Change name of INVENTORY_05 script and clean content to make it call the...

Change name of INVENTORY_05 script and clean content to make it call the required functions and generate the expected output

01_INVENTORY/INVENTORY_00_R_environment.R

@@ -101,3 +101,13 @@ MAP_TYPE                      <- "hybrid"
 ## Layout of panels for plotting GPS maps
 MAP_PLOT_PANEL_LAYOUT_NROW    <- 3
 MAP_PLOT_PANEL_LAYOUT_NCOL    <- 3
+
+
+
+
+
+######################################################################
+### SEED VALUE
+######################################################################
+## A global seed value to be used by set.seed() calls
+SEED <- 12345

01_INVENTORY/INVENTORY_02_list_all_inventory_participants.R

-## INVENTORY_02_list_all_inventory_participants.R
-## Date     : 2023/10/31
-## Author   : Thomas Obadia
-##
-## This script starts by fetching another one to dump the database
-## for the PvSTATEM Inventory project (hosted into REDCap).
-## It subsequently processes the inventory database to generate a list
-## of all individuals that were listed, and saves that list into
-## an output CSV file.
-######################################################################
-
-
-
-
-
-######################################################################
-### SOURCE THE DATABASE
-######################################################################
-if (!exists("DATA_EXTRACT_IS_RECENT") || DATA_EXTRACT_IS_RECENT) {
-  source("./01_INVENTORY/INVENTORY_01_dump_REDCap_database.R")
-}
-
-## Update DATA_EXTRACT_IS_RECENT_FLAG for future calls
-DATA_EXTRACT_IS_RECENT    <- as.logical(as.numeric(difftime(time1 = Sys.Date(), 
-                                                            time2 = DATA_EXTRACT_TS, 
-                                                            units = "days")) <= DATA_EXTRACT_EXPIRY_TIME_D)
-
-
-
-
-
-######################################################################
-### DERIVE LIST OF ALL INDIVIDUALS
-######################################################################
-inventory_list_p <- dat_inventory_raw %>% 
-  select(
-    # REDCap internal record_id
-    record_id, 
-    
-    # Items used to derive the house-and-household ID
-    country, clusterid, hid, hh_n, 
-    tidyselect::matches("^hh\\d{2}_subjid\\d{2}_(id|sex|agey)$")) %>% 
-  
-  # Prevent mis-interpretation of *_sex columns because 'F' can be FALSE in some context
-  mutate(across(ends_with("_sex"), function(x) {plyr::mapvalues(x, 
-                                                                from         = c(FALSE), 
-                                                                to           = c("F"), 
-                                                                warn_missing = FALSE)})) %>% 
-  
-  # Go from wide format to long to list household members by row, 
-  # then propagate age and sex to dedicated columns, to end up with
-  # a single row per individual
-  pivot_longer(cols             = starts_with("hh0"), 
-               names_to         = c("pivot_hh_n", "pivot_hh_subjid", "pivot_variable"), 
-               names_pattern    = c("^(hh\\d{2})_(subjid\\d{2})_(id|sex|agey)$"), 
-               values_transform = as.character) %>% 
-  pivot_wider(names_from  = "pivot_variable", 
-              values_from = "value") %>% 
-  mutate(agey = as.numeric(agey)) %>% 
-  extract(pivot_hh_n, 
-          into  = c("nested_hhid"), 
-          regex = "^hh(\\d{2})$") %>% 
-  extract(pivot_hh_subjid, 
-          into  = c("nested_subjid"), 
-          regex = "^subjid(\\d{2})$") %>% 
-  
-  # Add age as a categorical variable
-  mutate(agey_cat = case_when(country == "M" & agey < 1               ~ "y00_01",
-                              country == "M" & agey >= 1 & agey <= 5  ~ "y01_05",
-                              country == "M" & agey > 5  & agey <= 13 ~ "y05_13",
-                              country == "M" & agey > 13 & agey <= 24 ~ "y13_24", 
-                              country == "M" & agey > 24              ~ "y24_inf")) %>% 
-  
-  # Discard rows for whom no data was filled, i.e. empty placeholders in REDCap
-  filter(!is.na(sex) & !is.na(agey)) %>% 
-  
-  # Retain only columns of interest for derived data (list of everyone in inventory) 
-  select(
-    # REDCap internal record_id
-    record_id, 
-    
-    # Items used to derive the house-and-household ID
-    country, clusterid, hid, nested_hhid, nested_subjid, 
-    
-    # Actual demographics
-    sex, agey, agey_cat)
-
-
-
-
-
-######################################################################
-### WRITE LIST TO OUTPUT
-######################################################################
-## Name of output file
-INVENTORY_OUT_02_FILENAME <- paste0("INVENTORY_OUT_02_list_individuals", 
-                                    "_country-", 
-                                    paste(unique(inventory_list_p$country), collapse = "-"), 
-                                    "_timestamp-", 
-                                    strftime(Sys.time(), format = "%Y%m%d_%H%M%S"), 
-                                    ".csv")
-
-## Write to output file
-write.table(inventory_list_p, 
-            file      = paste0("./01_INVENTORY/outputs/", 
-                               INVENTORY_OUT_02_FILENAME), 
-            sep       = ",", 
-            dec       = ".", 
-            quote     = TRUE, 
-            col.names = TRUE, 
-            row.names = FALSE)
-
-
-
-
-
-######################################################################
-### CLEANUP
-######################################################################
-rm(INVENTORY_OUT_02_FILENAME)

