extract_metric: Add metrics to extracted sSummary

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

Add metrics to extracted sSummary

Description

This helper function adds metric values to an extract, like from extract_states() or extract_clusters(). E.g., the average value of a variable during a cluster or state instance might be of interest. The metrics must be specified by the user using the ... argument.

Usage

extract_metric(
  extracted_data,
  data,
  identifying.colname = state.count,
  Datetime.colname = Datetime,
  ...
)

Arguments

extracted_data	A dataframe containing cluster or state summaries, typically from extract_clusters() or extract_states().
data	The original dataset that produced extracted_data
identifying.colname	Name of the column in extracted_data that uniquely identifies each row (in addition to the groups. Expects a symbol. Defaults to state.count
Datetime.colname	Column name that contains the datetime in data. Defaults to "Datetime" which is automatically correct for data imported with LightLogR. Expects a symbol. This argument is only necessary if data does not contain the cluster.colname.
...	Arguments specifying the metrics to add summary. For example: "mean_lux" = mean(lux).

Details

The original data does not have to have the cluster/state information, but it will be computationally faster if it does.

Value

A dataframe containing the extracted data with added metrics.

Examples

# Extract clusters and add mean MEDI value
sample.data.environment |>
filter_Date(length = "2 days") |> 
extract_clusters(MEDI > 1000) |>
extract_metric(
  sample.data.environment,
  "mean_medi" = mean(MEDI, na.rm = TRUE)
) |>
dplyr::select(Id, state.count, duration, mean_medi)

# Extract states and add mean MEDI value
dataset <-
sample.data.environment |>
filter_Date(length = "2 days") |> 
 add_photoperiod(c(48.5, 9))

dataset |>
  extract_states(photoperiod.state) |>
  extract_metric(dataset, mean_lux = mean(MEDI)) |>
  dplyr::select(state.count, duration, mean_lux)

LightLogR documentation built on June 10, 2025, 5:12 p.m.