Complete configuration reference

All 189 live configuration keys are listed here with their normalized defaults and allowed values. This page is generated from analysis.DEFAULT_CONFIG through describe_config, so removed or undocumented keys fail the documentation checks.

A partial config or settings object may contain only the keys you change. Every result stores the complete normalized configuration in provenance.

Selection, core period, and actogram

Key	Type	Default	Allowed values	What it changes
start	nullable	null	—	Inclusive start of the analysis interval; null starts at the first sample.
end	nullable	null	—	Inclusive end of the analysis interval; null ends at the last sample.
exclusions	list	[]	—	Intervals treated as unavailable without altering the source recording.
analysis_channel	str	"activity"	—	Measurement key analysed; each channel keeps its declared sum or mean aggregation.
period_hours	float	24.0	—	Reference cycle used for folding, cosinor, and circular quantities.
period_min_hours	float	18.0	—	Shortest candidate period in spectral and instantaneous-phase searches.
period_max_hours	float	30.0	—	Longest candidate period in spectral and instantaneous-phase searches.
bin_minutes	int	15	—	Width of the regular analysis grid in minutes.
double_plot	bool	true	—	Show each actogram row beside the following cycle.
actogram_start_hours	float	0.0	—	Hour-valued control for actogram start in selection, core period, and actogram.
actogram_mode	str	"scaled"	scaled, threshold, quantile	Mapping from activity values to actogram marks.
actogram_threshold	float	1.0	—	Controls actogram threshold for selection, core period, and actogram.
actogram_quantiles	int	5	—	Controls actogram quantiles for selection, core period, and actogram.
actogram_y_scale	str	"fit"	fit, fixed	Controls actogram y scale for selection, core period, and actogram.
actogram_page_days	int	14	—	Controls actogram page days for selection, core period, and actogram.
cursor_start_hours	float	6.0	—	Hour-valued control for cursor start in selection, core period, and actogram.
cursor_end_hours	float	18.0	—	Hour-valued control for cursor end in selection, core period, and actogram.
bout_threshold	float	1.0	—	Controls bout threshold for selection, core period, and actogram.
bout_min_minutes	int	10	—	Minute-valued control for bout min in selection, core period, and actogram.
bout_max_gap_minutes	int	10	—	Minute-valued control for bout max gap in selection, core period, and actogram.
onset_off_hours	float	6.0	—	Hour-valued control for onset off in selection, core period, and actogram.
onset_on_hours	float	6.0	—	Hour-valued control for onset on in selection, core period, and actogram.
onset_threshold_percent	float	80.0	—	Controls onset threshold percent for selection, core period, and actogram.
onset_overrides	dict	{"onset":{},"offset":{}}	—	Explicit per-date onset or offset replacements retained in provenance.
show_marker_paths	bool	false	—	Controls show marker paths for selection, core period, and actogram.
show_marker_fits	bool	false	—	Controls show marker fits for selection, core period, and actogram.
fit1_start	nullable	null	—	Controls fit1 start for selection, core period, and actogram.
fit1_end	nullable	null	—	Controls fit1 end for selection, core period, and actogram.
fit2_start	nullable	null	—	Controls fit2 start for selection, core period, and actogram.
fit2_end	nullable	null	—	Controls fit2 end for selection, core period, and actogram.
phase_shift_day	nullable	null	—	Controls phase shift day for selection, core period, and actogram.
periodogram_alpha	float	0.01	—	Significance threshold used for periodogram.
periodogram_method	str	"lomb"	lomb, chi_square, f	Controls periodogram method for selection, core period, and actogram.

