emcee v3: A Python ensemble sampling toolkit for affine-invariant MCMC

Abstract

emcee is a Python library implementing a class of affine-invariant ensemble samplers for Markov chain Monte Carlo (MCMC). This package has been widely applied to probabilistic modeling problems in astrophysics where it was originally published, with some applications in other fields. When it was first released in 2012, the interface implemented in emcee was fundamentally different from the MCMC libraries that were popular at the time, such as PyMC, because it was specifically designed to work with "black box" models instead of structured graphical models. This has been a popular interface for applications in astrophysics because it is often non-trivial to implement realistic physics within the modeling frameworks required by other libraries. Since emcee's release, other libraries have been developed with similar interfaces, such as dynesty (Speagle 2019). The version 3.0 release of emcee is the first major release of the library in about 6 years and it includes a full re-write of the computational backend, several commonly requested features, and a set of new "move" implementations.

Published in the Journal for Open Source Software

References in corpus (1)

• emcee: The MCMC Hammer

Cited by in corpus (172)

• Early Release Science of the Exoplanet WASP-39b with JWST NIRSpec G395H
• Toward a Better Understanding of Cosmic Chronometers: A new measurement of H(z) at z~0.7
• Physics of Eclipsing Binaries. V. General Framework for Solving the Inverse Problem
• TESS Eclipsing Binary Stars. I. Short cadence observations of 4584 eclipsing binaries in Sectors 1-26
• Identification of carbon dioxide in an exoplanet atmosphere
• The Pantheon+ Analysis: SuperCal-Fragilistic Cross Calibration, Retrained SALT2 Light Curve Model, and Calibration Systematic Uncertainty
• Extended stellar systems in the solar neighborhood -- V. Discovery of coronae of nearby star clusters
• Earth shaped by primordial H${}_2$ atmospheres
• The Diversity and Variability of Star Formation Histories in Models of Galaxy Evolution
• GRB 221009A: Discovery of an Exceptionally Rare Nearby and Energetic Gamma-Ray Burst
• Line-by-line velocity measurements, an outlier-resistant method for precision velocimetry
• Revised and new proper motions for confirmed and candidate Milky Way dwarf galaxies
• Precision cosmology with voids in the final BOSS data
• zeus: A Python implementation of Ensemble Slice Sampling for efficient Bayesian parameter inference
• The eROSITA Final Equatorial-Depth Survey (eFEDS): X-ray Observable-to-Mass-and-Redshift Relations of Galaxy Clusters and Groups with Weak-Lensing Mass Calibration from the Hyper Suprime-Cam Subaru Strategic Program Survey
• Completeness of the Gaia-verse II: what are the odds that a star is missing from Gaia DR2?
• The surprising accuracy of isothermal Jeans modelling of self-interacting dark matter density profiles
• Massive neutrinos and cosmic composition
• Euclid: Forecasts from redshift-space distortions and the Alcock-Paczynski test with cosmic voids
• The Radial Acceleration Relation in CLASH Galaxy Clusters
• Cosmological Constraints from Galaxy Clusters and Groups in the eROSITA Final Equatorial Depth Survey
• Constraining the Hubble constant to a precision of about 1% using multi-band dark standard siren detections
• Chemical Evolution in the Milky Way: Rotation-based ages for APOGEE-Kepler cool dwarf stars
• The recent LMC-SMC collision: Timing and impact parameter constraints from comparison of Gaia LMC disk kinematics and N-body simulations
• Directly tracing the vertical stratification of molecules in protoplanetary disks
• A black hole detected in the young massive LMC cluster NGC 1850
• Binary Stars in the New Millennium
• High atmospheric metal enrichment for a Saturn-mass planet
• Introducing piXedfit -- a Spectral Energy Distribution Fitting Code Designed for Resolved Sources
• TOI-1452 b: SPIRou and TESS reveal a super-Earth in a temperate orbit transiting an M4 dwarf
• Constraining the cosmological parameters using gravitational wave observations of massive black hole binaries and statistical redshift information
• A new determination of the primordial helium abundance using the analyses of HII region spectra from SDSS
• Constraining the Cosmic Baryon Distribution with Fast Radio Burst Foreground Mapping
