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Changelog

Source: NEWS.md

LightLogR 0.9.0 Sunrise

This is a huge update for LightLogR, bringing many new features and twenty-two new functions

New functions & datasets

Light spectrum

  • spectral_reconstruction():reconstruct a spectral power distribution (SPD) from sensor channels that provide (normalized) counts, and a calibration matrix. Examples for such devices include the the ActLumus from Condor instruments, or the VEET from Meta Reality labs (after normalization of counts, e.g., through normalize_counts())

  • alphaopic.action.spectra: New dataset containing alphaopic action spectra (CIE S026) plus the photopic action spectrum in 1-nm wavelength steps.

  • spectral_integration(): integrate over all or just parts of the spectrum, including the option to weigh the spectrum with an action spectrum (e.g., from alphaopic.action.spectra)

Missing data

  • remove_partial_data(): remove groups with a below than user-specified amount of data

  • extract_gaps(): provides a start and end times, as well as durations for all gaps in the dataset.

  • has_gaps(), has_irregulars(); provide a logical feedback on whether a dataset has (implicit) gaps or irregular data.

  • gap_table() provides a comprehensive summary of available and missing data.

Metrics and summaries

  • durations(): calculate the groupwise duration of a dataset, based on datapoints, the dominant interval, and missing data

  • mean_daily() and mean_daily_metric(): give a three-row summary of weekday, weekend, and mean daily (numeric) values. mean_daily_metric() skips the prior metric calculation for duration-based metrics, and directly calculates the mean daily value.

  • extract_clusters(), add_clusters(): find clusters of a user-specified condition and either summarize them or add them to a dataset.

  • extract_states(), add_states(): provides a summary of every state in the dataset or add them to a dataset.

  • extract_metric(): add a calculation to extracted data, such as from extract_state() or extract_clusters().

  • summarize_numeric()/summarise_numeric(): calculate means across numeric values, ideal to summarize results from extract_state(), extract_gaps(), or extract_clusters.

  • Brown_cut(): divide light exposure variables into sections ≤1lx, ≤10lx, and ≥250lx according to Brown et al. 2022

  • log_zero_inflated() and `exp_zero_inflated(): apply or reverse a logarithmic transformation after adding a small value to a vector so as to provide zero values in logarithmic transformation, which is especially important for light exposure.

Visualizations

  • gg_gaps(): visualize gaps and shows instances of irregular data.

  • gg_state(): is an addon-function to gg_day() or gg_days(), which adds a state or cluster indicator to the plot

  • gg_heatmap(): visualize a condensed version of time series patterns, optionally as double plots.

Misc and Housekeeping

  • Import support for the ClouClip device.

  • number_states() added the option to just output a count number without the original state

  • gg_days(): jco_color = TRUE is now the default

Bug fixes

  • import_Dataset() no longer changes a pre-existing Id column (if it is not called Id). The function is also more informative for the daylight savings time handling in files with more than one Id.

  • gg_photoperiod() does no longer throw an error when the main plots y.axis is not based on a MEDI column.

  • gapless_Datetimes() now ignores groups with only a single measurement, instead of throwing an error. This function is the basis for all calculations regarding gaps.

LightLogR 0.5.4

  • changed the behavior of all metric functions that calculate an in-between value (such as the duration of light between 250 and 1000 lux). Up until now, the function would use inclusive bounds on both sides, i.e. the value of 250 lux and 1000 lux would be included in the calculation. This is now changed to right exclusive bounds, i.e. the value of 250 lux will still be included in the calculation, whereas 1000 lux will not. While of little practical difference in a realistic dataset (where exact values matching the threshold are likely not present), it is relevant when calculating, e.g., the time spent in various levels of light or any other variable. The sum of those times should always add up to the total time. With inclusive bounds on both sides, the sum could theoretically be larger, with right exclusive bounds it cannot.

