Render an Outbreak Report for Clinical Colleagues — episodic_report

Produces a self-contained HTML outbreak report for one cluster - the document you send to a treating physician, an infection prevention nurse, or a clinical colleague (e.g., a clinical microbiologist) who has neither an EpiSODIC account nor R installed. The report includes the epidemic curve, trend chart, the narrative summary shown in the dashboard, and (optionally) the case line list.

Usage

episodic_report_render(
  con,
  cluster_id,
  output_dir,
  user_id = NA,
  include_linelist = TRUE,
  small_count_threshold = NULL,
  episodic_config_path = Sys.getenv("EPISODIC_CONFIG", unset = NA),
  lang = Sys.getenv("EPISODIC_LANGUAGE"),
  qmd_path = Sys.getenv("EPISODIC_QUARTO_REPORT", unset = NA)
)

Arguments

con: A DBI::DBIConnection.
cluster_id: The cluster to report on.
output_dir: Directory the rendered HTML is written to. Created if it does not exist.
user_id: The id of the user requesting the report, or NA for an automated (cron) render.
include_linelist: If TRUE (default), the case line list is included in the report. Set to FALSE for a summary-only report, e.g. when sending outside your own organisation.
small_count_threshold: Small counts in the geography/institution breakdown tables are suppressed (shown as "<threshold") below this value, to avoid identifying individuals in a small population. Defaults to config$report$small_count_threshold.
episodic_config_path: The config path.
lang: Report language: "en", "ar", "nl", "fr", "de", "hi", "zh", or "es", or a regional variant of one ("en-US", "es-419"). Defaults to the EPISODIC_LANGUAGE environment variable, falling back to "en" if that is unset.
qmd_path: Path to the Quarto template to render. Defaults to the EPISODIC_QUARTO_REPORT environment variable, falling back to the shipped template if that is unset.

Value

Invisibly, a list with file_path (where the HTML was written), file_sha256, version_no, and report_id.

Details

Every render is kept, versioned, and logged to the database, including exactly which cases it contained - so what was sent out on a given date stays a fully recoverable record, even if the underlying data changes later.

By default the report uses EpiSODIC's own report template. If your organisation needs its own layout or branding, set the EPISODIC_QUARTO_REPORT environment variable to your own .qmd file; the default inst/report/episodic_default_report.qmd is a good starting point to copy and adapt.

The report is styled from the instance palette (episodic_palette()), the same colours and font as the dashboard: its charts are drawn in it, and an episodic.scss theme built from it is written beside the template, which the shipped template names as its theme. A custom template receives the palette as palette in its data and can name the same theme file.

Rendering requires Quarto to be installed separately (both the quarto R package and the Quarto command-line tool) - this function raises an informative error if it is not found.

Examples

if (FALSE) { # \dontrun{
# needs both the quarto R package and the Quarto CLI installed, plus a
# database with at least one detected cluster - see episodic_demo() for
# a populated one, and the app's rail for a cluster_id to render
db_path <- episodic_demo(launch = FALSE)
con <- episodic_db_connect(db_path)
episodic_report_render(con, cluster_id = 1, output_dir = tempdir())
DBI::dbDisconnect(con)
} # }