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Function dstats

dstats.Rd

The dstats function is used to find various patient lab value aggregations and calculations around an index date.

Usage

dstats(
  database,
  tables,
  code_list,
  index_date,
  index_days_start,
  index_days_end,
  allow_subset = FALSE
)

Arguments

database

database name to use

tables

names of tables to use in a dataset that is a list c("lab_result") or c("lab_result", "vitals_signs")

  • supported tables: lab_result and vitals_signs

code_list

user defined table with 3 mandatory columns:

  • mandatory columns

    • feature - the feature the exact code will roll up to and name of the column in the output (letters, numbers, underscores only, no spaces, not case sensitive)

    • code - exact code

    • code_system - RxNorm, LOINC, etc

  • optional columns

    • Supported columns are:

      • qualifier_num - looks across lab_result and vitals_signs num value fields at the same time

    • if a user only passes in lab_result or vitals_signs to dstats, the function checks only that table

    • users can create as many additional columns as they want, but column names must be unique and match the supported column names

    • syntax for qualifying lab numeric values:

      • '<=X': less than or equal to X

      • '<X': less than X

      • '>=X': greater than or equal to X

      • '>X': greater than X

      • '~=X': not equal to X

      • 'X:Y': between X and Y

    • syntax for qualifying lab categorical values

      • the user can enter any string they want - exact match

    • if cell is left blank, system skips and assumes no qualification for that code

    • one qualification of a code does not apply to the entire feature; in the case there is more than one code mapped to the feature - every code must be qualified

index_date

user defined table with two columns

  • patient_id

  • index_date

index_days_start

start period relative to index date in days

  • None means anytime

  • negative means before the index date

  • positive means after

index_days_end

end period relative to index date in days

  • None means anytime

  • negative means before the index date

  • positive means after

allow_subset

(optional argument) - checks whether the number of patients in the index event input table is the same as the dataset cohort number - would default to false, but if set to true would warn and continue

  • if TRUE and there are fewer patients in the index_date_df table, only returns the patient_ids present in index_date_df

Value

Returns a table with the following columns (unique key of the table is patient_id + feature)

  • patient_id

  • feature - each unique feature value per patient ID

  • min - the minimum lab value that appeared in time window defined by the user in relation to the index event

  • max - the maximum lab value that appeared in time window defined by the user in relation to the index event

  • median - the median of all lab values that appeared in time window defined by the user in relation to the index event.

    • If it is even values, take average of the 2.

  • mean - the mean of all lab values that appeared in time window defined by the user in relation to the index event

  • first - the first lab value that appeared in time window defined by the user in relation to the index event

    • If multiple values same day, system displays median

  • last - the last lab value that appeared in time window defined by the user in relation to the index event

    • If multiple values same day, system displays median

Details

dstats_table = dstats(database='covid_db', tables=c('procedure','diagnosis'), code_list=code_list, index_date=sg_index_date, index_days_start=-365, index_days_end=-1)
head(dstats_table)

| patient id | feature        | min | max | median | mean | first | last  |
|------------|----------------|-----|-----|--------|------|-------|-------|
| 1          | alkaline_phos  | 50  | 30  | 33     | 40   | 45    | 50    |
| 1          | aspartate_amin | 50  | 30  | 33     | 40   | 45    | 50    |
| 2          | alkaline_phos  | 50  | 30  | 33     | 40   | 45    | 50    |
| 2          | aspartate_amin | 50  | 30  | 33     | 40   | 45    | 50    |
| 3          | alkaline_phos  | 50  | 30  | 33     | 40   | 45    | 50    |
| 3          | aspartate_amin | 50  | 30  | 33     | 40   | 45    | 50    |