From 94eb3db7968ec9c096a7ae0d3a735ce9f30afe91 Mon Sep 17 00:00:00 2001
From: Thomas OBADIA <thomas.obadia@pasteur.fr>
Date: Thu, 22 May 2025 17:01:11 +0200
Subject: [PATCH] Make casting for REDCAP system variables explicit to address
changes in the redcapAPI methods
---
...NTERVENTIONAL_M0_01_dump_REDCap_database.R | 33 ++++++++++++-------
1 file changed, 22 insertions(+), 11 deletions(-)
diff --git a/03_INTERVENTIONAL_M0/INTERVENTIONAL_M0_01_dump_REDCap_database.R b/03_INTERVENTIONAL_M0/INTERVENTIONAL_M0_01_dump_REDCap_database.R
index 3740ebc..6e9f665 100644
--- a/03_INTERVENTIONAL_M0/INTERVENTIONAL_M0_01_dump_REDCap_database.R
+++ b/03_INTERVENTIONAL_M0/INTERVENTIONAL_M0_01_dump_REDCap_database.R
@@ -17,6 +17,7 @@
### SOURCE THE R ENVIRONMENT
######################################################################
source("./03_INTERVENTIONAL_M0/INTERVENTIONAL_M0_00_R_environment.R")
+source("./03_INTERVENTIONAL_M0/INTERVENTIONAL_M0_00_R_functions.R")
@@ -51,15 +52,15 @@ if (DATA_SOURCE_REDCAP_AHRI_INT_M0) {
# Passive Case Detection datasets
if (DATA_SOURCE_REDCAP_IPP_INT_PCD) {
RCON_IPP_INTERVENTIONAL_PCD <- redcapAPI::redcapConnection(url = Sys.getenv("REDCAP_IPP_API_URL"),
- token = Sys.getenv("REDCAP_IPP_API_TOKEN_INTERVENTIONAL_PCD"))
+ token = Sys.getenv("REDCAP_IPP_API_TOKEN_INTERVENTIONAL_PCD"))
}
if (DATA_SOURCE_REDCAP_IPM_INT_PCD) {
RCON_IPM_INTERVENTIONAL_PCD <- redcapAPI::redcapConnection(url = Sys.getenv("REDCAP_IPM_API_URL"),
- token = Sys.getenv("REDCAP_IPM_API_TOKEN_INTERVENTIONAL_PCD"))
+ token = Sys.getenv("REDCAP_IPM_API_TOKEN_INTERVENTIONAL_PCD"))
}
if (DATA_SOURCE_REDCAP_AHRI_INT_PCD) {
RCON_AHRI_INTERVENTIONAL_PCD <- redcapAPI::redcapConnection(url = Sys.getenv("REDCAP_AHRI_API_URL"),
- token = Sys.getenv("REDCAP_AHRI_API_TOKEN_INTERVENTIONAL_PCD"))
+ token = Sys.getenv("REDCAP_AHRI_API_TOKEN_INTERVENTIONAL_PCD"))
}
@@ -105,26 +106,36 @@ if (!DATA_EXTRACT_IS_RECENT_INT_M0) {
# Radio buttons reported as label instead of code
"radio" = castLabelCharacter,
"yesno" = castLabelCharacter,
- "dropdown" = castLabelCharacter
+ "dropdown" = castLabelCharacter,
+ "system" = castLabelCharacter
)) %>%
# Convert the '999' code to NA, except in Date/POSIX fields because it'll mess them up
mutate(across(-c(where(is.POSIXt),
- where(is.Date)), function(x) (ifelse(x == 999, NA, x)))) %>%
+ where(is.Date)), function(x) (ifelse(as.character(x) == "999", NA, x)))) %>%
# Add data source for convenience
mutate(data_source = RCON)
## Check for invalid records before moving on
print(reviewInvalidRecords(dat_interventional_m0_raw[[RCON]]))
+
+ ## Propagate baseline data to subsequent events
+ dat_interventional_m0_raw[[RCON]] <- propagate_unique_data(x = dat_interventional_m0_raw[[RCON]],
+ metadata = RCON_INTERVENTIONAL_M0[[RCON]]$metadata(),
+ events.from = c("participant_screening",
+ "eligibility_consent",
+ "identification_demographics",
+ "safety_of_study_drugs",
+ "final_status"))
}
- # Cleanup that loop
- rm(RCON)
-
# Concatenate all data into a single table
dat_interventional_m0_raw <- dat_interventional_m0_raw %>%
- bind_rows()
+ bind_rows()
+
+ # Cleanup that loop
+ rm(RCON)
## Passive Case Detection datasets
for (RCON in names(RCON_INTERVENTIONAL_PCD)) {
@@ -138,7 +149,8 @@ if (!DATA_EXTRACT_IS_RECENT_INT_M0) {
# Radio buttons reported as label instead of code
"radio" = castLabelCharacter,
"yesno" = castLabelCharacter,
- "dropdown" = castLabelCharacter
+ "dropdown" = castLabelCharacter,
+ "system" = castLabelCharacter
)) %>%
# Convert the '999' code to NA, except in Date/POSIX fields because it'll mess them up
@@ -228,4 +240,3 @@ rm(INTERVENTIONAL_M0_OUT_01_FILENAME,
DATA_EXTRACT_IS_RECENT_INT_M0 <- as.logical(difftime(time1 = Sys.Date(),
time2 = as.Date(ifelse(exists("DATA_EXTRACT_TS_INT_M0"), DATA_EXTRACT_TS_INT_M0, DATA_EXTRACT_TS_DEFAULT)),
units = "days") <= DATA_EXTRACT_EXPIRY_TIME_D)
-
--
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