https://lucasfr.r-universe.devRecent package updates in lucasfrR-universehttps://github.com/lucasfr.pnghttps://lucasfr.r-universe.devThu, 27 Aug 2026 00:54:08 GMTlucas.franca@northumbria.ac.uk (Lucas França)Provides profile-likelihood and general maximum-likelihood variance-components estimation of narrow-sense heritability (h2), household/common-environment effects (c2), and bivariate genetic and environmental correlations for quantitative traits in family cohort and twin studies. Additive genetic relationship matrices are built from pedigrees via 'kinship2', including monozygotic-twin relatedness overrides. Phenotypes are inverse-normal transformed internally. Likelihood-ratio tests use a one-sided chi-squared boundary correction equivalent to SOLAR Eclipse. Ninety-five percent confidence intervals are derived from the profile likelihood rather than Wald approximations. Batch estimation over many traits or trait pairs returns tidy data frames ready for downstream visualisation (forest plots, heatmaps) and includes Benjamini-Hochberg FDR correction for bivariate correlation batches.https://github.com/r-universe/circadia-bio/actions/runs/36223798952Thu, 27 Aug 2026 00:54:08 GMTRitable0.2.1successhttps://circadia-bio.r-universe.devhttps://github.com/circadia-bio/R-itablegetting-started.Rmdgetting-started.htmlGetting started with R-itable2026-05-28 12:50:572026-08-27 00:44:27twin-cohorts.Rmdtwin-cohorts.htmlTwin cohorts: MZ relatedness, household effects, and bivariate correlations2026-08-23 12:07:402026-08-27 00:44:27lucas.franca@northumbria.ac.uk (Lucas França)Provides tools for importing, parsing, and analysing raw actigraphy data from wrist-worn devices. Implements a full sleep analysis pipeline — off-wrist detection, main sleep period detection, nap detection, and WASO computation — validated epoch-for-epoch against the Condor circadiaBase Python reference pipeline using ActTrust hardware. Also computes standard non-parametric circadian rhythm variables (interdaily stability, intradaily variability, relative amplitude, L5, M10). Device-specific parameter presets can be swapped to adapt the pipeline to other actigraph models. Designed to complement slumbR in the Circadia Lab ecosystem.https://github.com/r-universe/circadia-bio/actions/runs/39944332999Mon, 24 Aug 2026 13:34:53 GMTzeitR0.1.8successhttps://circadia-bio.r-universe.devhttps://github.com/circadia-bio/zeitRactogram.Rmdactogram.htmlActogram visualisation2026-07-09 01:11:562026-07-09 01:11:56holidays.Rmdholidays.htmlClassifying free days: weekends and public holidays2026-07-08 23:47:232026-07-08 23:59:04raw-accelerometry.Rmdraw-accelerometry.htmlFrom raw accelerometry to PIM/TAT/ZCM activity counts2026-07-20 15:50:042026-07-20 15:50:04getting-started.Rmdgetting-started.htmlGetting started with zeitR2026-06-19 21:23:222026-06-20 00:28:23lids.Rmdlids.htmlLIDS: ultradian sleep-cycle dynamics from actigraphy2026-07-29 22:54:242026-07-29 22:54:24npcra.Rmdnpcra.htmlNon-parametric circadian rhythm analysis2026-06-20 00:28:232026-06-20 00:28:23physical-activity.Rmdphysical-activity.htmlPhysical activity intensity from ActTrust/GT3X+ counts2026-07-20 15:50:042026-07-20 15:50:04sleep-analysis.Rmdsleep-analysis.htmlSingle-recording sleep analysis2026-06-23 10:17:332026-08-24 13:28:06study-analysis.Rmdstudy-analysis.htmlStudy-level analysis2026-06-20 00:28:232026-06-20 00:28:23vallim-pipeline.Rmdvallim-pipeline.htmlThe Vallim pipeline: native sleep classification2026-07-07 01:06:172026-07-08 00:17:42lucas.franca@northumbria.ac.uk (Lucas França)Transforms standard R data frames into publication-ready tables across a handful of common archetypes found in biomedical and neuroscience manuscripts: descriptive/Table 1 with group comparisons, heritability and variance components, correlation and partial correlation, regression coefficients, and simple descriptive summaries. Provides a unified rendering pipeline targeting 'gt' (Word/PDF), 'reactable' (HTML), and LaTeX outputs, with consistent theming, domain/section grouping, footnote handling for transformed variables, and FDR annotation.https://github.com/r-universe/circadia-bio/actions/runs/39936719134Sat, 25 Jul 2026 21:21:13 GMTclerkR0.1.3successhttps://circadia-bio.r-universe.devhttps://github.com/circadia-bio/clerkRcorrelation.Rmdcorrelation.htmlCorrelation and partial correlation tables2026-06-26 15:08:382026-06-26 15:08:38descriptive-table1.Rmddescriptive-table1.htmlDescriptive tables (Table 1)2026-06-26 15:08:382026-06-26 15:08:38formatting-options.Rmdformatting-options.htmlFormatting options2026-07-20 15:52:302026-07-25 20:31:01getting-started.Rmdgetting-started.htmlGetting started with clerkR2026-06-26 15:08:382026-06-26 15:08:38heritability-ritable.Rmdheritability-ritable.htmlHeritability tables with R-itable and clerkR2026-06-26 14:38:382026-07-20 15:52:30regression.Rmdregression.htmlRegression coefficient tables2026-06-26 15:08:382026-06-26 15:08:38simple-descriptive.Rmdsimple-descriptive.htmlSimple descriptive tables2026-06-26 15:08:382026-06-26 15:08:38lucas.franca@northumbria.ac.uk (Lucas França)Serial communication and data retrieval for Axivity AX3/AX6 accelerometer devices: device discovery, status, settings, data download, and reading recorded '.cwa'/AX6 binary files. Wraps the Open Movement Project's 'OMAPI' C library (vendored in src/omapi, BSD 2-clause, Newcastle University; see src/omapi/LICENSE.TXT), rather than reimplementing the serial protocol or binary file format directly. Also reads Condor Instruments ActTrust '.txt' actigraphy exports into the same tidy epoch shape, as a device-agnostic actigraphy import layer. On Linux, device discovery requires 'libudev-dev' (Debian/Ubuntu) or 'systemd-devel' (Fedora/RHEL) to be installed separately -- see SystemRequirements. macOS and Windows use OS frameworks/APIs directly, with no separate install step. Part of the Circadia Lab R ecosystem.https://github.com/r-universe/circadia-bio/actions/runs/37455757163Tue, 21 Jul 2026 22:58:41 GMTaxR0.1.3successhttps://circadia-bio.r-universe.devhttps://github.com/circadia-bio/axRaxR.RmdaxR.htmlGetting started with axR2026-07-15 21:36:432026-07-15 21:36:43lucas.franca@northumbria.ac.uk (Lucas França)A staging- and signal-agnostic toolkit of complex systems measures for physiological time series: entropy (sample, permutation, approximate), fractal and multifractal analysis (Higuchi dimension, DFA, MFDFA), Lyapunov exponents, multiscale entropy, and recurrence quantification analysis. Core algorithms wrap established C/C++/Fortran reference implementations rather than reimplementing them in pure R, to preserve numerical parity with the original methods literature. Some wrapped reference implementations are GPL-licensed (see inst/COPYRIGHTS), which is why the package as a whole is licensed GPL (>= 2) rather than MIT. Designed to sit underneath other Circadia Lab and CoDe-Neuro Lab packages (mrpheus, hypnoR, zeitR, dynR) as a shared complexity-metrics layer, while remaining fully usable standalone on any numeric time series.https://github.com/r-universe/circadia-bio/actions/runs/38153401048Sun, 