  • Metrics intradaily_variability() and interdaily_stability() now use the population variance (divide by N), instead of the sample variance (divide by N-1). The legacy behavior can still be accessed by setting the argument use.samplevar = TRUE. #55

  • Metric IS now correctly uses the overall mean in relation to the variance, instead of the mean of hourly averages across days. #56

LightLogR 0.5.3

CRAN release: 2025-02-24

  • small cleanup changes for CRAN submission

LightLogR 0.5.2

  • passed 300 unit tests for LightLogR 🎉

  • normalize_counts() was added as a low-level helper function and the accompanying dataset gain.ratio.tables to facilitate calculating normalized sensor values when comparing across different sensors, e.g. to assess daylighting conditions based on UV, IR, and photopic sensing ranges. See documentation for more infos.

  • Update to the import function of GENEActiv devices, based on input from the author of the GGIR package. The timezone tz argument in LightLogR now is just set on the timestamp provided by the GGIR export, instead of shifting the datetime. This requires the correct setting of desiredtz/configtz arguments in GGIR during preprocessing.

LightLogR 0.5.1

  • refinement and cross-referencing in tutorials on photoperiod

  • fixing a bug in the photoperiod family of functions when using a timezone with a large offset to the coordinates where photoperiod is calculated and crosses a date.

LightLogR 0.5.0 “Civil dawn”

  • added a suite of functions to deal with photoperiod: photoperiod() and solar_noon() to calculate dusk, dawn, and noon times of the day. extract_photoperiod() and add_photoperiod() utilize datasets imported with LightLogR to calculate and deal with photoperiods in the context of your own datasets. gg_photoperiod() brings this functionality to the visualization tools of LightLogR in an easy and powerful way.

  • added the function number_states() that relabels states based on their non-consecutive appearance. This is especially useful when labelling photoperiod states, as the function will allow for an easy classifier of “day 1”, “day 2”, …, and “night 1”, “night 2”, …. These can be used to, e.g., calculate metrics for individual photoperiod sections throughout the observed time frame.

  • added a tutorial on the new functions Photoperiod. This also details how to calculate metrics based on photoperiod (#39).

  • implemented further changes in the paper.md based on the JOSS Reviews

LightLogR 0.4.3

LightLogR 0.4.2

  • updated the license to MIT: LightLogR is now permissively licensed

  • import functions will now give a warning message about identical observations in the provided data files, stop the import process and return a tibble with the duplicate rows. Through the remove_duplicates parameter, the user can decide to automatically remove these duplicates during import. Note: identical observations refers to identical rows when disregarding the filename.

LightLogR 0.4.1

  • added support for OcuWEAR devices

  • added support for MotionWatch 8 devices #32

  • added support for LIMO devices

  • added support for GENEActiv devices, when data was preprocessed with the GGIR package. The function import$GENEActiv_GGIR() takes the GGIR output and imports it with LightLogR naming schemes. #27

LightLogR 0.4.0 “Nautical dawn”

  • release on CRAN!

  • changed the supported.devices list to a function supported_devices() instead, so the documentation automatically updates with the list of supported devices. Similarly, ll_import_expr is now ll_import_expr().

  • added support for the Meta VEET device for visual experience measurements

  • added support for the Kronowise device

  • added support for the MPI melanopiQ Circadian Eye (Prototype)

  • rewrote the import function for Actiwatch_Spectrum, as the sample file the original was based off, had specific formatting to German standards. Now, the German version can still be called through Actiwatch_Spectrum_de, wheras the main function refers to the english/international format.

  • updated the landing page for the website with a list of supported devices and a table of metrics

  • small changes to documentation

LightLogR 0.3.8

CRAN release: 2024-07-04

  • Submission to CRAN

LightLogR 0.3.7 “Astronomical dawn”

  • Changes to the tutorial articles on the website

  • Integration of a community survey on the website and Github Readme.

LightLogR 0.3.6

  • bright_dark_period() now maintains the date when looping the data.

  • Added articles on Import & Cleaning, Metrics, and Visualizations to the website.

  • Added the option for more print rows of observation intervals during import.

  • Added the option to set a length for the dataset starting from the end in filter_Datetime() and family.

LightLogR 0.3.5

LightLogR 0.3.4

  • Backup to Zenodo, DOI and all

LightLogR 0.3.3

  • New and updated metric functions. LightLogR now contains 16 metric families with 60 sub-metrics.

LightLogR 0.3.2

  • added import functions for nanoLambdaand LightWatcher devices

  • new Logo!