• Toward a Better Understanding of Cosmic Chronometers: Stellar Population Properties of Passive Galaxies at Intermediate Redshift
• Accurate Estimation of Diffusion Coefficients and their Uncertainties from Computer Simulation
• The JWST Weather Report from the Nearest Brown Dwarfs I: multi-period JWST NIRSpec + MIRI monitoring of the benchmark binary brown dwarf WISE 1049AB
• HI intensity mapping with MeerKAT: 1/f noise analysis
• A $75\%$ Occurrence Rate of Debris Discs around F stars in the $\beta$ Pic Moving Group
• Cosmology with varying fundamental constants from hyperlight, coupled scalars
• First direct measurement of auroral and equatorial jets in the stratosphere of Jupiter
• Further Evidence of Modified Spin-down in Sun-like Stars: Pileups in the Temperature-Period Distribution
• Bayesian Inference of the Dense Matter Equation of State built upon Covariant Density Functionals
• Cluster Ages to Reconstruct the Milky Way Assembly (CARMA) I. The final word on the origin of NGC6388 and NGC6441
• Toward Robust Corrections for Stellar Contamination in JWST Exoplanet Transmission Spectra
• A Gravitational Redshift Measurement of the White Dwarf Mass-Radius Relation
• Detailed chemical abundances of stars in the outskirts of the Tucana II ultra-faint dwarf galaxy
• Solo dwarfs III: Exploring the orbital origins of isolated Local Group galaxies with Gaia Data Release 2
• Digging for relics of the past: the ancient and obscured bulge globular cluster NGC6256
• PSR J1641+3627F: a low-mass He white dwarf orbiting a possible high-mass neutron star in the globular cluster M13
• A Parameter-Masked Mock Data Challenge for Beyond-Two-Point Galaxy Clustering Statistics
• Modeling COVID-19 dynamics in Illinois under non-pharmaceutical interventions
• The Excitation Conditions of CN in TW Hya
• Gas Accretion Can Drive Turbulence in Galaxies
• Circumbinary discs for stellar population models
• Discovery of a double sequence of blue straggler stars in the core-collapsed globular cluster NGC 6256
• The white dwarf binary pathways survey V. The Gaia white dwarf plus AFGK binary sample and the identification of 23 close binaries
• Dust Populations in the Iconic Vega Planetary System Resolved by ALMA
• HAZMAT. VII. The Evolution of Ultraviolet Emission with Age and Rotation for Early M Dwarf Stars
• Masses of White Dwarf Binary Companions to Type Ia Supernovae Measured from Runaway Velocities
• First evidence of multi-iron sub-populations in the Bulge Fossil Fragment candidate Liller 1
• TOI-1695 b: A Water World Orbiting an Early M Dwarf in the Planet Radius Valley
• A New Method to Constrain the Appearance and Disappearance of Observed Jellyfish Galaxy Tails
• A new dynamical modeling of the WASP-47 system with CHEOPS observations
• Dissecting Nearby Galaxies with piXedfit: I. Spatially Resolved Properties of Stars, Dust, and Gas as Revealed by Panchromatic SED Fitting
• Digging into the Galactic Bulge: stellar population and structure of the poorly studied cluster NGC 6316
• A search for planetary companions around 800 pulsars from the Jodrell Bank pulsar timing programme
• Magnetic signatures on mixed-mode frequencies. II. Period spacings as a probe of the internal magnetism of red giants
• Spectroscopic Detection of a 2.9-hour Orbit in a Long Period Radio Transient
• The preferential orientation of magnetic switchbacks, implications for solar magnetic flux transport
• A clustering-based self-calibration of the richness-to-mass relation of CAMIRA galaxy clusters out to $z\approx 1.1$ in the Hyper Suprime-Cam survey
• SN2017jgh - A high-cadence complete shock cooling lightcurve of a SN IIb with the Kepler telescope
• Photometric detection of internal gravity waves in upper main-sequence stars. III. Comparison of amplitude spectrum fitting and Gaussian process regression using celerite2
• Transit Timing Variations in the three-planet system: TOI-270
• Progenitor Mass Distribution for 22 Historic Core-Collapse Supernovae
• The Dark Side of Using Dark Sirens to Constrain the Hubble-Lemaître Constant
• Beyond Point Masses. III. Detecting Haumea's Nonspherical Gravitational Field
• Beyond Point Masses. II. Non-Keplerian Shape Effects are Detectable in Several TNO Binaries
• Characterisation of the Warm-Jupiter TOI-1130 system with CHEOPS and photo-dynamical approach
• Modelling stellar activity with Gaussian process regression networks
