Package: LightLogR 0.10.6

Johannes Zauner

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

Import, processing, validation, and visualization of personal light exposure measurement data from wearable devices. The package implements features such as the import of data and metadata files, conversion of common file formats, validation of light logging data, verification of crucial metadata, calculation of common parameters, and semi-automated analysis and visualization.

Authors:Johannes Zauner [aut, cre], Manuel Spitschan [aut], Steffen Hartmeyer [aut], European Partnership on Metrology [fnd], Wellcome Trust [fnd], Reality Labs Research [fnd], Translational Sensory and Circadian Neuroscience Unit [cph]

LightLogR_0.10.6.tar.gz
LightLogR_0.10.6.zip(r-4.7-any)LightLogR_0.10.6.zip(r-4.6-any)LightLogR_0.10.6.zip(r-4.5-any)
LightLogR_0.10.6.tgz(r-4.6-any)LightLogR_0.10.6.tgz(r-4.5-any)
LightLogR_0.10.6.tar.gz(r-4.7-any)LightLogR_0.10.6.tar.gz(r-4.6-any)
LightLogR_0.10.6.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
LightLogR/json (API)

# Install 'LightLogR' in R:
install.packages('LightLogR', repos = c('https://tscnlab.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/tscnlab/lightlogr/issues

Pkgdown/docs site:https://tscnlab.github.io

Datasets:

On CRAN:

Conda:

dosimetrylighttime-series-analysiswearable-deviceswearable-sensors

6.37 score 20 stars 112 scripts 688 downloads 101 exports 103 dependencies

Last updated from:fd0b5c66b2. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK294
source / vignettesOK296
linux-releaseOK304
macos-releaseOK210
macos-oldrelOK238
windows-develOK215
windows-releaseOK254
windows-oldrelOK245
wasm-releaseOK171

Exports:%>%add_clustersadd_Date_coladd_photoperiodadd_statesadd_Time_colaggregate_Dateaggregate_Datetimebarroso_lighting_metricsbright_dark_periodBrown_checkBrown_cutBrown_recBrown2referencecentroidLECircular2Timecount_difftimecreate_Timedatacut_Datetimedata2referenceDatetime_breaksDatetime_limitsDatetime2Timedisparity_indexdominant_epochdosedst_change_handlerdst_change_summaryduration_above_thresholddurationsexp_zero_inflatedexponential_moving_averageextract_clustersextract_gapsextract_metricextract_photoperiodextract_statesfilter_Datefilter_Datetimefilter_Datetime_multiplefilter_Timeformat_coordinatesfrequency_crossing_thresholdgap_findergap_handlergap_tablegapless_Datetimesgg_daygg_daysgg_doubleplotgg_gapsgg_heatmapgg_overviewgg_photoperiodgg_stategg_stateshas_gapshas_irregularsimportimport_adjustmentimport_Datasetimport_Statechangesinterdaily_stabilityinterval2stateintradaily_variabilityjoin_datasetsll_import_exprlog_zero_inflatedmean_dailymean_daily_metricmidpointCEnormalize_countsnumber_statesnvRCnvRC_circadianBiasnvRC_circadianDisturbancenvRC_relativeAmplitudeErrornvRDnvRD_cumulative_responseperiod_above_thresholdphotoperiodpulses_above_thresholdremove_partial_datareverse2_transsample_groupssc2intervalsleep_int2Brownsolar_noonspectral_integrationspectral_reconstructionstyle_timesummarise_numericsummarize_numericsummary_metricssummary_overviewsummary_tablesupported_devicessupported_versionssymlog_transthreshold_for_durationtiming_above_threshold

Dependencies:base64encbigDbitbit64bitopsbootbslibcachemcircularclassclassIntclicliprcommonmarkcowplotcpp11crayoncurlDBIdigestdplyre1071evaluatefarverfastmapfontawesomefsgenericsggplot2ggsciggtextgluegridtextgtgtablegtExtrashighrhmshtmltoolshtmlwidgetsisobandjpegjquerylibjsonlitejuicyjuiceKernSmoothknitrlabelinglifecyclelitedownlubridatemagrittrmarkdownmemoisemimemvtnormpaletteerpillarpkgconfigpngprettyunitsprismaticprogressproxypurrrR6rappdirsRColorBrewerRcppreactablereactRreadrrematch2rlangrmarkdownrstudioapis2S7sassscalessfsliderstringistringrsuntoolstibbletidyrtidyselecttimechangetinytextzdbunitsutf8V8vctrsviridisLitevroomwarpwithrwkxfunxml2yaml

