From 5d6a6929328ca4ddbe1c2865246e1871834c9cd0 Mon Sep 17 00:00:00 2001 From: Guilhem Lavaux Date: Tue, 27 Jun 2023 08:12:18 +0200 Subject: [PATCH] Import doc from main --- docs/source/index.rst | 238 ++++++++++++++++++++++++++++++------------ 1 file changed, 170 insertions(+), 68 deletions(-) diff --git a/docs/source/index.rst b/docs/source/index.rst index ab6ee11..6264d75 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -42,78 +42,180 @@ Table of contents developer/copyright_and_authorship Citing ------- +^^^^^^ -If you are using |a| for your project, please cite the following articles for ARES2 and ARES3: +.. sectionauthor:: Florent Leclercq (last update: 20 June 2023) -* Jasche, Kitaura, Wandelt, 2010, MNRAS, 406, 1 (arxiv 0911.2493) -* Jasche & Lavaux, 2015, MNRAS, 447, 2 (arxiv 1402.1763) -* Lavaux & Jasche, 2016, MNRAS, 455, 3 (arxiv 1509.05040) -* Jasche & Lavaux, 2019, A&A, 625, A64 (arxiv 1806.11117) - -However, bear in mind that depending on the features that you are using you may want to cite other papers as well. -Here is a non-exhaustive list of those articles: - -* Model development: - - * HADES epoch: - - * HMC, exponential transform, linear bias: Jasche, Kitaura, Wandelt, 2010, 406, 1 (arXiv 0911.2493) - * HMC, exponential transform, power law bias: - - * Jasche, Leclercq, Wandelt, 2015 - * Jasche, Wandelt, 2012, MNRAS, 425, 1042 (arXiv 1106.2757) - - * Foreground/Robustification: - - * Jasche, Lavaux, 2017, A&A (arXiv:1706.08971) - * Porqueres, Kodi Ramanah, Jasche, Lavaux, 2019, A&A (arXiv: 1812.05113) - - * Cosmic expansion model: - - * Kodi Ramanah, Lavaux, Jasche, Wandelt, 2019, A&A (arXiv: 1808.07496) - - * Photometric redshifts - - * HADES with Photo-Z: Jasche & Wandelt, 2012, MNRAS, 425, 1042 (arXiv: 1106.2757) - - * Galaxy shear: - - * Porqueres, Heavens, Mortlock & Lavaux, 2021, MNRAS, 502, 3035 (arXiv 2011.07722) - * Porqueres, Heavens, Mortlock & Lavaux, 2022, MNRAS, 509, 3194 (arXiv 2108.04825) - - * Cosmic velocity field: - - * Prideaux-Ghee, Leclercq, Lavaux, Heavens, Jasche, 2022, MNRAS (arXiv: 2204.00023) - * Boruah, Lavaux, Hudson, 2022, MNRAS (arXiv 2111.15535) - - * BORG-PM - - * Jasche & Lavaux, 2019, A&A, 625, A64 (arXiv 1806.11117) - - * EFT bias model and likelihood - - * Schmidt, Elsner, Jasche, Nguyen, Lavaux, JCAP 01, 042 (2019) (arXiv:1808.02002) - * Schmidt, Cabass, Jasche, Lavaux, JCAP 11, 008 (2020) (arXiv:2004.06707) - -* Data applications - - * SDSS Main Galaxy sample: - * SDSS3 LRG sample: - - * Lavaux, Jasche & Leclercq, 2019, arXiv:1909.06396 - - * 2M++ sample: - - * Lavaux & Jasche, 2016, MNRAS, 455, 3 (arXiv 1509.05040) - * Jasche & Lavaux, 2019, A&A, 625, A64 (arXiv 1806.11117) - - -*HADES* and *BORG* papers have a different listing. - -For a full listing of publications from the Aquila consortium, please check the +The following section gives the references for the |ares|, |hades|, and |borg| algorithms and codes (including their direct application to real data, but excluding further scientific exploitation). +For the full list of publications from the Aquila consortium, please check the `Aquila website `_. +ARES +'''' + +References for the |ares| algorithm (linear data model, Wiener filtering with Gibbs sampling/messenger field) +are the following papers: + +* J. Jasche, F. S. Kitaura, B. D. Wandelt, T. A. Enßlin, *Bayesian power-spectrum inference for large-scale structure data*, + `Monthly Notices of the Royal Astronomical Society (2010) 406, 60 `_; + `arXiv:0911.2493 `_ + (linear data model, Wiener filtering and power spectrum inference with Gibbs sampling) +* J. Jasche, B. D. Wandelt, *Methods for Bayesian Power Spectrum Inference with Galaxy Surveys*, + `The Astrophysical Journal (2013) 779, 15 `_; + `arXiv:1306.1821 `_ + (luminosity-dependent galaxy bias, calibration of noise levels, reversible jump algorithm) +* J. Jasche, G. Lavaux, *Matrix-free large-scale Bayesian inference in cosmology*, + `Monthly Notices of the Royal Astronomical Society (2015) 447, 1204 `_; + `arXiv:1402.1763 `_ + (inference with messenger field) +* J. Jasche, G. Lavaux, *Bayesian power spectrum inference with foreground and target contamination treatment*, + `Astronomy and Astrophysics (2017) 606, A37 `_; + `arXiv:1706.08971 `_ + (joint inference of density field and known foregrounds) + +HADES +''''' + +References for the |hades| algorithm (log-normal data model, Hamiltonian Monte Carlo sampling, photometric redshift inference) are the following papers: + +* J. Jasche, F. S. Kitaura, *Fast Hamiltonian sampling for large-scale structure inference*, + `Monthly Notices of the Royal Astronomical Society (2010) 407, 29 `_; + `arXiv:0911.2496 `_ + (HMC method paper) +* J. Jasche, F. S. Kitaura, C. Li, T. A. Enßlin, *Bayesian non-linear