LightLogR 0.3.1

  • fixed bug in interval2state() that would dismiss the first state if it starts before the actual data

  • fixed a bug in interval2state() that would add other columns then the State column present in the interval dataset to the output dataset, but leave them empty. Added an example that shows how to add multiple columns to the output dataset correctly.

  • in aggregate_Datetime(), added the option to set the dominant.epoch, i.e., the most common interval, as the unit parameter, to effectively deal with irregular data.

LightLogR 0.3.0

  • Added the functions dst_change_summary() and dst_change_handler() to detect and deal with Daylight Savings. The functionality is also integrated into the import functions, so that a user can automatically apply it during the import process.

  • Added Steffen Hartmeyer as a collaborator, who added a number of light metrics from the lightdosimetry package.

  • Added the import_adjustment() function for more flexibility when importing light logger data that does not conform to the standard format. This goes hand in hand with the ll_import_expr list that contains specific expressions for all supported devices.

  • lots of bug fixes and improvements

LightLogR 0.2.2

  • Bugfix for LiDo import

  • Added import support for new devices: LiDo, DeLux, and Speccy

  • Removed minor inconsistencies in naming conventions. Also, all imported columns will have syntactic naming now

  • Added an option to all gap functions, to extend the gapless Datetime range to full days.

LightLogR 0.2.1

  • Exports the up to now internal function count_difftime() that is the basis for dominant_epoch(). But whereas the latter gets only the most common epoch, count_difftime() returns a table with the counts of all epochs. This is useful in conjunction with gap_finder(), to check the distribution of data intervals.

  • Added the gg_days() function to visualize multiple days of data in a single plot. Alongside come two helper functions, Datetime_limits() and Datetime_breaks(), to set the limits and breaks of the x-axis.

  • Added the filter_Datetime_multiple() function to filter for multiple Datetime ranges depending on certain conditions, e.g. different filter cutoffs for different participants. It wraps around filter_Datetime() or filter_Date().

  • Reworked the internals of the light logger data import functions. They now use a more straightforward function factory approach. For users the only visible change it that device specific functions now have the form import$device() instead of the old import.device().

  • Added the symlog_trans() function from a post on stack overflow. This function leads to a better visualization of light logger data, as a logarithmic transformation is necessary, but values of 0 are common. The function was integrated as a default for gg_day() and will likely be the basis of upcoming visualization functions.

  • Added the aggregate_Datetime() function to aggregate data to a given time interval.

  • Added the gg_overview() function to get a sense for the timeframe of measurement data.

  • Added the family of regularize functions to find and deal with implicit missing data. These functions include dominant_epoch(), gapless_Datetimes(), gap_handler(), and gap_finder().

  • A ton of updates to documentation, unit tests, and bug fixes.

LightLogR 0.2.0

  • Added Unit tests and documentation for all new functions.

  • To filter_Datetime() and filter_Date() added the option to filter for group specific dates.

  • Added the family of functions around States and Reference to import, process, and add states to light logger data, like sleep/wake times, wear times, or other data. This family includes import_Statechanges(), sc2interval(), ìnterval2state(), data2reference(), sleep_int2Brown(), Brown_check(), Brown_rec(), and Brown2reference().

  • Added the Article/Vignette “What´s in a Day” to demonstrate the LightLogR workflow.

  • Added the convenience function create_Timedata() to create a Time-of-Day column in datasets.

  • Added the family of filter_Datetime(), filter_Date() and filter_Time() functions to easily filter datasets.

  • Added unit tests for the first functions.

  • Added several helper functions to work with states like sleep or wear times.

  • Added an automatic ID creation at import and streamlined the import functions.

  • Added the function join_datasets to combine imported datasets with sensible constraints.

LightLogR 0.1.1

gg_day():

  • Added major grid marks for the y-axis.

  • Added a message when using start or end dates to make it clear, that only the Date portion of the input will be used.

  • Changed the behavior, when there is already a Day.data column present in the data. It will only create a new column if none is present, otherwise it will use the existing column for faceting (after factorization)

  • Added the option to create an interactive plot by feeding the plot to the [plotly] package.

LightLogR 0.1.0

  • Added a NEWS.md file to track changes to the package.