Pipeline-aware data quality report for health data — sus_data_quality

Reads sus_meta processing history to identify which climasus4r pipeline functions were applied, then produces a section-by-section quality assessment covering completeness, demographic distributions, date validity, ICD-10 codes, geographic coverage, and derived variables. Returns an overall quality score (0-100) and supports four output formats.

Usage

sus_data_quality_report(
  df,
  output_format = "console",
  output_file = NULL,
  save_file = TRUE,
  open_file = TRUE,
  check_icd = TRUE,
  check_dates = TRUE,
  top_n = 10,
  lang = "pt",
  verbose = TRUE
)

Arguments

df: A climasus_df or plain data.frame. Arrow objects are materialised automatically.
output_format: Character. One of "console" (default), "gt", "markdown", or "html". The "gt" format returns a gt_tbl object suitable for Quarto / R Markdown documents.
output_file: Character. File path for "markdown" and "html" formats. Defaults to a timestamped filename in the working directory.
save_file: Logical. For "markdown" and "html" formats, whether to write the report to disk. Default TRUE. Set to FALSE to only compute and return the metrics (e.g. $score) without creating a file.
open_file: Logical. When output_format = "html" and save_file = TRUE, automatically open the saved report in the system's default browser (via utils::browseURL()). Default TRUE. Only triggers in interactive sessions.
check_icd: Logical. Include ICD-10 quality section. Default TRUE.
check_dates: Logical. Include date validation section. Default TRUE.
top_n: Integer. Rows shown in frequency tables. Default 10.
lang: Character. Output language: "pt" (default), "en", "es".
verbose: Logical. Print progress messages. Default TRUE.

Value

Invisibly returns a named list of quality metrics (always available regardless of output_format):

$meta: Pipeline metadata from sus_meta
$pipeline: Functions detected in processing history
$overview: Row/column counts, duplicates, column types
$missing: Per-column missing values with quality flags
$demographics: Frequency tables for sex, race, age, education
$dates: Date range and validity per date column
$icd: ICD-10 frequency and validity
$geographic: Municipality and state coverage
$derived: Presence of expected derived variables
$score: Overall quality score 0-100

Examples

if (FALSE) { # \dontrun{
# Console report (default)
sus_data_quality_report(df, lang = "pt")

# gt table (for Quarto / R Markdown)
sus_data_quality_report(df, output_format = "gt", lang = "en")

# Save complete Markdown report
sus_data_quality_report(df, output_format = "markdown",
                        output_file = "reports/quality.md", lang = "pt")

# Save HTML report
sus_data_quality_report(df, output_format = "html",
                        output_file = "reports/quality.html")
} # }