Update table1_table_collation.R

opensafely · Sep 27, 2024 · 48b3077 · 48b3077
1 parent be54a58
commit 48b3077
Showing 1 changed file with 21 additions and 7 deletions.
diff --git a/analysis/collation_code/table1_table_collation.R b/analysis/collation_code/table1_table_collation.R
@@ -19,19 +19,33 @@ fs::dir_create(here("output", "collated", "descriptive"))
 # import table 1 by cohort
 collated_table1 = rbind(
   read_csv(here::here("output", "table1", paste0("table1_", cohort, 
-           "_2016_2017.csv"))) %>% mutate(subset = "2016_17"),
+           "_2016_2017.csv"))) %>% rename(N = 2) %>% 
+    mutate(N = ifelse(row_number() == 1, .[2, 2], N)) %>%
+    slice(-2) %>% mutate(subset = "2016_17") ,
   read_csv(here::here("output", "table1", paste0("table1_", cohort, 
-           "_2017_2018.csv"))) %>% mutate(subset = "2017_18"),
+           "_2017_2018.csv"))) %>% rename(N = 2) %>% 
+    mutate(N = ifelse(row_number() == 1, .[2, 2], N)) %>%
+    slice(-2) %>%  mutate(subset = "2017_18"),
   read_csv(here::here("output", "table1", paste0("table1_", cohort,
-           "_2018_2019.csv"))) %>% mutate(subset = "2018_19"),
+           "_2018_2019.csv"))) %>% rename(N = 2) %>% 
+    mutate(N = ifelse(row_number() == 1, .[2, 2], N)) %>%
+    slice(-2) %>%  mutate(subset = "2018_19"),
   read_csv(here::here("output", "table1", paste0("table1_", cohort, 
-           "_2019_2020.csv"))) %>% mutate(subset = "2019_20"),
+           "_2019_2020.csv"))) %>% rename(N = 2) %>% 
+    mutate(N = ifelse(row_number() == 1, .[2, 2], N)) %>%
+    slice(-2) %>%  mutate(subset = "2019_20"),
   read_csv(here::here("output", "table1", paste0("table1_", cohort, 
-           "_2020_2021.csv"))) %>% mutate(subset = "2020_21"),
+           "_2020_2021.csv"))) %>% rename(N = 2) %>% 
+    mutate(N = ifelse(row_number() == 1, .[2, 2], N)) %>%
+    slice(-2) %>%  mutate(subset = "2020_21"),
   read_csv(here::here("output", "table1", paste0("table1_", cohort, 
-           "_2021_2022.csv"))) %>% mutate(subset = "2021_22"),
+           "_2021_2022.csv"))) %>% rename(N = 2) %>% 
+    mutate(N = ifelse(row_number() == 1, .[2, 2], N)) %>%
+    slice(-2) %>%  mutate(subset = "2021_22"),
   read_csv(here::here("output", "table1", paste0("table1_", cohort, 
-           "_2022_2023.csv"))) %>% mutate(subset = "2022_23")
+           "_2022_2023.csv"))) %>% rename(N = 2) %>% 
+    mutate(N = ifelse(row_number() == 1, .[2, 2], N)) %>%
+    slice(-2) %>%  mutate(subset = "2022_23")
 )
 
 #save as csv