Rel

doc/BestillingerOgUtleveringer.R

@@ -3,6 +3,134 @@ library(norgast)
 # library(tidyverse)
 rm(list=ls())
 
+##### Uttrekk Søreide, pankreas 2016-2022, 22.10.2024 ##########################
+varnavn_kobl <- data.frame(
+  kol = c("mce.MCEID AS ForlopsID",
+          "mce.PATIENT_ID AS PasientId",
+          "mce.CENTREID AS AvdRESH",
+          "patient.SSN AS Fodselsnummer",
+          "patient.DECEASED AS Avdod",
+          "patient.DECEASED_DATE AS AvdodDato",
+          "centre.CENTRENAME AS SenterNavn",
+          "registration.PREVIOUS_WEIGHT AS Vekt6MndFoer",
+          "registration.PREVIOUS_WEIGHT_MISS AS Vekt6MndFoerUkjent",
+          "registration.ADMISSION_WEIGHT AS VektVedInnleggelse",
+          "registration.ADMISSION_WEIGHT_MISS AS VektVedInnleggelseUkjent",
+          "registration.HEIGHT AS Hoyde",
+          "registration.HEIGHT_MISS AS HoydeUkjent",
+          "registration.BMI AS BMI",
+          "registration.BMI_CATEGORY AS BMIKategori",
+          "registration.WEIGHTLOSS AS VekttapProsent",
+          "registration.DIABETES AS MedDiabetes",
+          "registration.CHEMOTHERAPY_ONLY AS KunCytostatika",
+          "registration.RADIATION_THERAPY_ONLY AS KunStraaleterapi",
+          "registration.CHEMORADIOTHERAPY AS KjemoRadioKombo",
+          "registration.WHO_ECOG_SCORE AS WHOECOG",
+          "registration.ALBUMIN AS Albumin",
+          "registration.CRP AS CRP",
+          "registration.GLASGOW_SCORE AS GlasgowScore",
+          "registration.MODIFIED_GLASGOW_SCORE AS ModGlasgowScore",
+          "registration.ASA AS ASA",
+          "registration.LUNG_DISEASE AS Lungesykdom",
+          "registration.HEART_DISEASE AS Hjertesykdom",
+          "registration.URGENCY AS Hastegrad",
+          "registration.ANESTHESIA_START AS AnestesiStartKl",
+          "registration.PRS_SCORE AS PRSScore",
+          "registration.OPERATION_DATE AS OpDato",
+          "registration.NCSP AS Hovedoperasjon",
+          "registration.ABLATION AS LeverAblasjon",
+          "registration.RECONSTRUCTION AS Rekonstruksjon",
+          "registration.RECONSTRUCTION_TYPE AS Rekonstruksjonstype",
+          "registration.ANASTOMOSIS_LEVEL AS Anastomoseniva",
+          "registration.ANASTOMOSIS AS NyAnastomose",
+          "registration.ANAL_GUARD_DISTANCE AS AvstandAnalVerge",
+          "registration.ANAL_GUARD_DISTANCE_MISS AS AvstandAnalVergeIkkeAkt",
+          "registration.TATME AS TaTME",
+          "registration.OSTOMY AS NyStomi",
+          "registration.ABDOMINAL_ACCESS AS Tilgang",
+          "registration.ROBOTASSISTANCE AS Robotassistanse",
+          "registration.THORAX_ACCESS AS ThoraxTilgang",
+          "registration.RELAPAROTOMY AS ReLapNarkose",
+          "registration.RELAPAROTOMY_YES AS ViktigsteFunn",
+          "registration.FINDINGS_SPESIFISER AS FunnSpesifiser",
+          "registration.RELAPAROTOMY_NO AS AnnenOpIAnestsi",
+          "registration.INTERVENTION_WITHOUT_ANESTHESIA AS IntUtenAnestesi",
+          "registration.PERCUTANEOUS_DRAINAGE AS PerkDrenasje",
+          "registration.HIGH_AMYLASE_CONCENTRATION AS HoyAmylaseKons",
+          "registration.LEAK_INTERVENTION AS EndoInterLekkasje",
+          "registration.BLEED_INTERVENTION AS EndoInterBlod",
+          "registration.ANGIO_INTERVENTION AS AngioInter",
+          "registration.LIQUID_DRAINAGE AS KunDrenasje",
+          "registration.SINGLE_ORGAN_FAILURE AS EttOrganSvikt",
+          "registration.MULTI_ORGAN_FAILURE AS MultiOrganSvikt",
+          "registration.IN_HOUSE_DEATH AS DodUnderOpphold",
+          "registration.IN_HOUSE_DEATH_DATE AS DodUnderOppholdDato",
+          "registration.ACCORDION_SCORE AS AccordionGrad",
+          "registration.DISCHARGE_DATE AS UtskrivelseDato",
+          "registration.BED_DAYS AS PostopLiggedogn",
+          "registration.ICD10 AS Hoveddiagnose",
+          "registration.DISCHARGE_TO AS UtskrevetTil",
+          "registration.STATUS AS RegistreringStatus",
