transfer from old repo

2026-08-19 09:27:27 +02:00 · 2026-08-19 09:27:27 +02:00 · 277e2b8cf3
commit 277e2b8cf3
parent cfa4a5f9cc
1111 changed files with 83736 additions and 0 deletions
--- a/follow-up/longterm-outcome.R
+++ b/follow-up/longterm-outcome.R
@ -0,0 +1,102 @@
+library(REDCapR)
+library(tidyverse)
+
+readRenviron("/Users/au301842/PAaSO/.Renviron")
+
+token <- Sys.getenv('STROKE_API')
+
+ds <-
+  redcap_read(
+    token = token,
+    redcap_uri = "https://redcap.au.dk/api/",
+    fields = c(
+      "forloebid",
+      "ageforloeb_patiente",
+      "sex_patiente",
+      "forloebdato_patiente",
+      "forloebtid_patiente",
+      "ankomstdato_basisske",
+      "ankomsttid_basisske",
+      "mrsfoer_basisske",
+      "symptdebexactdato_basisske",
+      "symptdebexacttid_basisske",
+      "modtagetsomtrombolysekandidat_basisske",
+      "vaskdiag_basisske",
+      "diagnosecerebraltinfarkt_basisske",
+      "nihss_basisske",
+      "id_tromboly",
+      "ankomsttidtrombol_tromboly",
+      "id_trombekt",
+      "mdmrs3_tremdrop",
+      "ankomstdatotrombek_trombekt"
+    )
+  )$data
+
+ds_filter <- ds |>  filter(diagnosecerebraltinfarkt_basisske=="TRUE")
+
+## Vector to correct arrival time
+tid_a <- substr(as.character(ds_filter$forloebtid_patiente),12,19)==""
+
+ds_mod <-
+  ds_filter |> mutate(mrsfoer_basisske=mrsfoer_basisske-2,
+                      mdmrs3_tremdrop=mdmrs3_tremdrop-1) |> 
+  transmute(onset=as_datetime(paste(substr(
+    as.character(ds_filter$symptdebexactdato_basisske), 1, 10
+  ), substr(as.character(ds_filter$symptdebexacttid_basisske), 12, 19)
+  )),
+  arrival = as_datetime(paste(substr(
+    as.character(ds_filter$forloebdato_patiente), 1, 10
+  ), ifelse(
+    tid_a,
+    substr(as.character(ds_filter$ankomsttid_basisske), 12, 19),
+    substr(as.character(ds_filter$forloebtid_patiente), 12, 19)
+  ))),
+  sex=sex_patiente,
+  age=ageforloeb_patiente,
+  nihss=nihss_basisske,
+  ivt=!is.na(id_tromboly),
+  evt=!is.na(id_trombekt),
+  mrs_0=factor(ifelse(!mrsfoer_basisske %in% 0:5,NA,mrsfoer_basisske)),
+  mrs_3=factor(ifelse(!mdmrs3_tremdrop %in% 0:5,NA,mdmrs3_tremdrop)),
+  delay=as.numeric(difftime(arrival,onset,units="mins")),
+  # delay_group=cut(delay,breaks = c(0,90,270,420,max(delay)),include.lowest = TRUE,labels = c("<90","90-270","270-420",">420")),
+  year=as.numeric(substr(as.character(arrival),1,4))
+  ) |> 
+  filter(delay<1440, delay>0) # Only include ptt presenting within 1 day, positive delay
+
+# FØR: 0=Uoplyst | 1=Ukendt | 2=0: Ingen symptomer | 3=1: Ingen synlig funktionsnedsættelse | 4=2: Nogen funktionsnedsættelse | 5=3: Moderat funktionsnesættelse | 6=4: Moderat-svær funktionsnedsættelse | 7=5: Svær funktionsnedsættelse
+# EFTER: 0=Ingen symptomer | 1=Ingen synlig funktionsnedsættelse | 2=Nogen funktionsnedsættelse | 3=Moderat funktionsnesættelse | 4=Moderat-svær funktionsnedsættelse | 5=Svær funktionsnedsættelse | 6=Død | 7=Levende, ukendt Ranking score | 8=Ikke tilgængelig info
+
+skimr::skim(ds_mod)
+
+tbl <- table(mRS=ds_mod$mrs_3, Group=ds_mod$delay_group, Strata=ds_mod$adm_year)
+  
+rankinPlot::grottaBar(tbl, groupName = "Group", scoreName = "mRS",strataName = "Strata")
+
+ds_sums <- ds_mod |> group_by(year) |> summarise(mrs_3_median=median(as.numeric(mrs_3)-1,na.rm=TRUE),
+                                      mrs_3_iqr=paste(quantile(as.numeric(mrs_3)-1,na.rm=TRUE),collapse = ", "),
+                                      nihss_median=median(nihss,na.rm=TRUE),
+                                      nihss_iqr=paste(quantile(nihss,na.rm=TRUE),collapse = ", "),
+                                      n=n(),
+                                      norm_days_frac=365.25/as.numeric(difftime(max(arrival),min(arrival),units = "days")),
+                                      n_norm=n*norm_days_frac,
+                                      ivt_n=sum(ivt),
+                                      ivt_f=sum(ivt)/n,
+                                      evt_n=sum(evt),
+                                      evt_f=sum(evt)/n)
+
+
+
+library(ggplot2)
+
+p1 <- ds_mod |> ggplot()+
+  geom_violin(aes(x=as.factor(year),y=as.numeric(mrs_3), fill = year))
+
+p2 <- ds_sums |> ggplot(aes(x=as.factor(year)))+
+  geom_line(aes(y=n_norm, group=1))
+
+ds_sums |> ggplot(aes(x=as.factor(year)))+
+  geom_line(aes(y=ivt_f, group=1))
+
+ds_sums |> ggplot(aes(x=as.factor(year)))+
+  geom_line(aes(y=evt_f, group=1))