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Update process_extract_ae.R #1020

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merged 2 commits into from
Oct 28, 2024
Merged

Update process_extract_ae.R #1020

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387fe86
Update process_extract_ae.R
lizihao-anu Oct 28, 2024
1b9991a
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lizihao-anu Oct 28, 2024
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15 changes: 12 additions & 3 deletions R/process_extract_ae.R
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Original file line number Diff line number Diff line change
Expand Up @@ -196,6 +196,8 @@ process_extract_ae <- function(data, year, write_to_disk = TRUE) {
col_type = readr::cols(
"ED Arrival Date" = readr::col_date(format = "%Y/%m/%d %T"),
"ED Arrival Time" = readr::col_time(""),
"ED Discharge Date" = readr::col_date(format = "%Y/%m/%d %T"),
"ED Discharge Time" = readr::col_time(""),
"ED Case Reference Number [C]" = readr::col_character(),
"CUP Marker" = readr::col_double(),
"CUP Pathway Name" = readr::col_character()
Expand All @@ -205,6 +207,8 @@ process_extract_ae <- function(data, year, write_to_disk = TRUE) {
dplyr::rename(
record_keydate1 = "ED Arrival Date",
keytime1 = "ED Arrival Time",
record_keydate2 = "ED Discharge Date",
keytime2 = "ED Discharge Time",
case_ref_number = "ED Case Reference Number [C]",
cup_marker = "CUP Marker",
cup_pathway = "CUP Pathway Name"
Expand All @@ -217,6 +221,8 @@ process_extract_ae <- function(data, year, write_to_disk = TRUE) {
# Remove any duplicates
dplyr::distinct(.data$record_keydate1,
.data$keytime1,
.data$record_keydate2,
.data$keytime2,
.data$case_ref_number,
.keep_all = TRUE
)
Expand All @@ -225,9 +231,12 @@ process_extract_ae <- function(data, year, write_to_disk = TRUE) {
# Join data--------------------------------------------

matched_ae_data <- outfile %>%
dplyr::left_join(
ae_cup_clean,
by = c("record_keydate1", "keytime1", "case_ref_number")
dplyr::left_join(ae_cup_clean,
by = c(
"record_keydate1", "keytime1",
"record_keydate2", "keytime2",
"case_ref_number"
)
) %>%
dplyr::arrange(
.data$chi,
Expand Down