Process Data from Wearable Light Loggers and Optical Radiation Dosimeters

Documentation for package ‘LightLogR’ version 0.10.0

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-- A --

add_clusters	Find and extract clusters from a dataset
add_Date_col	Create a Date column in the dataset
add_photoperiod	Calculate photoperiod and boundary times
add_states	Add states to a dataset based on groups and start/end times
add_Time_col	Create a Time-of-Day column in the dataset
aggregate_Date	Aggregate dates to a single day
aggregate_Datetime	Aggregate Datetime data
alphaopic.action.spectra	Alphaopic (+ photopic) action spectra

-- B --

barroso_lighting_metrics	Circadian lighting metrics from Barroso et al. (2014)
bright_dark_period	Brightest or darkest continuous period
Brown2reference	Add Brown et al. (2022) reference illuminance to a dataset
Brown_check	Check whether a value is within the recommended illuminance/MEDI levels by Brown et al. (2022)
Brown_cut	Create a state column that cuts light levels into sections by Brown et al. (2022)
Brown_rec	Set the recommended illuminance/MEDI levels by Brown et al. (2022)

-- C --

centroidLE	Centroid of light exposure
Circular2Time	Convert circular time columns to hms
count_difftime	Counts the Time differences (epochs) per group (in a grouped dataset)
create_Timedata	create_Timedata
cut_Datetime	Create Datetime bins for visualization and calculation

-- D --

data2reference	Create reference data from other data
Datetime2Time	Convert Datetime columns to Time columns
Datetime_breaks	Create a (shifted) sequence of Datetimes for axis breaks
Datetime_limits	Find or set sensible limits for Datetime axis
disparity_index	Disparity index
dominant_epoch	Determine the dominant epoch/interval of a dataset
dose	Calculate the dose (value·hours)
dst_change_handler	Handle jumps in Daylight Savings (DST) that are missing in the data
dst_change_summary	Get a summary of groups where a daylight saving time change occurs.
durations	Calculate duration of data in each group
duration_above_threshold	Duration above/below threshold or within threshold range

-- E --

exponential_moving_average	Exponential moving average filter (EMA)
exp_zero_inflated	Add a defined number to a numeric and log transform it
extract_clusters	Find and extract clusters from a dataset
extract_gaps	Extract gap episodes from the data
extract_metric	Add metrics to extracted sSummary
extract_photoperiod	Calculate photoperiod and boundary times
extract_states	Extract summaries of states

-- F --

filter_Date	Filter Datetimes in a dataset.
filter_Datetime	Filter Datetimes in a dataset.
filter_Datetime_multiple	Filter multiple times based on a list of arguments.
filter_Time	Filter Times in a dataset.
format_coordinates	Format coordinates as a readable string
frequency_crossing_threshold	Frequency of crossing light threshold

-- G --

gain.ratio.tables	Gain / Gain-ratio tables to normalize counts
gapless_Datetimes	Create a gapless sequence of Datetimes
gap_finder	Check for and output gaps in a dataset
gap_handler	Fill implicit gaps in a light logger dataset
gap_table	Tabular summary of data and gaps in all groups
gg_day	Create a simple Time-of-Day plot of light logger data, faceted by Date
gg_days	Create a simple datetime plot of light logger data, faceted by group
gg_doubleplot	Double Plots
gg_gaps	Visualize gaps and irregular data
gg_heatmap	Plot a heatmap across days and times of day
gg_overview	Plot an overview of dataset intervals with implicit missing data
gg_photoperiod	Add photoperiods to gg_day() or gg_days() plots
gg_state	Add states to gg_day() or gg_days() plots
gg_states	Add states to gg_day() or gg_days() plots

-- H --

has_gaps	Does a dataset have implicit gaps
has_irregulars	Does a dataset have irregular data

-- I --

import	Import a light logger dataset or related data
import_adjustment	Adjust device imports or make your own
import_Dataset	Import a light logger dataset or related data
import_Statechanges	Import data that contain 'Datetimes' of 'Statechanges'
interdaily_stability	Interdaily stability (IS)
interval2state	Adds a state column to a dataset from interval data
intradaily_variability	Intradaily variability (IV)

-- J --

Join similar Datasets

-- L --

ll_import_expr	Get the import expression for a device
log_zero_inflated	Add a defined number to a numeric and log transform it

-- M --

mean_daily	Calculate mean daily metrics from daily summary
mean_daily_metric	Calculate mean daily metrics from Time Series
midpointCE	Midpoint of cumulative light exposure.

-- N --

normalize_counts	Normalize counts between sensor outputs
number_states	Number non-consecutive state occurrences
nvRC	Non-visual circadian response
nvRC_circadianBias	Performance metrics for circadian response
nvRC_circadianDisturbance	Performance metrics for circadian response
nvRC_metrics	Performance metrics for circadian response
nvRC_relativeAmplitudeError	Performance metrics for circadian response
nvRD	Non-visual direct response
nvRD_cumulative_response	Cumulative non-visual direct response

-- P --

period_above_threshold	Length of longest continuous period above/below threshold
photoperiod	Calculate photoperiod and boundary times
pulses_above_threshold	Pulses above threshold

-- R --

remove_partial_data	Remove groups that have too few data points
reverse2_trans	Create a reverse transformation function specifically for date scales

-- S --

sample.data.environment	Sample of wearable data combined with environmental data
sample.data.irregular	Sample of highly irregular wearable data
sample_groups	Sample groups from a grouped dataset
sc2interval	Statechange (sc) Timestamps to Intervals
sleep_int2Brown	Recode Sleep/Wake intervals to Brown state intervals
solar_noon	Calculate photoperiod and boundary times
spectral_integration	Integrate spectral irradiance with optional weighting
spectral_reconstruction	Reconstruct spectral irradiance from sensor counts
style_time	Style (date)times as times
summarise_numeric	Summarize numeric columns in dataframes to means
summarize_numeric	Summarize numeric columns in dataframes to means
summary_metrics	Light exposure summary table helpers
summary_overview	Light exposure summary table helpers
summary_table	Light exposure summary table helpers
supported_devices	Get all the supported devices in LightLogR
supported_versions	Get all the supported device-formats in LightLogR
symlog_trans	Scale positive and negative values on a log scale

-- T --

threshold_for_duration	Find threshold for given duration
timing_above_threshold	Mean/first/last timing above/below threshold.