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Renders signal detection report

run_report.Rd

The function supports the generation of a single-pathogen and multi-pathogen report when `report_format = "HTML"`. For Word (DOCX) output, only single-pathogen reports are currently supported.

Usage

run_report(
  data,
  report_format = "HTML",
  method = "FarringtonFlexible",
  number_of_weeks = 6,
  pathogens = NULL,
  strata = c("county", "age_group"),
  tables = TRUE,
  output_file = NULL,
  output_dir = ".",
  signals_padded = NULL,
  signals_agg = NULL,
  intervention_date = NULL,
  custom_logo = NULL,
  custom_theme = NULL
)

Arguments

data

data.frame containing surveillance data in linelist format following the format specified in `input_metadata`

report_format

character, format of the report: "HTML" or "DOCX"

method

a character string, signal detection method to be used. One of "FarringtonFlexible", "EARS" , "CUSUM", "Mean", "Timetrend", "Harmonic", "Harmonic with timetrend", "Step harmonic", "Step harmonic with timetrend". You can retrieve the full list using [names(available_algorithms())].

number_of_weeks

integer, number of weeks for which signals are generated

pathogens

A character vector specifying which pathogens to include in the report. If `NULL` (default), all pathogens present in `data`, `signals_padded`, or `signals_agg` are used. Multi-pathogen reports are supported only for HTML output.

strata

A character vector specifying the columns to stratify. If `NULL` no strata are used. If precomputed signals are provided this argument is ignored and strata are inferred from the provided signals. Defaults to c("county", "age_group") when no precomputed signals were provided.

tables

Logical, default TRUE. True if Signal Detection Tables should be included in report. Only used for DOCX reports, the parameter is ignored for HTML reports.

output_file

A character string specifying the name of the output file (without directory path). If `NULL` (default), the file name is automatically generated to be SignalDetectionReport. See render for more details.

output_dir

A character string specifying the output directory for the rendered output file (default is ".", which means the rendered file will be saved in the current working directory. See render for more details. `NULL` is used when running the report from shiny app which will take the Downloads folder as default option for saving.

signals_padded

A tibble of precomputed and padded signals containing a `pathogen` column. If multiple pathogens are present, the tibble should represent all of them stacked together (e.g., using `dplyr::bind_rows()`). Defaults to `NULL`, in which case the signal data will be computed from the linelist within the `run_report()` function. If not `NULL`, the provided `signals_padded` is used as-is, and signals are not recomputed.

signals_agg

A tibble of aggregated signals containing a `pathogen` column. If multiple pathogens are included, the tibble should represent all of them stacked together (e.g., using `dplyr::bind_rows()`). Defaults to `NULL`, in which case the aggregated signals are computed from the linelist within the `run_report()` function. If not `NULL`, the provided `signals_agg` is used directly and signals are not recomputed.

intervention_date

A date object or character of format yyyy-mm-dd or NULL specifying the date for the intervention. This can be used for interrupted timeseries analysis. It only works with the following methods: "Mean", "Timetrend", "Harmonic", "Harmonic with timetrend", "Step harmonic", "Step harmonic with timetrend". Default is NULL which indicates that no intervention is done.

A character string with a path to a png or svg logo, to replace the default United4Surveillance logo. Only used when `report_format` is `"HTML"`.

custom_theme

A bslib::bs_theme() to replace the default United4Surveillance theme. This is mainly used to change colors. See the bslib documentation for all parameters. Use version = "3" to keep the navbar intact. Only used when `report_format` is `"HTML"`.

Value

the compiled document is written into the output file, and the path of the output file is returned; see render

Details

If executed as a standalone function, all filtering must be performed beforehand. This function is also invoked within the app.

See also

[names(available_algorithms())]

Examples