Extended period estimation

Key	Type	Default	Allowed values	What it changes
period_method	str	"lomb"	chi_square, ejtk, f, fft_nlls, jtk, lomb, mesa, mfourfit, spectrum_resampling	Single estimator used by estimate_period.
period_methods	list	["lomb"]	—	Estimators requested by compare_periods; the default runs Lomb-Scargle only.
phase_reference	str	"zero"	zero, window	Origin used when a period estimator reports phase.
phase_units	str	"hours"	hours, circadian	Unit used for reported phase.
period_detrend	str	"none"	als, amp&baseline, amp_baseline, asls, asymmetric-least-squares, asymmetric_least_squares, baseline, bicubic, cubic, degree6, diff, difference, first-difference, first_difference, frequency, huber, kernel, linear, loess, lowess, median, moving_average, moving_median, none, poly3, poly6, polynomial, robust, robust_linear, running_mean, running_median, savgol, savitzky-golay, savitzky_golay	Baseline-removal method applied before extended period estimation.
period_detrend_window_hours	float	24.0	—	Hour-valued control for period detrend window in extended period estimation.
period_detrend_polynomial_degree	int	3	—	Polynomial degree used when period detrending is polynomial.
period_detrend_min_valid_fraction	float	0.5	—	Minimum valid fraction required inside a detrending window.
period_detrend_bandwidth_hours	nullable	null	—	Kernel bandwidth used by kernel baseline detrending.
period_detrend_low_cut_hours	float	45.0	—	Longest period retained by frequency-filter detrending.
period_detrend_high_cut_hours	float	4.0	—	Shortest period retained by frequency-filter detrending.
period_detrend_filter_order	int	2	—	Digital-filter order used by frequency-filter detrending.
period_detrend_lowess_fraction	nullable	null	—	Finite-record fraction used by each LOWESS local fit; null derives it from the detrending window.
period_detrend_lowess_iterations	int	3	—	Robust residual-reweighting passes used by LOWESS detrending.
period_detrend_asls_smoothness	float	1000000.0	—	Second-difference smoothness penalty used by asymmetric least-squares detrending.
period_detrend_asls_asymmetry	float	0.01	—	Weight given to points above an asymmetric least-squares baseline.
period_detrend_asls_iterations	int	10	—	Reweighting passes used by asymmetric least-squares detrending.
nlls_max_components	int	5	—	Controls nlls max components for extended period estimation.
nlls_circadian_min	nullable	null	—	Legacy name for the FFT-NLLS component-selection lower bound, in hours. Null follows period_min_hours, including ultradian searches.
nlls_circadian_max	nullable	null	—	Legacy name for the FFT-NLLS component-selection upper bound, in hours. Null follows period_max_hours, including infradian searches.
nlls_improvement_alpha	float	0.05	—	Significance threshold used for nlls improvement.
mesa_model_length	nullable	null	—	Controls mesa model length for extended period estimation.
chi_square_spline_interval_hours	nullable	null	—	Hour-valued control for chi square spline interval in extended period estimation.
chi_square_normalisation	str	"sokolove_bushell"	legacy, sokolove_bushell	Controls chi square normalisation for extended period estimation.
mfourfit_harmonics	int	4	—	Controls mfourfit harmonics for extended period estimation.
mfourfit_step_hours	float	0.05	—	Hour-valued control for mfourfit step in extended period estimation.
sr_iterations	int	1000	—	Number of iterations used by sr.
sr_bandwidth	nullable	null	—	Controls sr bandwidth for extended period estimation.
sr_trim_high_frequency	bool	true	—	Controls sr trim high frequency for extended period estimation.
sr_grid_points	int	256	—	Controls sr grid points for extended period estimation.
sr_seed	int	20260901	—	Deterministic random seed used for sr.

JTK_CYCLE and empirical JTK_CYCLE

Key	Type	Default	Allowed values	What it changes
jtk_periods	list	[20.0,24.0,28.0]	—	Template periods tested by JTK_CYCLE and empirical JTK_CYCLE.
jtk_asymmetries	nullable	null	—	Optional active:inactive waveform ratios for JTK templates; null uses symmetric templates.
jtk_phase_step_hours	nullable	null	—	Hour-valued control for jtk phase step in jtk_cycle and empirical jtk_cycle.
ejtk_permutations	int	1000	—	Number of random permutations used by ejtk.
jtk_correction	str	"bh"	bh, bonferroni, sidak, none	Multiple-testing correction used for jtk.
jtk_alpha	float	0.05	—	Significance threshold used for jtk.
jtk_seed	int	20260901	—	Deterministic random seed used for jtk.
jtk_max_points	int	96	—	Controls jtk max points for jtk_cycle and empirical jtk_cycle.

