Simple summary

side projects/post_stroke_sleep.R

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+# ------------------------------------------------------------------------------
+# Setup
+# ------------------------------------------------------------------------------
+
+token=names(suppressWarnings(read.csv("/Users/au301842/pss_redcap_token.csv",colClasses = "character")))
+uri="https://redcap.au.dk/api/"
+
+library(REDCapR)
+library(gtsummary)
+source("https://raw.githubusercontent.com/agdamsbo/daDoctoR/master/R/dob_extract_cpr_function.R")
+
+library(lubridate)
+
+# ------------------------------------------------------------------------------
+# Data download
+# ------------------------------------------------------------------------------
+
+dta <- redcap_read_oneshot(
+  redcap_uri   = uri,
+  token        = token,
+  forms = "baggrund"
+)$data |>
+  mutate(kon=factor(ifelse(as.integer(substr(cpr, start = 11, stop = 11)) %%2 == 0,  # Sex determination
+                           "female", "male")),
+         dob=as.Date(ifelse(redcap_event_name=="inclusion_arm_1",dob_extract_cpr(cpr),NA),origin="1970-01-01"), # Date of birth
+         age=trunc(time_length(difftime(indlagt,dob),"years"))) |>
+  select(-c("cpr","name"))
+
+dta<-dta[!is.na(dta$debut),]
+
+# ------------------------------------------------------------------------------
+# Table 1
+# ------------------------------------------------------------------------------
+
+vars<-c("kon","age","nihss_acute","diagnosis","psg_performed","interview")
+
+dta|>
+  tbl_summary(missing = "ifany",
+              include = all_of(vars),
+              missing_text="(Missing)"#,
+              #label = lab_sel(labels_all,tbl1_vars)
+  )|>
+  add_n()|>
+  as_gt() |>
+  # modify with gt functions
+  gt::tab_header("Baseline Characteristics") |>
+  gt::tab_options(
+    table.font.size = "small",
+    data_row.padding = gt::px(1)) 
+
+