Format Text for Outbreak Reports and the Dashboard

Small HTML formatting helpers used when building dossier text, both in the dashboard and in the Quarto outbreak report template. Both are exported so that a custom report template of your own (set via EPISODIC_QUARTO_REPORT) can use the same formatting as the shipped one. Input text is always HTML-escaped first, so the result is safe to pass on to shiny::HTML().

Usage

episodic_ui_italicise_taxon(pathogen)

episodic_ui_code_join(detectors, sep = ", ")

Arguments

pathogen

A character vector of pathogen display names.

detectors

A character vector of detector names.

sep

Separator between entries.

Value

A character vector (or, for episodic_ui_code_join(), a single string), safe to pass to shiny::HTML().

Details

episodic_ui_italicise_taxon() italicises pathogen names that AMR recognises as a taxonomic binomial (e.g. Escherichia coli), following standard microbiological convention. Names it does not recognise (e.g. "Influenza A", a virus type rather than a species) are left as-is.

episodic_ui_code_join() renders a vector of detector names (e.g. "farrington", "same_place") as inline <code>, joined into one string - useful when listing which detectors flagged a cluster.

Examples

episodic_ui_italicise_taxon(c("Escherichia coli", "Influenza A"))
#> [1] "<i>Escherichia coli</i>" "Influenza A"            
episodic_ui_code_join(c("farrington", "same_place"))
#> [1] "<code>farrington</code>, <code>same_place</code>"