12 Jul 2026 23:44:12 GMTRtractor0.1.0successhttps://circadia-bio.r-universe.devhttps://github.com/circadia-bio/Rtractorentropy-and-complexity.Rmdentropy-and-complexity.htmlEntropy and multiscale complexity2026-07-12 23:25:582026-07-12 23:29:31getting-started.Rmdgetting-started.htmlGetting started with Rtractor2026-07-12 02:23:282026-07-12 23:25:58multifractal-methods.Rmdmultifractal-methods.htmlMultifractal methods: MFDMA vs Chhabra-Jensen2026-07-12 23:25:582026-07-12 23:25:58lucas.franca@northumbria.ac.uk (Lucas França)Provides a staging-agnostic layer for hypnogram ingestion, sleep architecture metric computation, cycle segmentation, and transition analysis. Accepts full AASM-staged hypnograms (W / N1 / N2 / N3 / REM) from mrpheus and coarser actigraphy-derived hypnograms (W / Sleep / Quiet sleep) from zeitR; all metric functions degrade gracefully depending on staging resolution. Includes publication-ready plotting with a shared Circadia Lab colour palette. Designed as the hypnogram layer of the Circadia Lab ecosystem, feeding into syncR::sync().https://github.com/r-universe/circadia-bio/actions/runs/37915234560Sat, 11 Jul 2026 11:47:21 GMThypnoR0.1.1successhttps://circadia-bio.r-universe.devhttps://github.com/circadia-bio/hypnoRgetting-started.Rmdgetting-started.htmlGetting started with hypnoR2026-06-27 09:59:092026-07-11 11:16:07lucas.franca@northumbria.ac.uk (Lucas França)Raw physiological signal analysis for biological rhythms research. Provides ingestion, artefact detection, event detection, and feature extraction for multi-modal physiological recordings including polysomnography (EDF/EDF+), MRI-concurrent physiological logs (Philips PMU), and EEG. Covers cardiac rhythm (QRS detection, HRV), respiratory rhythm (apnoea detection, respiratory indices), and neural oscillations (sleep spindles, slow oscillations, automatic AASM sleep staging via a pre-trained LightGBM model ported from YASA; Vallat & Walker, 2021). Exports staged hypnograms to hypnor and derived metrics to syncR. Part of the Circadia Lab R ecosystem at Northumbria University.https://github.com/r-universe/circadia-bio/actions/runs/37110726662Wed, 08 Jul 2026 22:16:43 GMTmrpheus0.1.4successhttps://circadia-bio.r-universe.devhttps://github.com/circadia-bio/mrpheussleep-staging.Rmdsleep-staging.htmlAutomatic AASM Sleep Staging2026-07-05 22:10:552026-07-05 22:10:55getting-started.Rmdgetting-started.htmlGetting started with mrpheus2026-06-27 14:06:352026-07-05 22:10:55mri-physiology.Rmdmri-physiology.htmlMRI physiological signal processing2026-07-04 12:41:222026-07-04 21:45:13eeg-preprocessing.Rmdeeg-preprocessing.htmlPSG Preprocessing Pipeline2026-07-06 01:13:272026-07-06 01:17:31spectral-analysis.Rmdspectral-analysis.htmlSpectral Analysis of Sleep EEG2026-07-06 01:17:312026-07-06 01:17:31lucas.franca@northumbria.ac.uk (Lucas França)Provides the shared visual identity for the Circadia Lab R ecosystem: colour palettes, ggplot2 theme, and ggplot2 scales. Palettes cover qualitative, sequential, and diverging use cases anchored on the lab's brand colours. Designed to be used alongside zeitR, slumbR, tallieR, and syncR.https://github.com/r-universe/circadia-bio/actions/runs/37298787143Tue, 07 Jul 2026 11:23:46 GMTcircadia0.1.0successhttps://circadia-bio.r-universe.devhttps://github.com/circadia-bio/circadiadiverging-palettes.Rmddiverging-palettes.htmlDiverging palettes2026-06-24 23:16:572026-07-07 11:23:03getting-started.Rmdgetting-started.htmlGetting started with circadia2026-06-24 