From d8b28181fc6406318f2c97b4b6105d67c058b8c9 Mon Sep 17 00:00:00 2001
From: Thomas OBADIA <thomas.obadia@pasteur.fr>
Date: Mon, 2 Jun 2025 10:57:48 +0200
Subject: [PATCH] Refactor loading of R environment content (global variables
and functions) so that all environment from 00_COMMON is always sourced and
available in other projects.
---
00_COMMON/COMMON_00_R_environment.R | 42 ++++++----
01_INVENTORY/INVENTORY_00_R_environment.R | 4 +-
.../OBSERVATIONAL_00_R_environment.R | 2 +-
.../INTERVENTIONAL_M0_00_R_environment.R | 83 ++++++++++++++++++-
4 files changed, 110 insertions(+), 21 deletions(-)
diff --git a/00_COMMON/COMMON_00_R_environment.R b/00_COMMON/COMMON_00_R_environment.R
index 4512b79..0b74807 100644
--- a/00_COMMON/COMMON_00_R_environment.R
+++ b/00_COMMON/COMMON_00_R_environment.R
@@ -24,6 +24,15 @@ require(ggthemes)
+######################################################################
+### CUSTOM R ENVIRONMENT & FUNCTIONS
+######################################################################
+source("./00_COMMON/COMMON_00_R_functions.R")
+
+
+
+
+
######################################################################
### RUN TEST CODE
######################################################################
@@ -48,7 +57,7 @@ PVSTATEM_STUDY_TITLE <- "PvSTATEM"
######################################################################
-### PARTICIPANT IDENTIFIER
+### PARTICIPANT & SAMPLE IDENTIFIERS
######################################################################
## Global variable storing country codes (named vector)
# - E: Ethiopia
@@ -71,21 +80,6 @@ PVSTATEM_TIMEPOINT <- c("Observational" = "OB",
"Evaluation round 2" = "D",
"Passive Case Detection" = "PCD")
-## Global variable storing sample type codes (named vector)
-PVSTATEM_SAMPLE_TYPE_CODE <- c("Case Report Form" = "CRF",
- "Patient Information Sheet" = "PIS",
- "Sampling Sheet" = "SAS",
- "G6PD results" = "G6P",
- "Heparin tube" = "HEP",
- "EDTA" = "EDT",
- "Dried Blood Spot" = "DBS",
- "Bloodsmear" = "BLS",
- "Rapid Diagnostic Test" = "RDT",
- "Serum" = "SER",
- "Red Blood Cell pellet" = "RBC",
- "Cryo stabilat" = "CRY",
- "Additional spare" = "SPA")
-
## Global variable storing the possible values for aliquot number (vector)
PVSTATEM_ALIQUOT_RANGE <- 1:3
@@ -95,17 +89,31 @@ PVSTATEM_LABELS_PER_ROW <- 7
PVSTATEM_LABELS_PER_COL <- 17
PVSTATEM_LABELS_PER_SHEET <- PVSTATEM_LABELS_PER_ROW * PVSTATEM_LABELS_PER_COL
+
+
+
+
+######################################################################
+### RANDOMIZATION LIST
+######################################################################
## Global variables storing cluster randomization list
+PVSTATEM_RANDOMIZATION_E <- NULL
PVSTATEM_RANDOMIZATION_M <- read.table(file = "./00_COMMON/resources/randomisation.csv",
header = TRUE,
dec = ".",
sep = ",") %>%
select(-X) %>%
rename(cluster = cluster.ID) %>%
- mutate(cluster = gsub(pattern = "M",
+ mutate(country = "M",
+ cluster = gsub(pattern = "M",
replacement = "",
x = cluster)) %>%
mutate(cluster = sprintf(cluster, fmt = "%02s")) %>%
mutate(n_enroll_max = case_when(randomisation == 0 ~ 255,
randomisation == 1 ~ ceiling(size * 1.10),
.default = NA))
+
+
+
+PVSTATEM_RANDOMIZATION <- PVSTATEM_RANDOMIZATION_E %>%
+ bind_rows(PVSTATEM_RANDOMIZATION_M)
diff --git a/01_INVENTORY/INVENTORY_00_R_environment.R b/01_INVENTORY/INVENTORY_00_R_environment.R
index e559d2d..d500368 100644
--- a/01_INVENTORY/INVENTORY_00_R_environment.R
+++ b/01_INVENTORY/INVENTORY_00_R_environment.R
@@ -28,9 +28,9 @@ require(ggmap) # More general set of methods
######################################################################
-### CUSTOM R FUNCTIONS
+### CUSTOM R ENVIRONMENT & FUNCTIONS
######################################################################
-source("./00_COMMON/COMMON_00_R_functions.R")
+source("./00_COMMON/COMMON_00_R_environment.R")
