Integrate PICDB into RICU (#5)

* Add picdb.json. * Some fewer rows. * Add "easy" entries to concept dicts. * Add 'sub_var': 'itemid' * Add some 'defaults' values. * Get rid of surgery vital signs. * load_difftime and id_win_helper for picdb. * Add picdb to startup datasets * Update row counts: chartevents, labevents --------- Co-authored-by: Manuel Burger <[email protected]>
ratschlab · Mar 6, 2024 · 8e5c060 · 8e5c060
1 parent 0be6b80
commit 8e5c060
Show file tree

Hide file tree

Showing 15 changed files with 1,404 additions and 48 deletions.
diff --git a/R/data-load.R b/R/data-load.R
@@ -178,6 +178,18 @@ load_difftime.sic_tbl <- function(x, rows, cols = colnames(x),
   load_eiau(x, {{ rows }}, cols, id_hint, time_vars, sec_as_mins)
 }
 
+#' @rdname load_src
+#' @export
+# copy-pasted from mimic_tbl
+load_difftime.picdb_tbl <- function(x, rows, cols = colnames(x),
+                                   id_hint = id_vars(x),
+                                   time_vars = ricu::time_vars(x), ...) {
+
+  warn_dots(...)
+
+  load_mihi(x, {{ rows }}, cols, id_hint, time_vars)
+}
+
 #' @rdname load_src
 #' @export
 load_difftime.character <- function(x, src, ...) {

diff --git a/R/data-utils.R b/R/data-utils.R
@@ -361,6 +361,35 @@ id_win_helper.miiv_env <- function(x) {
   order_rename(res, ids, sta, end)
 }
 
+#' @rdname data_utils
+#' @export
+# copy-pasted from mimic
+id_win_helper.picdb_env <- function(x) {
+
+  merge_inter <- function(x, y) {
+    merge(x, y, by = intersect(colnames(x), colnames(y)))
+  }
+
+  get_id_tbl <- function(tbl, id, start, end, aux) {
+    as_src_tbl(x, tbl)[, c(id, start, end, aux)]
+  }
+
+  cfg <- sort(as_id_cfg(x), decreasing = TRUE)
+
+  ids  <- field(cfg, "id")
+  sta <- field(cfg, "start")
+  end  <- field(cfg, "end")
+
+  res <- Map(get_id_tbl, field(cfg, "table"), ids, sta,
+             end, c(as.list(ids[-1L]), list(NULL)))
+  res <- Reduce(merge_inter, res)
+
+  res <- res[, c(sta, end) := lapply(.SD, as_dt_min, get(sta[1L])),
+             .SDcols = c(sta, end)]
+
+  order_rename(res, ids, sta, end)
+}
+
 #' @export
 id_win_helper.default <- function(x) stop_generic(x, .Generic)
 

diff --git a/R/utils-file.R b/R/utils-file.R
@@ -193,7 +193,7 @@ auto_attach_srcs <- function() {
   res <- sys_env("RICU_SRC_LOAD", unset = NA_character_)
 
   if (is.na(res)) {
-    c("mimic", "mimic_demo", "eicu", "eicu_demo", "hirid", "aumc", "miiv", "sic")
+    c("mimic", "mimic_demo", "eicu", "eicu_demo", "hirid", "aumc", "miiv", "sic", "picdb")
   } else {
     strsplit(res, ",")[[1L]]
   }

diff --git a/inst/extdata/config/concept-dict/blood_gas.json b/inst/extdata/config/concept-dict/blood_gas.json
@@ -71,6 +71,16 @@
                     "table": "laboratory",
                     "sub_var": "LaboratoryID"
                 }
+            ],
+            "picdb": [
+                {
+                    "table": "labevents",
+                    "ids": [
+                        5211,
+                        5249
+                    ],
+                    "sub_var": "itemid"
+                }
             ]
         }
     },
@@ -144,7 +154,8 @@
                     "table": "laboratory",
                     "sub_var": "LaboratoryID"
                 }
-            ]
+            ],
+            "picdb": []
         }
     },
     "fio2": {
@@ -246,7 +257,8 @@
                     "table": "data_float_h",
                     "sub_var": "DataID"
                 }
-            ]
+            ],
+            "picdb": []
         }
     },
     "hbco": {
@@ -282,6 +294,15 @@
                     "sub_var": "variableid",
                     "class": "hrd_itm"
                 }
+            ],
+            "picdb": [
+                {
+                    "table": "labevents",
+                    "ids": [
+                        5219
+                    ],
+                    "sub_var": "itemid"
+                }
             ]
         }
     },
@@ -356,6 +377,15 @@
                     "table": "laboratory",
                     "sub_var": "LaboratoryID"
                 }
+            ],
+            "picdb": [
+                {
+                    "table": "labevents",
+                    "ids": [
+                        5227
+                    ],
+                    "sub_var": "itemid"
+                }
             ]
         }
     },
@@ -416,6 +446,15 @@
                     "table": "labevents",
                     "sub_var": "itemid"
                 }
+            ],
+            "picdb": [
+                {
+                    "table": "labevents",
+                    "ids": [
+                        5228
+                    ],
+                    "sub_var": "itemid"
+                }
             ]
         }
     },
@@ -490,6 +529,16 @@
                     "table": "laboratory",
                     "sub_var": "LaboratoryID"
                 }
+            ],
+            "picdb": [
+                {
+                    "table": "labevents",
+                    "ids": [
+                        5235,
+                        5236
+                    ],
+                    "sub_var": "itemid"
+                }
             ]
         }
     },
@@ -559,6 +608,19 @@
                     "table": "laboratory",
                     "sub_var": "LaboratoryID"
                 }
+            ],
+            "picdb": [
+                {
+                    "table": "labevents",
+                    "ids": [
+                        5237,
+                        5238,
+                        5373,
+                        5374,
+                        5386
+                    ],
+                    "sub_var": "itemid"
+                }
             ]
         }
     },
@@ -636,6 +698,16 @@
                     "table": "laboratory",
                     "sub_var": "LaboratoryID"
                 }
+            ],
+            "picdb": [
+                {
+                    "table": "labevents",
+                    "ids": [
+                        5239,
+                        5244
+                    ],
+                    "sub_var": "itemid"
+                }
             ]
         }
     },
@@ -683,7 +755,8 @@
                     "table": "labevents",
                     "sub_var": "itemid"
                 }
-            ]
+            ],
+            "picdb": []
         }
     }
 }