14:53:572026-06-24 14:53:57qualitative-palettes.Rmdqualitative-palettes.htmlQualitative palettes2026-06-24 23:16:572026-06-24 23:16:57sequential-palettes.Rmdsequential-palettes.htmlSequential palettes2026-06-24 23:16:572026-07-07 11:23:03lucas.franca@northumbria.ac.uk (Lucas França)An R port of the Python dynfc library for computing dynamic connectivity (dynFC) representations from multivariate neurophysiological timeseries, including BOLD fMRI, EEG, LFP, and related signals. Implements sliding-window Pearson correlation (Hansen et al., 2015), edge-centric cofluctuation analysis (Esfahlani et al., 2020; Faskowitz et al., 2020), instantaneous phase-locking via the Hilbert transform, dynamic phase-locking matrices (dPL), the LEiDA leading-eigenvector framework (Cabral et al., 2017; Lord et al., 2019), and the Kuramoto order parameter with metastability and Shannon entropy. Part of the Circadia Lab R ecosystem.https://github.com/r-universe/circadia-bio/actions/runs/37283538310Mon, 06 Jul 2026 21:02:48 GMTdynR0.1.5successhttps://circadia-bio.r-universe.devhttps://github.com/circadia-bio/dynRsliding-window-fc.Rmdsliding-window-fc.htmlCorrelation-based dynamic FC: sliding windows and edge cofluctuations2026-06-28 08:30:012026-06-28 23:10:57getting-started.Rmdgetting-started.htmlGetting started with dynR2026-06-28 08:30:012026-06-28 23:10:57phase-based-fc.Rmdphase-based-fc.htmlPhase-based dynamic FC: Hilbert transform, LEiDA, and Kuramoto2026-06-28 08:30:012026-06-28 23:12:45lucas.franca@northumbria.ac.uk (Lucas França)Analysis of Blood-Oxygen-Level-Dependent (BOLD) fMRI data for sleep and circadian research. Receives preprocessed derivatives from fMRIPrep and transforms them into analysis-ready outputs: atlas-agnostic parcellation with an extensible atlas schema, ROI-level timeseries extraction, voxelwise signal metrics (tSNR, GLM contrasts), and functional connectivity matrices. Exports parcellated BOLD data directly to syncR for integration with actigraphy, polysomnography, and questionnaire data in a unified participant-indexed database. Part of the Circadia Lab R ecosystem at Northumbria University. fmriprep gets you clean data. boldR gets you useful data.https://github.com/r-universe/circadia-bio/actions/runs/36540813805Mon, 29 Jun 2026 05:22:50 GMTboldR0.1.0successhttps://circadia-bio.r-universe.devhttps://github.com/circadia-bio/boldRgetting-started.Rmdgetting-started.htmlGetting started with boldR2026-06-27 22:46:262026-06-27 22:46:26lucas.franca@northumbria.ac.uk (Lucas França)syncR is the integrator and coordinator of the Circadia Lab R ecosystem. It pulls sociodemographic and questionnaire data from tallieR, sleep diary data from slumbR, and actigraphy-derived circadian metrics from zeitR into a single unified, participant-indexed database. syncR::sync() — pulling everything into alignment, just like the SCN does.https://github.com/r-universe/circadia-bio/actions/runs/36541369700Mon, 29 Jun 2026 05:19:56 GMTsyncR0.1.0successhttps://circadia-bio.r-universe.devhttps://github.com/circadia-bio/syncRsyncR.RmdsyncR.htmlGetting started with syncR2026-06-23 20:41:182026-06-23 22:05:21lucas.franca@kcl.ac.uk (Lucas França)Provides tidy tools for quantifying brain state dynamics from functional connectivity time series. Computes fractional occupancy, mean dwell time, and Markov-chain transition probabilities across discrete brain states derived from clustering methods such as k-means or hidden Markov models.https://github.com/r-universe/code-neuro/actions/runs/36693640570Sun, 31 May 