From 802dc5c613797db6d672b1d6194f0d53aa6a4f1f Mon Sep 17 00:00:00 2001
From: Thomas OBADIA <tobadia@ml24-0166.corp.pasteur.fr>
Date: Wed, 4 Dec 2024 15:18:32 +0100
Subject: [PATCH] Now that IPM data from the observational study are available,
I need to split the curation rule (that fixes the agey calculation) by
country, because only the data from Ethiopia suffered from that bug.
---
.../OBSERVATIONAL_00_R_environment.R | 5 +--
.../OBSERVATIONAL_02_curate_REDCap_raw_data.R | 32 +++++++++++++------
2 files changed, 25 insertions(+), 12 deletions(-)
diff --git a/02_OBSERVATIONAL/OBSERVATIONAL_00_R_environment.R b/02_OBSERVATIONAL/OBSERVATIONAL_00_R_environment.R
index ef3c615..d1987f2 100644
--- a/02_OBSERVATIONAL/OBSERVATIONAL_00_R_environment.R
+++ b/02_OBSERVATIONAL/OBSERVATIONAL_00_R_environment.R
@@ -44,7 +44,7 @@ dotenv::load_dot_env("./02_OBSERVATIONAL/.env")
# - TRUE : data will be dumped
# - FALSE: data will not be dumped
DATA_SOURCE_REDCAP_IPP_OBS <- FALSE
-DATA_SOURCE_REDCAP_IPM_OBS <- FALSE
+DATA_SOURCE_REDCAP_IPM_OBS <- TRUE
DATA_SOURCE_REDCAP_AHRI_OBS <- TRUE
@@ -89,4 +89,5 @@ SEED <- 12345
## the raw data dumped from REDCap or not.
# - TRUE : curation rule will be enforced
# - FALSE: curation rule will not be enforced (default)
-CURATE_DATA_RECALCULATE_AGEY <- TRUE
+CURATE_DATA_RECALCULATE_AGEY_ETHIOPIA <- TRUE
+CURATE_DATA_RECALCULATE_AGEY_MADAGASCAR <- FALSE
diff --git a/02_OBSERVATIONAL/OBSERVATIONAL_02_curate_REDCap_raw_data.R b/02_OBSERVATIONAL/OBSERVATIONAL_02_curate_REDCap_raw_data.R
index 3c0c2a1..9be600b 100644
--- a/02_OBSERVATIONAL/OBSERVATIONAL_02_curate_REDCap_raw_data.R
+++ b/02_OBSERVATIONAL/OBSERVATIONAL_02_curate_REDCap_raw_data.R
@@ -32,16 +32,28 @@ source("./02_OBSERVATIONAL/OBSERVATIONAL_01_dump_REDCap_database.R")
## Start from the raw dataset generated in OBSERVATIONAL_01_dump_REDCap_database.R
dat_observational_curated <- dat_observational_raw %>%
# Go through each curation flag
- mutate(agey = case_when(CURATE_DATA_RECALCULATE_AGEY & (dob_yn %in% c(1, "Yes") & !is.na(dob)) ~ round(x = as.numeric(difftime(time1 = visdat,
- time2 = dob,
- units = "days")) / 365.25,
- digits = 0),
- CURATE_DATA_RECALCULATE_AGEY & (dob_yn %in% c(0, "No") | is.na(dob)) ~ round(x = as.numeric(difftime(time1 = visdat,
- time2 = as.Date(x = calc_dob_from_myob,
- format = "%d-%m-%Y"),
- units = "days")) / 365.25,
- digits = 0),
- .default = agey))
+ mutate(
+ # agey: distinct curation flages for Ethiopia & Madagascar
+ agey = case_when(CURATE_DATA_RECALCULATE_AGEY_ETHIOPIA & country %in% c("E", "Ethiopia") & (dob_yn %in% c(1, "Yes") & !is.na(dob)) ~ round(x = as.numeric(difftime(time1 = visdat,
+ time2 = dob,
+ units = "days")) / 365.25,
+ digits = 0),
+ CURATE_DATA_RECALCULATE_AGEY_ETHIOPIA & country %in% c("E", "Ethiopia") & (dob_yn %in% c(0, "No") | is.na(dob)) ~ round(x = as.numeric(difftime(time1 = visdat,
+ time2 = as.Date(x = calc_dob_from_myob,
+ format = "%d-%m-%Y"),
+ units = "days")) / 365.25,
+ digits = 0),
+
+ CURATE_DATA_RECALCULATE_AGEY_MADAGASCAR & country %in% c("M", "Madagascar") & (dob_yn %in% c(1, "Yes") & !is.na(dob)) ~ round(x = as.numeric(difftime(time1 = visdat,
+ time2 = dob,
+ units = "days")) / 365.25,
+ digits = 0),
+ CURATE_DATA_RECALCULATE_AGEY_MADAGASCAR & country %in% c("M", "Madagascar") & (dob_yn %in% c(0, "No") | is.na(dob)) ~ round(x = as.numeric(difftime(time1 = visdat,
+ time2 = as.Date(x = calc_dob_from_myob,
+ format = "%d-%m-%Y"),
+ units = "days")) / 365.25,
+ digits = 0),
+ .default = agey))
--
GitLab