01_INVENTORY/INVENTORY_05_generate_list_of_participants_for_observational_study.R

 ## INVENTORY_05_select_list_function.R
 ## Date     : 2024/02/02
-## Author   : Eliharintsoa Rajaoranimirana
+## Author   : Eliharintsoa Rajaoranimirana, Thomas Obadia
 ##
 ## This script provides functions to sample from the population from 
 ## the inventory project and generate a list of participants of 
@@ -11,6 +11,67 @@
 
 
 
-myfunction(32, 20)
+######################################################################
+### SOURCE THE DATABASE
+######################################################################
+if (!exists("DATA_EXTRACT_IS_RECENT") || DATA_EXTRACT_IS_RECENT) {
+  source("./01_INVENTORY/INVENTORY_01_dump_REDCap_database.R")
+}
+
+## Update DATA_EXTRACT_IS_RECENT_FLAG for future calls
+DATA_EXTRACT_IS_RECENT    <- as.logical(as.numeric(difftime(time1 = Sys.Date(), 
+                                                            time2 = DATA_EXTRACT_TS, 
+                                                            units = "days")) <= DATA_EXTRACT_EXPIRY_TIME_D)
+
+
+
+
+
+######################################################################
+### REPLICABILITY
+######################################################################
+set.seed(seed = SEED)
+
+
 
-save_multiple_cluster(c(3,4), c(10,5))
+
+
+######################################################################
+### GENERATE SAMPLING LIST
+######################################################################
+observational_list_p <- get_target_list_for_observational_study(x        = inventory_list_p, 
+                                                                n_target = 270)
+
+
+
+
+
+######################################################################
+### WRITE LIST TO OUTPUT
+######################################################################
+## Name of output file
+INVENTORY_OUT_05_FILENAME <- paste0("INVENTORY_OUT_05_list_participants_for_observational_study", 
+                                    "_country-", 
+                                    paste(unique(observational_list_p$country), collapse = "-"), 
+                                    "_timestamp-", 
+                                    strftime(Sys.time(), format = "%Y%m%d_%H%M%S"), 
+                                    ".csv")
+
+## Write to output file
+write.table(observational_list_p, 
+            file      = paste0("./01_INVENTORY/outputs/", 
+                               INVENTORY_OUT_05_FILENAME), 
+            sep       = ",", 
+            dec       = ".", 
+            quote     = TRUE, 
+            col.names = TRUE, 
+            row.names = FALSE)
+
+
+
+
+
+######################################################################
+### CLEANUP
+######################################################################
+rm(INVENTORY_OUT_05_FILENAME)