA_data <- function(data) { #nolint
]$n
)
)
database_specific_results <- data.frame(
reason = gsub(
",.*$",
"",
unlist(
strsplit(
as.character(
data[
grep(
"database_specific_results",
data[, 1]
),
]$n
),
split = "; "
)
)
),
n = gsub(
".*,",
"",
unlist(
strsplit(
as.character(
data[
grep(
"database_specific_results",
data[, 1]
),
]$n
),
split = "; "
)
database_specific_results <- split_reason_n(
unlist(
strsplit(
as.character(
data[
grep(
"database_specific_results",
data[, 1]
),
]$n
),
split = "; "
)
)
)
register_specific_results <- data.frame(
reason = gsub(
",.*$",
"",
unlist(
strsplit(
as.character(
data[
grep(
"register_specific_results",
data[, 1]
),
]$n
),
split = "; "
)
)
),
n = gsub(
".*,",
"",
unlist(
strsplit(
as.character(
data[
grep(
"register_specific_results",
data[, 1]
),
]$n
),
split = "; "
)
register_specific_results <- split_reason_n(
unlist(
strsplit(
as.character(
data[
grep(
"register_specific_results",
data[, 1]
),
]$n
),
split = "; "
)
)
)
Expand Down Expand Up @@ -1445,39 +1418,18 @@ PRISMA_data <- function(data) { #nolint
]$n
)
)
dbr_excluded <- data.frame(
reason = gsub(
",.*$",
"",
unlist(
strsplit(
as.character(
data[
grep(
"dbr_excluded",
data[, 1]
),
]$n
),
split = "; "
)
)
),
n = gsub(
".*,",
"",
unlist(
strsplit(
as.character(
data[
grep(
"dbr_excluded",
data[, 1]
),
]$n
),
split = "; "
)
dbr_excluded <- split_reason_n(
unlist(
strsplit(
as.character(
data[
grep(
"dbr_excluded",
data[, 1]
),
]$n
),
split = "; "
)
)
)
Expand All @@ -1491,39 +1443,18 @@ PRISMA_data <- function(data) { #nolint
]$n
)
)
other_excluded <- data.frame(
reason = gsub(
",.*$",
"",
unlist(
strsplit(
as.character(
data[
grep(
"other_excluded",
data[, 1]
),
]$n
),
split = "; "
)
)
),
n = gsub(
".*,",
"",
unlist(
strsplit(
as.character(
data[
grep(
"other_excluded",
data[, 1]
),
]$n
),
split = "; "
)
other_excluded <- split_reason_n(
unlist(
strsplit(
as.character(
data[
grep(
"other_excluded",
data[, 1]
),
]$n
),
split = "; "
)
)
)
Expand Down