https://circadia-bio.r-universe.devRecent package updates in circadia-bioR-universehttps://github.com/circadia-bio.pnghttps://circadia-bio.r-universe.devThu, 02 Jul 2026 21:19:47 GMTlucas.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/28624654807Thu, 02 Jul 2026 21:19:47 GMTdynR0.1.2successhttps://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)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/28555566608Mon, 29 Jun 2026 05:23:35 GMTclerkR0.1.2successhttps://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 options2026-06-27 01:31:262026-06-27 01:42:16getting-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 14:38:382026-06-26 23:00:00regression.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)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/28555570514Mon, 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)Raw polysomnography (PSG) signal analysis for sleep and circadian research. Provides EDF/EDF+ ingestion, artefact detection, spectral analysis, sleep event detection (spindles, slow oscillations), automatic AASM sleep staging via a pre-trained LightGBM model (ported from YASA; Vallat & Walker, 2021), and respiratory and cardiac metrics. Exports staged hypnograms directly to hypnor and PSG-derived metrics to syncR. Part of the Circadia Lab R ecosystem.https://github.com/r-universe/circadia-bio/actions/runs/28555569073Mon, 29 Jun 2026 05:21:25 GMTmrpheus0.1.0successhttps://circadia-bio.r-universe.devhttps://github.com/circadia-bio/mrpheusgetting-started.Rmdgetting-started.htmlGetting started with mrpheus2026-06-27 14:06:352026-06-27 14:06:35lucas.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 via theme_circadia(). Designed as the hypnogram layer of the Circadia Lab ecosystem, feeding into syncR::sync().https://github.com/r-universe/circadia-bio/actions/runs/28555567860Mon, 29 Jun 2026 05:20:45 GMThypnoR0.1.0successhttps://circadia-bio.r-universe.devhttps://github.com/circadia-bio/hypnoRgetting-started.Rmdgetting-started.htmlGetting started with hypnoR2026-06-27 09:59:092026-06-27 09:59:09lucas.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/28555565544Mon, 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@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/28555562526Mon, 29 Jun 2026 05:18:54 GMTzeitR0.1.0successhttps://circadia-bio.r-universe.devhttps://github.com/circadia-bio/zeitRgetting-started.Rmdgetting-started.htmlGetting started with zeitR2026-06-19 21:23:222026-06-20 00:28:23npcra.Rmdnpcra.htmlNon-parametric circadian rhythm analysis2026-06-20 00:28:232026-06-20 00:28:23sleep-analysis.Rmdsleep-analysis.htmlSingle-recording sleep analysis2026-06-23 10:17:332026-06-23 10:17:33study-analysis.Rmdstudy-analysis.htmlStudy-level analysis2026-06-20 00:28:232026-06-20 00:28:23lucas.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/28555561316Wed, 24 Jun 2026 23:46:23 GMTcircadia0.1.0successhttps://circadia-bio.r-universe.devhttps://github.com/circadia-bio/circadiadiverging-palettes.Rmddiverging-palettes.htmlDiverging palettes2026-06-24 23:16:572026-06-24 23:16:57getting-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 23:16:572026-06-24 23:16:57lucas.franca@northumbria.ac.uk (Lucas França)Provides profile-likelihood variance-components estimation of narrow-sense heritability (h2) for quantitative traits in family cohort studies. Additive genetic relationship matrices are built from pedigrees via 'kinship2'. 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 returns tidy data frames ready for downstream visualisation (forest plots, heatmaps).https://github.com/r-universe/circadia-bio/actions/runs/28557278993Mon, 08 Jun 2026 11:41:14 GMTRitable0.1.0successhttps://circadia-bio.r-universe.devhttps://github.com/circadia-bio/R-itablegetting-started.Rmdgetting-started.htmlGetting started with R-itable2026-05-28 12:50:572026-06-08 11:41:14lucas.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/28555564758Fri, 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/28555563401Thu, 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