• Multi-probe analysis of the galaxy cluster CL J1226.9+3332: Hydrostatic mass and hydrostatic-to-lensing bias
• Bayesian inference of the dense matter equation of state built upon extended Skyrme interactions
• Kinematic unrest of low mass galaxy groups
• Spitzer thermal phase curve of WASP-121 b
• A 99-minute Double-lined White Dwarf Binary from SDSS-V
• On dust evolution in planet-forming discs in binary systems. II -- Comparison with Taurus and $\rho$ Ophiuchus (sub-)millimetre observations: discs in binaries have small dust sizes
• Joint Modeling of Radial Velocities and Photometry with a Gaussian Process Framework
• Improving the Cosmological Constraints by Inferring the Formation Channel of Extreme-mass-ratio Inspirals
• Differentiable Predictions for Large Scale Structure with SHAMNet
• A decade of radial-velocity monitoring of Vega and new limits on the presence of planets
• The Distance and Dynamical History of the Virgo Cluster Ultradiffuse Galaxy VCC 615
• Mass-Velocity Dispersion Relation in HIFLUGCS Galaxy Clusters
• Advice on describing Bayesian analysis of neutron and X-ray reflectometry
• Detection of Contact Binary Candidates Observed By TESS Using Autoencoder Neural Network
• Molecular gas and dust properties in $z>7$ quasar hosts
• The luminosity functions of kilonovae from binary neutron star mergers under different equation of states
• Trends in Spitzer Secondary Eclipses
• Faint Stars in a Faint Galaxy: II. The Low Mass Stellar Initial Mass Function of the Boötes I Ultrafaint Dwarf Spheroidal Galaxy
• The ultra narrow FRB20191107B, and the origins of FRB scattering
• Analytic Light Curve for Mutual Transits of Two Bodies Across a Limb-darkened Star
• A comparison of Bayesian sampling algorithms for high-dimensional particle physics and cosmology applications
• Debiased Galaxy Cluster Pressure Profiles from X-ray Observations and Simulations
• A young white dwarf orbiting PSR J1835-3259B in the bulge globular cluster NGC 6652
• FX UMa: A New Heartbeat Binary System with Linear and Non-linear Tidal Oscillations and delta Sct Pulsations
• Dark-siren Cosmology with Decihertz Gravitational-wave Detectors
• A Distinct Radial Acceleration Relation across Brightest Cluster Galaxies and Galaxy Clusters
• A Method of Rapidly Deriving Late-type Contact Binary Parameters and Its Application in the Catalina Sky Survey
• Seasonal Changes in the Atmosphere of HD 80606b Observed with JWST's NIRSpec/G395H
• Vertical CO surfaces as a probe for protoplanetary disk mass and carbon depletion
• The Baltimore Oriole's Nest: Cool Winds from the Inner and Outer Parts of a Star-Forming Galaxy at z=1.3
• The U.S. Naval Observatory VLBI Spectroscopic Catalog
• Detached Eclipsing Binaries in Compact Hierarchical Triples: Triple-lined systems BD+44 2258 and KIC 06525196
• Kepler-80 Revisited: Assessing the Participation of a Newly Discovered Planet in the Resonant Chain
• Mass-Velocity Dispersion Relation in MaNGA Brightest Cluster Galaxies
• Dark skies of the slightly eccentric WASP-18 b from its optical-to-infrared dayside emission
• A Photometric in-depth look at the core-collapsed globular cluster NGC 6284
• Very High Energy Afterglow of Structured Jets: GW 170817 and Prospects for Future Detections
• Evidence of a fraction of LIGO/Virgo/KAGRA events coming from active galactic nuclei
• Quantitative grain size estimation on airless bodies from the negative polarization branch. II. Dawn mission targets (4) Vesta and (1) Ceres
• Exploiting the transit timing capabilities of Ariel
• V772 Cas: an ellipsoidal HgMn star in an eclipsing binary
• The C-Band All-Sky Survey (C-BASS): New Constraints on the Integrated Radio Spectrum of M 31
• Multi-frequency analysis of the ALMA and VLA high resolution continuum observations of the substructured disc around CI Tau. Preference for sub-mm-sized low-porosity amorphous carbon grains
• High-Precision Redshifts for Type Ia Supernovae with the Nancy Grace Roman Space Telescope P127 Prism
• The hydrostatic-to-lensing mass bias from resolved X-ray and optical-IR data
• The strange case of Na I in the atmosphere of HD209458 b: Reconciling low- and high-resolution spectroscopic observations G
• Discovery of four new EL CVn-type binaries in the Gaia eclipsing binaries
• XENONnT WIMP Search: Signal & Background Modeling and Statistical Inference
