summary_table: Light exposure summary table helpers

In LightLogR: Process Data from Wearable Light Loggers and Optical Radiation Dosimeters

Light exposure summary table helpers

Description

These helpers create a publication-ready summary table for light logger datasets. Users can either calculate the metrics, generate overview counts, or render the complete gt table.

This function creates a tibble that gives some high level information about a dataset: How many participants are in there, the number of participant days, how many participant days are complete above a given threshold, how much data is missing, and (if provided) what the photoperiod is.

Usage

summary_overview(
  dataset,
  Variable.colname = MEDI,
  coordinates = NULL,
  location = NULL,
  site = NULL,
  Datetime.colname = Datetime,
  Id.colname = Id,
  threshold.missing = 0.2,
  programmatic.use = FALSE,
  handle.gaps = TRUE
)

summary_metrics(
  dataset,
  Variable.colname = MEDI,
  Datetime.colname = Datetime,
  Id.colname = Id,
  threshold.missing = 0.2,
  programmatic.use = FALSE,
  handle.gaps = TRUE
)

summary_table(
  dataset,
  coordinates = NULL,
  location = NULL,
  site = NULL,
  color = "grey",
  Variable.colname = MEDI,
  Datetime.colname = Datetime,
  Id.colname = Id,
  threshold.missing = 0.2,
  Variable.label = "melanopic EDI (lx)",
  histograms = TRUE
)

Arguments

dataset	A data frame containing light logger data.
Variable.colname	Column containing light exposure values. Expects a symbol; defaults to MEDI for compatibility with the built-in datasets.
coordinates	Optional numeric vector of length two containing latitude and longitude (in that order). If supplied, photoperiod information is calculated when the dataset does not already contain a photoperiod column.
location	Optional location description (e.g. city name).
site	Optional site description (e.g. country or study site).
Datetime.colname	Column containing the timestamp information. Expects a symbol; defaults to Datetime.
Id.colname	Column containing the participant identifier. Expects a symbol; defaults to Id.
threshold.missing	Proportion of missing data (per participant-day) tolerated before a day is considered incomplete.
programmatic.use	Whether the function is used by another function. This determines the number of columns to be output. Default is FALSE
handle.gaps	Whether gaps in the data should be handled. Sets the argument in remove_partial_data(). Default is TRUE.
color	Color used for histogram accents in the metrics section.
Variable.label	Label used in the table footnote to describe the light variable.
histograms	Logical indicating whether histogram spark lines should be added for metrics where applicable.

Details

The function is used within summary_table().

Value

A tibble with overview metrics (type, name, mean, SD, min, max, plot). A location_string attribute is attached to the result for use in summary_table(). If programmatic.use = FALSE, type, SD and plot are removed.

A tibble with summarized metrics across participant-days and participant-level stability measures. Columns are compatible with summary_table().

A gt table.

Examples

sample.data.environment |> summary_overview()
sample.data.irregular |> summary_overview()

sample.data.environment |> 
filter_Date(length = "3 days") |> 
summary_metrics()
  

#sample.data.environment |> summary_table(coordinates = c(47,9))

LightLogR documentation built on Nov. 28, 2025, 5:09 p.m.