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