source("./01_INVENTORY/INVENTORY_00_R_functions.R")
diff --git a/02_OBSERVATIONAL/OBSERVATIONAL_00_R_environment.R b/02_OBSERVATIONAL/OBSERVATIONAL_00_R_environment.R
index 96a07bb..222a8b2 100644
--- a/02_OBSERVATIONAL/OBSERVATIONAL_00_R_environment.R
+++ b/02_OBSERVATIONAL/OBSERVATIONAL_00_R_environment.R
@@ -30,7 +30,7 @@ require(tidyverse) # Data manipulation made easy
######################################################################
### CUSTOM R FUNCTIONS
######################################################################
-source("./00_COMMON/COMMON_00_R_functions.R")
+source("./00_COMMON/COMMON_00_R_environment.R")
diff --git a/03_INTERVENTIONAL_M0/INTERVENTIONAL_M0_00_R_environment.R b/03_INTERVENTIONAL_M0/INTERVENTIONAL_M0_00_R_environment.R
index c542eb5..6dea859 100644
--- a/03_INTERVENTIONAL_M0/INTERVENTIONAL_M0_00_R_environment.R
+++ b/03_INTERVENTIONAL_M0/INTERVENTIONAL_M0_00_R_environment.R
@@ -30,7 +30,7 @@ require(tidyverse) # Data manipulation made easy
######################################################################
### CUSTOM R FUNCTIONS
######################################################################
-source("./00_COMMON/COMMON_00_R_functions.R")
+source("./00_COMMON/COMMON_00_R_environment.R")
source("./03_INTERVENTIONAL_M0/INTERVENTIONAL_M0_00_R_functions.R")
@@ -109,3 +109,84 @@ CURATE_DATA_RECALCULATE_AGEY_MADAGASCAR <- FALSE
+
+######################################################################
+### REDCAP LABELLING
+######################################################################
+## Depending on casting functions, results from redcapAPI::exportRecordsTyped()
+## may be label-based or raw codes, whever a coding mechanism is involved.
+## The following global variables will store both codes and labels to be used as
+## a dictionary when checking if a coded data matches an expected category
+# Global variable: labeling of country for Ethiopia
+REDCAP_LABELS_RADIO_COUNTRY_E <- c("Ethiopia",
+ "Ethiopie",
+ "E")
+
+# Global variable: labeling of country for Madagascar
+REDCAP_LABELS_RADIO_COUNTRY_E <- c("Madagascar",
+ "Madagasikara",
+ "M")
+
+# Global variable: labeling of 'Yes' categorical value
+REDCAP_LABELS_RADIO_YES <- c(1,
+ "Yes",
+ "Oui",
+ "Eny")
+
+# Global variable: labeling of 'No' categorical value
+REDCAP_LABELS_RADIO_NO <- c(0,
+ "No",
+ "Non",
+ "Tsia")
+
+# Global variable: labeling of 1/0/0 in Pf/pan RDTs
+REDCAP_LABELS_RADIO_RDT_PF_PAN_100 <- c("RDT_M_100",
+ "100 (Negative)",
+ "100")
+
+# Global variable: labeling of 1/1/0 in Pf/pan RDTs
+REDCAP_LABELS_RADIO_RDT_PF_PAN_110 <- c("RDT_M_110",
+ "110 (Non-falciparum)",
+ "110")
+
+# Global variable: labeling of 1/0/1 in Pf/pan RDTs
+REDCAP_LABELS_RADIO_RDT_PF_PAN_101 <- c("RDT_M_101",
+ "101 (P. falciparum)",
+ "101")
+
+# Global variable: labeling of 1/1/1 in Pf/pan RDTs
+REDCAP_LABELS_RADIO_RDT_PF_PAN_111 <- c("RDT_M_111",
+ "111 (P. falciparum or mixed)",
+ "111")
+
+# Global variable: labeling of 1/0/0 in Pf/Pv RDTs
+REDCAP_LABELS_RADIO_RDT_PF_PV_100 <- c("RDT_E_100",
+ "100 (Negative)",
+ "100",
+ "Mihiba")
+
+# Global variable: labeling of 1/1/0 in Pf/Pv RDTs
+REDCAP_LABELS_RADIO_RDT_PF_PV_110 <- c("RDT_E_110",
+ "110 (P. vivax)",
+ "110",
+ "P. vivax")
+
+# Global variable: labeling of 1/0/1 in Pf/Pv RDTs
+REDCAP_LABELS_RADIO_RDT_PF_PV_101 <- c("RDT_E_101",
+ "101 (P. falciparum)",
+ "101",
+ "P. falciparum")
+
+# Global variable: labeling of 1/1/1 in Pf/Pv RDTs
+REDCAP_LABELS_RADIO_RDT_PF_PV_111 <- c("RDT_E_111",
+ "111 (Mixed)",
+ "111",
+ "Mixed")
+
+# Global variable: labeling of 'Checked' checkboxes
+REDCAP_LABELS_CHECKBOX_CHECKED <- c("Checked",
+ "1")
+
+# Global variable: labeling of 'Unchecked' checkboxes
+REDCAP_LABELS_CHECKBOX_UNCHECKED <- c("Unchecked",
+ "0")
--
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