2026 14:32:30 GMTstateR0.1.0successhttps://code-neuro.r-universe.devhttps://github.com/CoDe-Neuro/stateRgetting-started.Rmdgetting-started.htmlGetting started with stateR2026-05-31 13:51:022026-05-31 13:51:02grouped-pipeline.Rmdgrouped-pipeline.htmlGrouped pipeline: testing across states2026-05-31 13:51:022026-05-31 14:11:40markov-transitions.Rmdmarkov-transitions.htmlMarkov transition probabilities2026-05-31 13:51:022026-05-31 14:11:40lucas.franca@kcl.ac.uk (Lucas G. S. França)Wraps glm(), lme4::lmer(), and binomial glm() with a permutation loop to compute nonparametric p-values. For each model, ptestR generates a null distribution of the test statistic by randomly rearranging the outcome variable, then computes p.perm as the proportion of permuted statistics at least as extreme as the observed one. This approach requires far fewer distributional assumptions than standard Wald or likelihood-ratio tests, making it well-suited to neuroimaging, EEG, and other biomedical datasets with repeated measures and small samples.https://github.com/r-universe/code-neuro/actions/runs/36693838665Sun, 31 May 2026 13:24:36 GMTptestR0.1.1successhttps://code-neuro.r-universe.devhttps://github.com/CoDe-Neuro/ptestRgetting-started.Rmdgetting-started.htmlGetting started with ptestR2026-05-31 13:20:242026-05-31 13:20:24grouped-analysis.Rmdgrouped-analysis.htmlGrouped analysis across features2026-05-31 13:20:242026-05-31 13:24:36mixed-effects-models.Rmdmixed-effects-models.htmlPermutation tests for mixed-effects models2026-05-31 13:20:242026-05-31 13:20:24lucas.franca@northumbria.ac.uk (Lucas França)A companion package for the ScoreMe app (https://scoreme.circadia-lab.uk). Provides tools to import participant JSON exports, re-score validated questionnaires, and assemble tidy wide and long study-level data frames ready for downstream analysis in R. Stable instruments: ESS, ISI, DBAS-16, MEQ, PSQI, RU-SATED, STOP-BANG, KSS, MCTQ. Beta instruments (scoring ported from ScoreMe, not yet independently validated in tallieR): PHQ-2, PHQ-9, PHQ-15, GAD-7, GAD-2, BDI-II, BAI, DASS-21, PANSS, STAI-S, STAI-T, WHOQOL-BREF, MacArthur SSS, IPAQ-S, GPAQ, GSQ, AQ-10.https://github.com/r-universe/circadia-bio/actions/runs/36541332239Fri, 22 May 2026 12:30:07 GMTtallieR0.2.0successhttps://circadia-bio.r-universe.devhttps://github.com/circadia-bio/tallieRcustom-instruments.Rmdcustom-instruments.htmlCustom instruments in tallieR2026-05-22 12:30:072026-05-22 12:30:07getting-started.Rmdgetting-started.htmlGetting started with tallieR2026-05-14 15:29:242026-05-22 12:30:07longitudinal-data.Rmdlongitudinal-data.htmlLongitudinal data in tallieR2026-05-22 12:30:072026-05-22 12:30:07reliability-analysis.Rmdreliability-analysis.htmlReliability analysis in tallieR2026-05-22 12:30:072026-05-22 12:30:07lucas.franca@northumbria.ac.uk (Lucas França)A companion package for the Sleep Diaries app (https://sleepdiaries.circadia-lab.uk). Provides tools to import participant JSON exports, compute standard sleep variables (sleep onset latency, total sleep time, sleep efficiency, WASO, etc.), re-score validated sleep questionnaires (ESS, ISI, DBAS-16, MEQ, PSQI, RU-SATED, STOP-BANG, MCTQ), and assemble tidy study-level data frames ready for downstream analysis.https://github.com/r-universe/circadia-bio/actions/runs/39232405809Thu, 14 May 2026 17:48:52 GMTslumbR0.1.0successhttps://circadia-bio.r-universe.devhttps://github.com/circadia-bio/slumbRgetting-started.Rmdgetting-started.htmlGetting started with slumbR2026-05-13 22:23:352026-05-13 22:23:35