• Radii, masses, and transit-timing variations of the three-planet system orbiting the naked-eye star TOI-396
• When the Stars Align: A 5 σ Concordance of Planetary Nebulae Major Axes in the Centre of our Galaxy
• Satellite galaxy abundance dependency on cosmology in Magneticum simulations
• In-depth characterization of the Kepler-10 three-planet system with HARPS-N radial velocities and Kepler transit timing variations
• Is binning always sinning? The impact of time-averaging for exoplanet phase curves
• Pulse Timing Discovery of a Three-Day Companion to the Hot Subdwarf BPM 36430
• A Ghost in Boötes: The Least Luminous Disrupted Dwarf Galaxy
• From Barthel Randers Kropina Geometries to the Accelerating Universe: A Brief Review of Recent Advances in Finslerian Cosmology
• HYPERION: broad-band X-ray-to-near-infrared emission of Quasars in the first billion years of the Universe
• Galaxy And Mass Assembly (GAMA): $\mathbf{z}\sim 0$ Galaxy Luminosity Function down to $\mathbf{L}\sim 10^6{\mathbf{L}}_{\odot }$ via Clustering Based Redshift Inference
• Exoplanets Prediction in Multiplanetary Systems
• Measurements and models of enhanced recombination following inner-shell vacancies in liquid xenon
• Tidally Heated Sub-Neptunes, Refined Planetary Compositions, and Confirmation of a Third Planet in the TOI-1266 System
• Cosmology with voids from the Nancy Grace Roman Space Telescope
• The Circumbinary Disk of HD 34700A: I. CO gas kinematics indicate spirals, infall, and vortex motions
• Revisiting the Local Star-Forming Galaxies Observed in the HETDEX Pilot Survey
• Detecting the inner regions of discs around sources of microlensing with Roman Space Telescope
• Galaxy cluster mass bias from projected mass maps: The Three Hundred-NIKA2 LPSZ twin samples
• Probing populations of dark stellar remnants in the globular clusters 47 Tuc and Terzan 5 using pulsar timing
• Cool Interstellar Medium as an Evolutionary Tracer in ALMA-Observed Local Dusty Early-Type Galaxies
• Measurement of the evolving galaxy luminosity and mass function using clustering-based redshift inference
• Molecules with ALMA at Planet-forming Scales (MAPS XVIII): Kinematic Substructures in the Disks of HD 163296 and MWC 480
• Structural parameters, chronological age and dynamical age of the LMC globular cluster NGC 1754
• Searching for Low-mass Population III Stars Disguised as White Dwarfs
• Perturbation theory challenge for cosmological parameters estimation II.: Matter power spectrum in redshift space
• Characterisation of the eclipsing post-common-envelope binary TIC 60040774
• Constraining the halo-ISM connection through multi-transition carbon monoxide line-intensity mapping
• Exploiting the high-resolution NIKA2 data to study the intracluster medium and dynamical state of ACT-CL J0240.0+0116
• PANCO2: a new software to measure pressure profiles from resolved thermal SZ observations
• Far-infrared to centimeter emission of very nearby galaxies with archival data
• Compact CO emission and no evidence of radial drift. ALMA observations of the faintest planet-forming disks in Lupus
• Brans-Dicke-like field for co-varying $G$ and $c$: observational constraints
• Fixing effective range parameters in elastic $\alpha$-${}^{12}$C scattering: an impact on resonant $2_4^{+}$ state of ${}^{16}$O and $S_{E2}$ factor of ${}^{12}$C($\alpha$,$\gamma$)${}^{16}$O
• Re-examining the Bayesian colour excess estimation for the local star-forming galaxies observed in the HETDEX Pilot Survey
• X-ray Observations of 1ES 1959+650 in its high activity state in 2016-2017 with AstroSat and Swift
• lintsampler: Easy random sampling via linear interpolation
• The SNIa Runaway LP 398-9: Detection of Circumstellar Material and Surface Rotation
• Magellan/IMACS spectroscopy of Grus I: A low metallicity ultra-faint dwarf galaxy
• Thermal Sunyaev-Zel'dovich effect at the core of CL J1226.9+3332 revealed by NOEMA
• Confirmation of Fe I on MASCARA-5 b's Dayside Observed With EXPRES
• Granulation on a quiet K dwarf: HD 166620 I. Spectral signatures as a function of line-formation temperature
• Capability for detection of GW190521-like binary black holes with TianQin
• Markov chain Monte Carlo Detector Tomography applied to a NbTiN nanobridge
• Gas and Dust Shadows in the TW Hydrae Disk
• Cross-correlations between mm-wave line-intensity mapping and weak lensing surveys: preliminary consideration of long-term prospects