Merge pull request #7 from jmjmfasdf/main

lecture slide, code edit

code/datatable-3-CCI.R

@@ -27,12 +27,17 @@ code.cci <- list(
 cciscore <- c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 6, 6, 2)
 names(cciscore) <- names(code.cci)
 
+# info.cci <- mclapply(names(code.cci), function(x){
+#   merge(data.asd[, .(RN_INDI, Indexdate)], 
+#         m40[like(MCEX_SICK_SYM, paste(code.cci[[x]], collapse = "|"))][order(MDCARE_STRT_DT), .SD[1], keyby = "RN_INDI"][, .(RN_INDI, inidate = MDCARE_STRT_DT)],
+#         by = "RN_INDI", all.x = T)[, ev := as.integer(Indexdate >= as.Date(as.character(inidate), format = "%Y%m%d"))][, ev := ifelse(is.na(ev), 0, ev)][]$ev * cciscore[x]
+# }, mc.cores = 4) %>% do.call(cbind, .) %>% cbind(rowSums(.))
+# colnames(info.cci) <- c(paste0("Prev_", names(code.cci)), "CCI")
 
-
+# rolling merge in 365 days 위의 결과와 같게 하려면 roll=Inf, 365일 내로 보려면 roll=365
 info.cci <- mclapply(names(code.cci), function(x){
-  merge(data.asd[, .(RN_INDI, Indexdate)], 
-        m40[like(MCEX_SICK_SYM, paste(code.cci[[x]], collapse = "|"))][order(MDCARE_STRT_DT), .SD[1], keyby = "RN_INDI"][, .(RN_INDI, inidate = MDCARE_STRT_DT)],
-        by = "RN_INDI", all.x = T)[, ev := as.integer(Indexdate > as.Date(as.character(inidate), format = "%Y%m%d"))][, ev := ifelse(is.na(ev), 0, ev)][]$ev * cciscore[x]
-}, mc.cores = 4) %>% do.call(cbind, .) %>% cbind(rowSums(.))
+  data.asd[, MDCARE_STRT_DT := Indexdate]
+  dt <- m40[like(MCEX_SICK_SYM, paste(code.cci[[x]], collapse = "|"))][, MDCARE_STRT_DT := as.Date(as.character(MDCARE_STRT_DT), format = "%Y%m%d")][, .(RN_INDI, MDCARE_STRT_DT, Incidate = MDCARE_STRT_DT)]  
+  dt[, .SD[1], keyby = c("RN_INDI", "MDCARE_STRT_DT")][data.asd, on = c("RN_INDI", "MDCARE_STRT_DT"), roll = 365][, ev := as.integer(!is.na(Incidate))][]$ev * cciscore[x]
+}, mc.cores = 4) %>%  do.call(cbind, .) %>% cbind(rowSums(.))
 colnames(info.cci) <- c(paste0("Prev_", names(code.cci)), "CCI")
-

code/datatable-4-prevdrug.R

@@ -13,9 +13,17 @@ code.drug <- list(
 )
 
 
+# info.prevmed <- mclapply(code.drug, function(x){
+#   merge(data.asd,
+#         m60[GNL_NM_CD %in% x][order(MDCARE_STRT_DT), .SD[1], keyby = "RN_INDI"][, .(RN_INDI, inidate = MDCARE_STRT_DT)],
+#         by = "RN_INDI", all.x = T)[, ev := as.integer(Indexdate >= as.Date(as.character(inidate), format = "%Y%m%d"))][, ev := ifelse(is.na(ev), 0, ev)][]$ev
+# }, mc.cores = 3) %>% do.call(cbind, .)
+# colnames(info.prevmed) <- paste0("Prev_", names(code.drug))
+
+# rolling merge in 365 days 위의 결과와 같게 하려면 roll=Inf, 365일 내로 보려면 roll=365
 info.prevmed <- mclapply(code.drug, function(x){
-  merge(data.asd,
-        m60[GNL_NM_CD %in% x][order(MDCARE_STRT_DT), .SD[1], keyby = "RN_INDI"][, .(RN_INDI, inidate = MDCARE_STRT_DT)],
-        by = "RN_INDI", all.x = T)[, ev := as.integer(Indexdate > as.Date(as.character(inidate), format = "%Y%m%d"))][, ev := ifelse(is.na(ev), 0, ev)][]$ev
+  data.asd[, MDCARE_STRT_DT := Indexdate]
+  dt <- m60[GNL_NM_CD %in% x][, MDCARE_STRT_DT := as.Date(as.character(MDCARE_STRT_DT), format = "%Y%m%d")][, .(RN_INDI, MDCARE_STRT_DT, inidate = MDCARE_STRT_DT)] 
+  dt[, .SD[1], keyby = c("RN_INDI", "MDCARE_STRT_DT")][data.asd, on = c("RN_INDI", "MDCARE_STRT_DT"), roll = 365][, ev := as.integer(!is.na(inidate))][]$ev
 }, mc.cores = 3) %>% do.call(cbind, .)
-colnames(info.prevmed) <- paste0("Prev_", names(code.drug))
+colnames(info.prevmed) <- paste0("Prev_", names(code.drug))

code/datatable-5-outcome.R

@@ -1,12 +1,18 @@
 ## MI after indexdate
 
 source("code/inclusion.R")
-info.MI <- merge(data.asd[, .(RN_INDI, Indexdate)], 
-                 m40[like(MCEX_SICK_SYM, paste(code.cci[["MI"]], collapse = "|"))][, .(RN_INDI, MIdate = MDCARE_STRT_DT)], by = "RN_INDI", all.x = T) %>% 
-  .[Indexdate < as.Date(as.character(MIdate), format = "%Y%m%d")] %>% 
-  .[order(MIdate), .(MI = 1, MIday = as.integer(as.Date(as.character(MIdate), format = "%Y%m%d") - Indexdate)[1]), keyby = "RN_INDI"]
-
-
+# info.MI <- merge(data.asd[, .(RN_INDI, Indexdate)], 
+#                  m40[like(MCEX_SICK_SYM, paste(code.cci[["MI"]], collapse = "|"))][, .(RN_INDI, MIdate = MDCARE_STRT_DT)], by = "RN_INDI", all.x = T) %>% 
+#   .[Indexdate <= as.Date(as.character(MIdate), format = "%Y%m%d")] %>% 
+#   .[order(MIdate), .(MI = 1, MIday = as.integer(as.Date(as.character(MIdate), format = "%Y%m%d") - Indexdate)[1]), keyby = "RN_INDI"]
+
+# rolling merge 위의 결과와 같게 하려면 roll=-Inf, 365일 내로 보려면 roll=365
+data.asd[, MDCARE_STRT_DT := Indexdate]
+info.MI <- m40 %>% 
+  .[like(MCEX_SICK_SYM, paste(code.cci[["MI"]], collapse = "|")), .(RN_INDI, MDCARE_STRT_DT = as.Date(as.character(MDCARE_STRT_DT), format = "%Y%m%d"), MIdate = as.Date(as.character(MDCARE_STRT_DT), format = "%Y%m%d"))] %>%
+  .[data.asd, on = c("RN_INDI", "MDCARE_STRT_DT"), roll = -Inf] %>% 
+  .[Indexdate <= MIdate] %>% 
+  .[order(MIdate), .(MI = 1, MIday = as.integer(MIdate - Indexdate)[1]), keyby = "RN_INDI"]
 
 
 data.final <- cbind(data.asd, info.cci, info.prevmed) %>% merge(info.MI, by = "RN_INDI", all.x = T) %>% .[, `:=`(MI = as.integer(!is.na(MI)),