From 9fcf3c4b18e87081e205297f47138ac71b3ba7d3 Mon Sep 17 00:00:00 2001
From: Linda Nab <linda.nab@thedatalab.org>
Date: Sun, 12 Nov 2023 14:18:10 +0000
Subject: [PATCH] describe trt outc same day

---
 .../describe_trt_outcm_same_day.R             | 71 +++++++++++++++++++
 project.yaml                                  |  8 +++
 2 files changed, 79 insertions(+)
 create mode 100644 analysis/data_properties/describe_trt_outcm_same_day.R

diff --git a/analysis/data_properties/describe_trt_outcm_same_day.R b/analysis/data_properties/describe_trt_outcm_same_day.R
new file mode 100644
index 0000000..1c5541b
--- /dev/null
+++ b/analysis/data_properties/describe_trt_outcm_same_day.R
@@ -0,0 +1,71 @@
+################################################################################
+#
+# Number of people treated and experiencing an outcome on same day
+# 
+# This script can be run via an action in project.yaml using one argument
+# - 'period' /in {ba1, ba2} --> period 
+#
+# Depending on 'period' the output of this script is:
+# empty file ./output/data_properties/trt_outcm_same_day.csv
+################################################################################
+
+################################################################################
+# 0.0 Import libraries + functions
+################################################################################
+library(readr)
+library(dplyr)
+library(fs)
+library(here)
+library(purrr)
+
+################################################################################
+# 0.1 Create directories for output
+################################################################################
+output_dir <- here("output", "data_properties")
+fs::dir_create(output_dir)
+
+################################################################################
+# 0.2 Import command-line arguments
+################################################################################
+
+################################################################################
+# 0.3 Import data
+################################################################################
+file_names <- paste0(c("", "ba2_"), "data_processed.rds")
+data <-
+  map(.x = fs::path(here("output", "data"), file_names),
+      .f = ~ read_rds(.x))
+names(data) <- c("ba1", "ba2")
+
+################################################################################
+# Number of pt treated + outcome on same day
+################################################################################
+out <- 
+  imap(.x = data,
+       .f = ~ 
+         .x %>%
+         filter(status_primary %in% c("covid_hosp_death", "noncovid_death", "dereg") & 
+                  treatment == "Treated" &
+                  treatment_date == min_date_all) %>%
+         group_by(status_primary, .drop = "FALSE") %>%
+         summarise(n = n()) %>%
+         filter(status_primary != "none") %>%
+         mutate(period = .y, .before = status_primary)
+  ) %>% bind_rows()
+# Set rounding and redaction thresholds
+rounding_threshold = 6
+redaction_threshold = 8
+out_red <-
+  out %>%
+  mutate(n = if_else(n > 0 & n <= redaction_threshold,
+                     "[REDACTED]",
+                     plyr::round_any(n, rounding_threshold) %>% as.character()
+                     )
+         )
+################################################################################
+#  Save output
+################################################################################
+write_csv(out,
+          path(output_dir, "trt_outcm_same_day.csv"))
+write_csv(out_red,
+          path(output_dir, "trt_outcm_same_day_red.csv"))
diff --git a/project.yaml b/project.yaml
index 417cffb..32f79b0 100644
--- a/project.yaml
+++ b/project.yaml
@@ -229,6 +229,14 @@ actions:
       moderately_sensitive:
         csv: output/data_properties/ba2_sense_checks.txt
 
+  describe_trt_outcm_same_day:
+    run: r:latest analysis/data_properties/describe_trt_outcm_same_day.R
+    needs: [data_process, data_process_ba2]
+    outputs:
+      moderately_sensitive:
+        csv1: output/data_properties/trt_outcm_same_day.csv
+        csv2: output/data_properties/trt_outcm_same_day_red.csv
+
   ## # # # # # # # # # # # # # # # # # # # 
   ## # # # # # # # # # # # # # # # # # # # 
   ## 1 MAIN ANALYSIS - COX