Module 4 - Covariate Feasibility

Compares a target cohort against a comparator on baseline covariates: standardized mean differences (SMD love-plot data), a per-arm prevalence table, and a simple power calculation. Maps to HARPER Sec.4 (comparability). Runs only when a comparator_id is supplied.

Usage

run_covariates(
  con,
  cdm_schema,
  cohort_table,
  cohort_id,
  comparator_id,
  vocab_schema = "vocab",
  covariate_window = c(-365, 0),
  top_n = 20,
  smd_warn_threshold = 0.1,
  power_baseline_rate = 0.15,
  power_effect_rate = 0.3,
  power_sig_level = 0.05,
  power_warn_threshold = 0.8
)

Arguments

con

A live DBI connection (see cdm_connect()).

cdm_schema

Schema holding the clinical CDM tables.

cohort_table

Cohort table, schema-qualified, containing both arms.

cohort_id

Integer cohort definition id of the target arm.

comparator_id

Integer cohort definition id of the comparator arm.

vocab_schema

Schema holding the vocabulary tables. Default "vocab".

covariate_window

Length-2 numeric c(pre, post) days defining the baseline window relative to index for comorbidity/drug covariates. Default c(-365, 0).

top_n

Number of top conditions/drugs to profile. Default 20.

smd_warn_threshold

Absolute SMD above which a covariate is flagged imbalanced. Default 0.1 (standard).

power_baseline_rate, power_effect_rate

Assumed comparator and target event rates for the two-proportion power calculation. Defaults 0.15, 0.30.

power_sig_level

Significance level for the power calculation. Default 0.05.

power_warn_threshold

Power below this value flags a WARN. Default 0.80.

Value

A named list: smd_table, prevalence_table, power, flags.

Examples

if (requireNamespace("duckdb", quietly = TRUE)) {
  con <- example_cdm()
  # The demo CDM ships two arms: target = 1, comparator = 2.
  res <- run_covariates(con, cdm_schema = "main", cohort_table = "cohort",
                        cohort_id = 1, comparator_id = 2, vocab_schema = "main")
  res$smd_table
  res$power
  cdm_disconnect(con)
}