Codages manquants (exhaustivité)

donnees.R

@@ -8,6 +8,7 @@ date <- "04/12/2015"
 user <- ""
 password <- ""
 
+# Ovalide
 read.csv2("listOvalide.csv") %>%
 {
   apply(., 1, . %>%
@@ -27,6 +28,7 @@ read.csv2("listOvalide.csv") %>%
   names(OvalideP) <<- .$name
 }
 
+# RUM + structure + calcul durée de séjour
 src_mysql("pmsi_dim", "livenne.chu-nancy.fr", user = user, password = password) %>%
   tbl(sql("SELECT idhosp, idrss, idrum, date_entree, date_sortie, cmd, um FROM fix116
           UNION
@@ -36,7 +38,7 @@ src_mysql("pmsi_dim", "livenne.chu-nancy.fr", user = user, password = password)
          date_sortie = date_sortie %>% as.Date,
          annee_sortie = year(date_sortie),
          mois_sortie = month(date_sortie)) %>%
-  filter(annee_sortie > annee - 3) %>% # Données rum/rss depuis 3 ans
+  filter(annee_sortie > annee - 3) %>% # Données rum/rss depuis 3 ans
   left_join(src_mysql("pmsi_dim_nom", "livenne.chu-nancy.fr", user = user, password = password) %>%
             tbl("structure") %>%
             filter(um != "") %>%
@@ -44,29 +46,45 @@ src_mysql("pmsi_dim", "livenne.chu-nancy.fr", user = user, password = password)
             arrange(um, uf_date_ferm) %>%
             distinct %>%
             collect %>%
-            add_rownames(var = "dummy") %>% # Dédoublonnage : 1 um -> 1 couple libellés
+            add_rownames(var = "dummy") %>% # Dédoublonnage : 1 um -> 1 couple libellés
             group_by(um) %>%
               filter(dummy == last(dummy)) %>%
               select(-dummy, -uf_date_ferm) %>%
-              ungroup) %>%
-  mutate(idrss = ifelse(idhosp %>% str_detect("^13"), str_c("m", idrss), idrss)) %>% # Dédoublonnage rss maternité 2013
+            ungroup) %>%
+  mutate(idrss = ifelse(idhosp %>% str_detect("^13"), str_c("m", idrss), idrss)) %>% # Dédoublonnage rss maternité 2013
   mutate(idhosp = idhosp %>% str_replace_all(" ", "")) %>%
-  mutate(duree_rum = date_sortie - date_entree) %>% # durée rum
+  mutate(duree_rum = date_sortie - date_entree) %>% # durée rum
   left_join(group_by(., idrss) %>%
             summarise(duree_rss = sum(duree_rum))) -> rum
 
+# GAM et structure --> hospit non codées
 src_mysql("pmsi_dim", "livenne.chu-nancy.fr", user = user, password = password) %>%
   tbl("mvt_gam") %>%
-  select(idhosp, date_entree, date_sortie, uf) %>%
-  filter(date_sortie != "") %>%
+  select(idhosp, date_entree, date_sortie, uf, pass_typ, type_resp) %>%
+  filter(pass_typ != "EXT",
+         type_resp == "H") %>%
+  distinct %>%
   collect %>%
   mutate(date_entree = as.Date(date_entree),
          date_sortie = as.Date(date_sortie)) %>%
-  filter(date_sortie >= as.Date(str_c(annee, "01", "01", sep = "-")),
-         date_sortie < as.Date(str_c(annee, mois, "01", sep = "-")) + period(1, "month")) %>%
-  distinct -> gam
-
-gam %>%
-  anti_join(rum, by="idhosp")
+  anti_join(filter(., is.na(date_sortie) | date_sortie >= as.Date(str_c(annee, mois, "01", sep = "-")) + period(1, "month")),
+            by = "idhosp") %>% # supprimer séjours non terminés à la fin de la période étudiée
+  filter(date_sortie >= as.Date(str_c(annee, "01", "01", sep = "-"))) %>%
+  select(-pass_typ, -type_resp) %>%
+  left_join(src_mysql("pmsi_dim_nom", "livenne.chu-nancy.fr", user = user, password = password) %>%
+            tbl("structure") %>%
+            filter(um != "") %>%
+            select(uf, service, service_libelle, pole, pole_libelle) %>%
+            distinct %>%
+            collect, by = "uf") %>%
+  anti_join(rum, by="idhosp") %>% # supprimer séjours codés
+  arrange(idhosp, date_sortie) %>%
+  filter(!(service %in% c("5110", "5140", "1700", "1170", "1600", "2350")),
+         !is.na(service)) %>%
+  group_by(idhosp) %>%
+  summarise(date_entree = first(date_entree),
+            date_sortie = last(date_sortie),
+            service_libelle= last(service_libelle),
+            pole_libelle = last(pole_libelle)) -> gam
 
 save(Ovalide, OvalideP, annee, mois, rum, gam, date, file = "donnees.Rdata")