+          "readmission.OWN_INSTITUTION AS ReinnlEgenInst",
+          "readmission.OTHER_INSTITUTIONS AS ReinnlAndreInst",
+          "readmission.CONTROL AS AktivKontroll",
+          "readmission.PHYSICAL_CONTROL AS FysiskKontroll",
+          "readmission.PHONE_CONTROL AS TelefonKontroll",
+          "readmission.RELAPAROTOMY AS OppfReLapNarkose",
+          "readmission.RELAPAROTOMY_YES AS OppfViktigsteFunn",
+          "readmission.FINDINGS_SPESIFISER AS OppfFunnSpesifiser",
+          "readmission.RELAPAROTOMY_NO AS OppfAnnenOpIAnestsi",
+          "readmission.INTERVENTION_WITHOUT_ANESTHESIA AS OppfIntUtenAnestesi",
+          "readmission.PERCUTANEOUS_DRAINAGE AS OppfPerkDrenasje",
+          "readmission.HIGH_AMYLASE_CONCENTRATION AS OppfHoyAmylaseKons",
+          "readmission.LEAK_INTERVENTION AS OppfEndoInterLekkasje",
+          "readmission.BLEED_INTERVENTION AS OppfEndoInterBlod",
+          "readmission.ANGIO_INTERVENTION AS OppfAngioInter",
+          "readmission.LIQUID_DRAINAGE AS OppfKunDrenasje",
+          "readmission.SINGLE_ORGAN_FAILURE AS OppfEttOrganSvikt",
+          "readmission.MULTI_ORGAN_FAILURE AS OppfMultiOrganSvikt",
+          "readmission.IN_HOUSE_DEATH AS OppfDodUnderOpphold",
+          "readmission.IN_HOUSE_DEATH_DATE AS OppfDodUnderOppholdDato",
+          "readmission.ACCORDION_SCORE AS OppfAccordionGrad",
+          "readmission.STATUS AS OppfStatus")) %>%
+  tidyr::separate(col="kol", into=c("dbnavn", "rapporteket"), sep = " AS ") %>%
+  dplyr::mutate(dbnavn = toupper(dbnavn))
+# dplyr::as_tibble() %>%
+# tidyr::separate(col="dbnavn", into=c("skjema", "dbnavn"), sep = "\\." )
+
+utlevernavn <- readr::read_csv2("~/mydata/norgast/utlevering_soreide.csv",
+                                    locale = readr::locale(encoding = "Latin1"))
+utlevernavn <- utlevernavn %>% dplyr::mutate(variabel_id = sub("_", ".", variabel_id))
+utlevernavn1 <- utlevernavn$variabel_id %>% unique()
+utlevernavn <- readr::read_csv2("~/mydata/norgast/varnavn_utlevering_v2.csv",
+                                locale = readr::locale(encoding = "Latin1"))
+utlevernavn <- utlevernavn %>% dplyr::mutate(variabel_id = sub("_", ".", variabel_id))
+utlevernavn2 <- utlevernavn$variabel_id %>% unique()
+rappnavn_utlevering <- varnavn_kobl %>%
+  dplyr::filter(dbnavn %in% c(utlevernavn1, utlevernavn2))
+
+RegData <- norgast::NorgastHentRegData()
+RegData <- norgast::NorgastPreprosess(RegData)
+kobling <- readr::read_csv2("~/mydata/norgast/NoRGast_koblingstabell_datadump_30.09.2024.csv")
+
+utlevering <- RegData %>%
+  dplyr::filter(Aar %in% 2016:2022 &
+                  ncsp_lowercase %in% c("jlc10", "jlc11", "jlc30", "jlc31")) %>%
+  dplyr::select(c(rappnavn_utlevering$rapporteket,
+                  "PasientID", "PasientKjonn", "AvdRESH", "SykehusNavn", "ForlopsID", "Alder")) %>%
+  merge(kobling, by.x = "PasientID", by.y = "PID") %>%
+  mutate(fdato = paste0(substr(SSN, 1,2), ".", substr(SSN, 3,4), ".", substr(SSN, 5,6))) %>%
+  select(-"SSN") %>%
+  mutate(ncsp_kode = stringr::str_extract(Hovedoperasjon, "^[^\\s]+"),
+         ncsp_tekst = stringr::str_extract(Hovedoperasjon, "\\s.+"),
+         icd10_kode = stringr::str_extract(Hoveddiagnose, "^[^\\s]+"),
+         icd10_tekst = stringr::str_extract(Hoveddiagnose, "\\s.+"))
+
+openxlsx::write.xlsx(utlevering, "~/mydata/norgast/textbook_outcomes_pancreas_okt2024.xlsx")
+write.csv2(utlevering, "~/mydata/norgast/textbook_outcomes_pancreas_okt2024.csv",
+           row.names = F, fileEncoding = "Latin1", na = "")
+
+
 ###### Komorbiditet NPR 30.09.2024 ########################################
 RegData <- norgast::NorgastHentRegData() %>%
   norgast::NorgastPreprosess() %>%

docker-compose.yml

@@ -11,7 +11,7 @@ services:
   dev:
     depends_on:
       - db
-    image: rapporteket/norgast-dev:main
+    image: rapporteket/norgast-dev:weekly
     volumes:
       - ~/.ssh:/home/rstudio/.ssh
       - ~/.gitconfig:/home/rstudio/.gitconfig