Circular and instantaneous analyses

Key	Type	Default	Allowed values	What it changes
circular_test	str	"permutation"	permutation, watson_williams	Controls circular test for circular and instantaneous analyses.
circular_permutations	int	2000	—	Number of random permutations used by circular.
circular_min_resultant	float	0.7	—	Minimum phase concentration before the parametric circular test is considered.
circular_alpha	float	0.05	—	Significance threshold used for circular.
circular_seed	int	0	—	Deterministic random seed used for circular.
circular_correction	str	"sidak"	bh, bonferroni, sidak, none	Multiple-testing correction used for circular.
instantaneous_band_min_hours	nullable	null	—	Hour-valued control for instantaneous band min in circular and instantaneous analyses.
instantaneous_band_max_hours	nullable	null	—	Hour-valued control for instantaneous band max in circular and instantaneous analyses.
instantaneous_edge_trim_cycles	float	1.5	—	Filter-edge duration removed from each end, measured in cycles.

Phase response and longitudinal analyses

Key	Type	Default	Allowed values	What it changes
prc_reference	str	"nocturnal"	nocturnal, diurnal	Controls prc reference for phase response and longitudinal analyses.
prc_marker	str	"onset"	onset, peak	Controls prc marker for phase response and longitudinal analyses.
prc_min_onsets	int	5	—	Controls prc min onsets for phase response and longitudinal analyses.
prc_min_animals	int	8	—	Controls prc min animals for phase response and longitudinal analyses.
prc_harmonics	int	1	—	Controls prc harmonics for phase response and longitudinal analyses.
prc_dead_zone_hours	float	0.5	—	Hour-valued control for prc dead zone in phase response and longitudinal analyses.
prc_comparison_alpha	float	0.05	—	Significance threshold used for prc comparison.
prc_comparison_correction	str	"sidak"	—	Multiple-testing correction used for prc comparison.
longitudinal_min_subjects	int	3	—	Minimum independent subjects required by longitudinal.
longitudinal_min_epochs	int	3	—	Controls longitudinal min epochs for phase response and longitudinal analyses.
longitudinal_alpha	float	0.05	—	Significance threshold used for longitudinal.
longitudinal_correction	str	"sidak"	—	Multiple-testing correction used for longitudinal.
longitudinal_sphericity	str	"greenhouse_geisser"	—	Controls longitudinal sphericity for phase response and longitudinal analyses.

Splitting and dose response

Key	Type	Default	Allowed values	What it changes
splitting_min_days	float	10.0	—	Minimum valid days required by splitting.
splitting_min_separation_hours	float	0.5	—	Hour-valued control for splitting min separation in splitting and dose response.
splitting_alpha	float	0.05	—	Significance threshold used for splitting.
splitting_hold_days	int	3	—	Controls splitting hold days for splitting and dose response.
splitting_harmonic_tolerance	float	1.0	—	Controls splitting harmonic tolerance for splitting and dose response.
dose_min_levels	int	4	—	Controls dose min levels for splitting and dose response.
dose_alpha	float	0.05	—	Significance threshold used for dose.
dose_ct_tolerance_hours	float	2.0	—	Hour-valued control for dose ct tolerance in splitting and dose response.
dose_bootstrap	int	2000	—	Controls dose bootstrap for splitting and dose response.