Readme and manuals

Help Manual

Help pageTopics
Create a Date column in the datasetadd_Date_col
Add states to a dataset based on groups and start/end timesadd_states
Create a Time-of-Day column in the datasetadd_Time_col
Aggregate dates to a single dayaggregate_Date
Aggregate Datetime dataaggregate_Datetime
Alphaopic (+ photopic) action spectraalphaopic.action.spectra
Circadian lighting metrics from Barroso et al. (2014)barroso_lighting_metrics
Brightest or darkest continuous periodbright_dark_period
Check whether a value is within the recommended illuminance/MEDI levels by Brown et al. (2022)Brown_check
Create a state column that cuts light levels into sections by Brown et al. (2022)Brown_cut
Set the recommended illuminance/MEDI levels by Brown et al. (2022)Brown_rec
Add Brown et al. (2022) reference illuminance to a datasetBrown2reference
Centroid of light exposurecentroidLE
Convert circular time columns to hmsCircular2Time
Counts the Time differences (epochs) per group (in a grouped dataset)count_difftime
create_Timedatacreate_Timedata
Create Datetime bins for visualization and calculationcut_Datetime
Create reference data from other datadata2reference
Create a (shifted) sequence of Datetimes for axis breaksDatetime_breaks
Find or set sensible limits for Datetime axisDatetime_limits
Convert Datetime columns to Time columnsDatetime2Time
Disparity indexdisparity_index
Determine the dominant epoch/interval of a datasetdominant_epoch
Calculate the dose (value·hours)dose
Handle jumps in Daylight Savings (DST) that are missing in the datadst_change_handler
Get a summary of groups where a daylight saving time change occurs.dst_change_summary
Duration above/below threshold or within threshold rangeduration_above_threshold
Calculate duration of data in each groupdurations
Exponential moving average filter (EMA)exponential_moving_average
Find and extract clusters from a datasetadd_clusters extract_clusters
Extract gap episodes from the dataextract_gaps
Add metrics to extracted sSummaryextract_metric
Extract summaries of statesextract_states
Filter Datetimes in a dataset.filter_Date filter_Datetime
Filter multiple times based on a list of arguments.filter_Datetime_multiple
Filter Times in a dataset.filter_Time
Format coordinates as a readable stringformat_coordinates
Frequency of crossing light thresholdfrequency_crossing_threshold
Gain / Gain-ratio tables to normalize countsgain.ratio.tables
Check for and output gaps in a datasetgap_finder
Fill implicit gaps in a light logger datasetgap_handler
Tabular summary of data and gaps in all groupsgap_table
Create a gapless sequence of Datetimesgapless_Datetimes
Create a simple Time-of-Day plot of light logger data, faceted by Dategg_day
Create a simple datetime plot of light logger data, faceted by groupgg_days
Double Plotsgg_doubleplot
Visualize gaps and irregular datagg_gaps
Plot a heatmap across days and times of daygg_heatmap
Plot an overview of dataset intervals with implicit missing datagg_overview
Add photoperiods to gg_day() or gg_days() plotsgg_photoperiod
Add states to gg_day() or gg_days() plotsgg_state
Add states to gg_day() or gg_days() plotsgg_states
Does a dataset have implicit gapshas_gaps
Does a dataset have irregular datahas_irregulars
Adjust device imports or make your ownimport_adjustment
Import a light logger dataset or related dataimport import_Dataset
Import data that contain 'Datetimes' of 'Statechanges'import_Statechanges
Interdaily stability (IS)interdaily_stability
Adds a state column to a dataset from interval datainterval2state
Intradaily variability (IV)intradaily_variability
Join similar Datasetsjoin_datasets
Get the import expression for a devicell_import_expr
Add a defined number to a numeric and log transform itexp_zero_inflated log_zero_inflated
Calculate mean daily metrics from daily summarymean_daily
Calculate mean daily metrics from Time Seriesmean_daily_metric
Midpoint of cumulative light exposure.midpointCE
Normalize counts between sensor outputsnormalize_counts
Number non-consecutive state occurrencesnumber_states
Non-visual circadian responsenvRC
Performance metrics for circadian responsenvRC_circadianBias nvRC_circadianDisturbance nvRC_metrics nvRC_relativeAmplitudeError
Non-visual direct responsenvRD
Cumulative non-visual direct responsenvRD_cumulative_response
Length of longest continuous period above/below thresholdperiod_above_threshold
Calculate photoperiod and boundary timesadd_photoperiod extract_photoperiod photoperiod solar_noon
Pulses above thresholdpulses_above_threshold
Remove groups that have too few data pointsremove_partial_data
Create a reverse transformation function specifically for date scalesreverse2_trans
Sample groups from a grouped datasetsample_groups
Sample of wearable data combined with environmental datasample.data.environment
Sample of highly irregular wearable datasample.data.irregular
Statechange (sc) Timestamps to Intervalssc2interval
Recode Sleep/Wake intervals to Brown state intervalssleep_int2Brown
Integrate spectral irradiance with optional weightingspectral_integration
Reconstruct spectral irradiance from sensor countsspectral_reconstruction
Style (date)times as timesstyle_time
Summarize numeric columns in dataframes to meanssummarise_numeric summarize_numeric
Light exposure summary table helperssummary_metrics summary_overview summary_table
Get all the supported devices in LightLogRsupported_devices
Get all the supported device-formats in LightLogRsupported_versions
Scale positive and negative values on a log scalesymlog_trans
Find threshold for given durationthreshold_for_duration
Mean/first/last timing above/below threshold.timing_above_threshold