Standardize visit-level data

Turns visit-level emergency department data (one row per visit) into the input expected by ts_counts(): a data.table with columns key (patient identifier), date, diagnosis_codes (space-separated ICD-10-CM codes), and severity ("A" = admitted, "V" = visit only).

Usage

ts_visits(
  data,
  key = "key",
  date = "date",
  codes = "diagnosis_codes",
  admitted = "severity"
)

ts_visits_nssp(data)

Arguments

data

A data.frame with one row per visit.

key, date, codes, admitted

Names of the columns in data holding the patient identifier, visit date (or date-time), diagnosis codes (separated by spaces, commas, or semicolons), and admission status (logical, 0/1, or "A"/"V"). Missing admission status is treated as not admitted.

Value

A data.table.

Details

ts_visits_nssp() is a shortcut for NSSP ESSENCE DataDetails extracts (columns C_Unique_Patient_ID, C_Visit_Date_Time, DischargeDiagnosis, and HasBeenAdmitted).

Examples

visits <- read.csv(system.file("extdata", "toy_visits.csv", package = "treescanr"))
ts_visits(visits) |> head()
#>       key       date     diagnosis_codes severity
#>    <char>     <Date>              <char>   <char>
#> 1: P00016 2025-03-01        R10822 A0221        A
#> 2: P00027 2025-03-01              R62.59        V
#> 3: P01136 2025-03-01 R62.51 A08.11 R19.0        V
#> 4: P01366 2025-03-01   R1931 A0811 R1905        V
#> 5: P01420 2025-03-01               R19.2        V
#> 6: P01585 2025-03-01   R6883 A0811 R1902        V