Entrainment, masking, feeding, and sleep

Key	Type	Default	Allowed values	What it changes
entrainment_reference	str	"cycle_off"	—	Controls entrainment reference for entrainment, masking, feeding, and sleep.
entrainment_zeitgeber	str	"light"	—	Controls entrainment zeitgeber for entrainment, masking, feeding, and sleep.
entrainment_marker	str	"onset"	—	Controls entrainment marker for entrainment, masking, feeding, and sleep.
entrainment_min_days	int	5	—	Minimum valid days required by entrainment.
entrainment_alpha	float	0.05	—	Significance threshold used for entrainment.
reentrainment_criterion_sd	float	2.0	—	Controls reentrainment criterion sd for entrainment, masking, feeding, and sleep.
reentrainment_hold_days	int	3	—	Controls reentrainment hold days for entrainment, masking, feeding, and sleep.
reentrainment_min_days_each_side	int	4	—	Controls reentrainment min days each side for entrainment, masking, feeding, and sleep.
masking_control_days	int	7	—	Controls masking control days for entrainment, masking, feeding, and sleep.
masking_min_control_days	int	3	—	Controls masking min control days for entrainment, masking, feeding, and sleep.
masking_alpha	float	0.05	—	Significance threshold used for masking.
faa_window_hours	float	3.0	—	Hour-valued control for faa window in entrainment, masking, feeding, and sleep.
faa_hold_days	int	3	—	Controls faa hold days for entrainment, masking, feeding, and sleep.
faa_criterion_sd	float	2.0	—	Controls faa criterion sd for entrainment, masking, feeding, and sleep.
faa_min_days	int	5	—	Minimum valid days required by faa.
faa_fast_days	list	[]	—	Controls faa fast days for entrainment, masking, feeding, and sleep.
faa_alpha	float	0.05	—	Significance threshold used for faa.
sleep_immobility_minutes	float	1.0	—	Minute-valued control for sleep immobility in entrainment, masking, feeding, and sleep.
sleep_activity_threshold	float	0.0	—	Controls sleep activity threshold for entrainment, masking, feeding, and sleep.

Ultradian and temperature analyses

Key	Type	Default	Allowed values	What it changes
ultradian_min_hours	float	2.0	—	Hour-valued control for ultradian min in ultradian and temperature analyses.
ultradian_max_hours	float	8.0	—	Hour-valued control for ultradian max in ultradian and temperature analyses.
ultradian_min_samples_per_cycle	float	8.0	—	Controls ultradian min samples per cycle for ultradian and temperature analyses.
ultradian_min_relative_amplitude	float	0.05	—	Controls ultradian min relative amplitude for ultradian and temperature analyses.
compensation_band_low	float	0.8	—	Controls compensation band low for ultradian and temperature analyses.
compensation_band_high	float	1.2	—	Controls compensation band high for ultradian and temperature analyses.
compensation_alpha	float	0.05	—	Significance threshold used for compensation.

Differential, paired, and predictive analyses

Key	Type	Default	Allowed values	What it changes
differential_compared	list	["mesor","amplitude","phase"]	—	Controls differential compared for differential, paired, and predictive analyses.
differential_free_period	bool	false	—	Controls differential free period for differential, paired, and predictive analyses.
differential_rhythmic_alpha	float	0.05	—	Significance threshold used for differential rhythmic.
differential_min_units	int	3	—	Controls differential min units for differential, paired, and predictive analyses.
differential_correction	str	"sidak"	bh, bonferroni, sidak, none	Multiple-testing correction used for differential.
differential_alpha	float	0.05	—	Significance threshold used for differential.
paired_min_subjects	int	3	—	Minimum independent subjects required by paired.
paired_correction	str	"sidak"	—	Multiple-testing correction used for paired.
paired_alpha	float	0.05	—	Significance threshold used for paired.
prediction_t_min_hours	float	20.0	—	Hour-valued control for prediction t min in differential, paired, and predictive analyses.
prediction_t_max_hours	float	28.0	—	Hour-valued control for prediction t max in differential, paired, and predictive analyses.
prediction_t_step_hours	float	0.1	—	Hour-valued control for prediction t step in differential, paired, and predictive analyses.
prediction_max_cycles	int	60	—	Controls prediction max cycles for differential, paired, and predictive analyses.
prediction_tolerance_hours	float	0.5	—	Hour-valued control for prediction tolerance in differential, paired, and predictive analyses.
two_process_min_transitions	int	20	—	Controls two process min transitions for differential, paired, and predictive analyses.
two_process_min_days	int	5	—	Minimum valid days required by two process.
two_process_min_phases	int	4	—	Controls two process min phases for differential, paired, and predictive analyses.
two_process_max_iterations	int	2000	—	Number of iterations used by two process max.
two_process_restarts	int	4	—	Independent optimiser restarts used by two process.
two_process_step_minutes	float	10.0	—	Minute-valued control for two process step in differential, paired, and predictive analyses.
two_process_parameter_span	float	1.5	—	Controls two process parameter span for differential, paired, and predictive analyses.
two_process_timing_tolerance	float	0.1	—	Controls two process timing tolerance for differential, paired, and predictive analyses.
two_process_mismatch_tie	float	0.02	—	Controls two process mismatch tie for differential, paired, and predictive analyses.

Study, synchrony, spatial, coupling, dispersion, and power

Key	Type	Default	Allowed values	What it changes
study_max_recordings	int	200	—	Controls study max recordings for study, synchrony, spatial, coupling, dispersion, and power.
study_figure_formats	list	["svg"]	—	Controls study figure formats for study, synchrony, spatial, coupling, dispersion, and power.
synchrony_min_cells	int	10	—	Minimum independent inputs required by synchrony.
synchrony_min_contributing	int	5	—	Controls synchrony min contributing for study, synchrony, spatial, coupling, dispersion, and power.
synchrony_alpha	float	0.05	—	Significance threshold used for synchrony.
spatial_min_points	int	6	—	Minimum independent inputs required by spatial.
spatial_alpha	float	0.05	—	Significance threshold used for spatial.
spatial_permutations	int	2000	—	Number of random permutations used by spatial.
spatial_collinear_ratio	float	0.001	—	Controls spatial collinear ratio for study, synchrony, spatial, coupling, dispersion, and power.
coupling_alpha	float	0.05	—	Significance threshold used for coupling.
coupling_min_cycles	int	3	—	Controls coupling min cycles for study, synchrony, spatial, coupling, dispersion, and power.
coupling_window_cycles	int	2	—	Controls coupling window cycles for study, synchrony, spatial, coupling, dispersion, and power.
period_dispersion_min_cycles	int	3	—	Controls period dispersion min cycles for study, synchrony, spatial, coupling, dispersion, and power.
period_dispersion_alpha	float	0.05	—	Significance threshold used for period dispersion.
power_simulations	int	400	—	Controls power simulations for study, synchrony, spatial, coupling, dispersion, and power.
power_max_n	int	64	—	Controls power max n for study, synchrony, spatial, coupling, dispersion, and power.
power_target	float	0.8	—	Controls power target for study, synchrony, spatial, coupling, dispersion, and power.
power_max_seconds	float	600.0	—	Controls power max seconds for study, synchrony, spatial, coupling, dispersion, and power.
power_interval_alpha	float	0.05	—	Significance threshold used for power interval.
power_seed	int	0	—	Deterministic random seed used for power.

Spectral display, schedules, and colours

Key	Type	Default	Allowed values	What it changes
fft_blackman_harris	bool	false	—	Controls fft blackman harris for spectral display, schedules, and colours.
fft_spectrum	str	"power"	amplitude, power	Controls fft spectrum for spectral display, schedules, and colours.
wavelet_cycles	float	6.0	—	Controls wavelet cycles for spectral display, schedules, and colours.
lights_on	float	7.0	—	Controls lights on for spectral display, schedules, and colours.
lights_off	float	19.0	—	Controls lights off for spectral display, schedules, and colours.
lighting_schedule	list	[]	—	Dated light-state intervals used instead of a repeating simple schedule.
zeitgeber_schedule	list	[]	—	Dated light, food, or other cue intervals used by entrainment analyses.
ld_start	nullable	null	—	Controls ld start for spectral display, schedules, and colours.
ld_end	nullable	null	—	Controls ld end for spectral display, schedules, and colours.
dd_start	nullable	null	—	Controls dd start for spectral display, schedules, and colours.
dd_end	nullable	null	—	Controls dd end for spectral display, schedules, and colours.
actogram_activity_color	str	"#111111"	—	SVG colour used for actogram activity.
actogram_light_color	str	"#ffffff"	—	SVG colour used for actogram light.
actogram_dark_color	str	"#d6d6d6"	—	SVG colour used for actogram dark.
onset_color	str	"#c0392b"	—	SVG colour used for onset.
offset_color	str	"#2878b5"	—	SVG colour used for offset.
protocol_preset	str	"custom"	—	Name recorded in provenance for the selected settings preset.