large-scale structure inference of the Sloan Digital + Sky Survey Data Release 7*, + `Monthly Notices of the Royal Astronomical Society (2010) 409, 355 `_; + `arXiv:0911.2498 `_ + (data application with log-normal data model) +* J. Jasche, B. D. Wandelt, *Bayesian inference from photometric redshift surveys*, + `Monthly Notices of the Royal Astronomical Society (2012) 425, 1042 `_; + `arXiv:1106.2757 `_ + (method paper: joint inference of density and photometric redshifts) + +BORG +'''' + +Methodological papers that shall be cited when referring to the |borg| algorithm (inference with a structure formation model and Hamiltonian Monte Carlo) are the following: + +* J. Jasche, B. D. Wandelt, *Bayesian physical reconstruction of initial conditions from large-scale structure surveys*, + `Monthly Notices of the Royal Astronomical Society (2013) 432, 894 `_; + `arXiv:1203.3639 `_ + (original BORG method paper with differentiable LPT data model and HMC) +* J. Jasche, F. Leclercq, B. D. Wandelt, *Past and present cosmic structure in the SDSS DR7 main sample*, + `Journal of Cosmology and Astroparticle Physics (2015) 01, 036 `_; + `arXiv:1409.6308 `_ + (luminosity-dependent galaxy bias, power-law bias model, calibration of noise levels) +* G. Lavaux, J. Jasche, *Unmasking the masked Universe: the 2M++ catalogue through Bayesian eyes*, + `Monthly Notices of the Royal Astronomical Society (2016) 455, 3169 `_; + `arXiv:1509.05040 `_ + (data model with redshift-space distortions) +* J. Jasche, G. Lavaux, *Physical Bayesian modelling of the non-linear matter distribution: New insights into the nearby universe*, + `Astronomy and Astrophysics (2019) 625, A64 `_; + `arXiv:1806.11117 `_ + (BORGPM: particle-mesh data model, observer velocity sampling, "heating up" the likelihood) +* G. Lavaux, J. Jasche, F. Leclercq, *Systematic-free inference of the cosmic matter density field from SDSS3-BOSS data*, + `arXiv:1909.06396 `_ + (data model with light-cone effects, quadratic form bias model) + +Data application papers of |borg| are the following: + +* J. Jasche, F. Leclercq, B. D. Wandelt, *Past and present cosmic structure in the SDSS DR7 main sample*, + `Journal of Cosmology and Astroparticle Physics (2015) 01, 036 `_; + `arXiv:1409.6308 `_ + (application to SDSS DR7 main galaxy sample) +* G. Lavaux, J. Jasche, *Unmasking the masked Universe: the 2M++ catalogue through Bayesian eyes*, + `Monthly Notices of the Royal Astronomical Society (2016) 455, 3169 `_; + `arXiv:1509.05040 `_ + (application to 2M++, LPT data model) +* J. Jasche, G. Lavaux, *Physical Bayesian modelling of the non-linear matter distribution: New insights into the nearby universe*, + `Astronomy and Astrophysics (2019) 625, A64 `_; + `arXiv:1806.11117 `_ + (application to 2M++, PM data model) +* G. Lavaux, J. Jasche, F. Leclercq, *Systematic-free inference of the cosmic matter density field from SDSS3-BOSS data*, + `arXiv:1909.06396 `_ + (application to SDSS3 BOSS, LPT data model) + +Additional papers extend the |borg| algorithm and shall be cited depending on the context. The list includes (but may not be limited to): + +* Foregrounds/Systematic effects: + + * J. Jasche, G. Lavaux, *Bayesian power spectrum inference with foreground and target contamination treatment*, + `Astronomy and Astrophysics (2017) 606, A37 `_; + `arXiv:1706.08971 `_ + (joint inference of density field and known foregrounds) + * N. Porqueres, D. Kodi Ramanah, J. Jasche, G. Lavaux, *Explicit Bayesian treatment of unknown foreground contaminations + in galaxy surveys*, + `Astronomy and Astrophysics (2019) 624, A115 `_; + `arXiv:1812.05113 `_ + (robust likelihood for unknown foregrounds effects) + +* Cosmic expansion model (Alcock-Paczynski effect): + + * D. Kodi Ramanah, G. Lavaux, J. Jasche, B. Wandelt, *Cosmological inference from Bayesian forward modelling + of deep galaxy redshift surveys*, + `Astronomy and Astrophysics (2019) 621, A69 `_; + `arXiv:1808.07496 `_ + (Alcock-Paczynski expansion test) + +* Lyman-α forest: + + * N. Porqueres, J. Jasche, G. Lavaux, T. Enßlin, *Inferring high-redshift large-scale structure dynamics from the Lyman-α forest*, + `Astronomy and Astrophysics (2019) 630, A151 `_; + `arXiv:1907.02973 `_ (Lyman alpha data model) + * N. Porqueres, O. Hahn, J. Jasche, G. Lavaux, *A hierarchical field-level inference approach to reconstruction from + sparse Lyman-α forest data*, + `Astronomy and Astrophysics (2020) 642, A139 `_; + `arXiv:2005.12928 `_ + +* Weak lensing (cosmic shear): + + * N. Porqueres, A. Heavens, D. Mortlock, G. Lavaux, *Bayesian forward modelling of cosmic shear data*, + `Monthly Notices of the Royal Astronomical Society (2021) 502, 3035 `_; + `arXiv:2011.07722 `_ + (original BORG-WL paper) + * N. Porqueres, A. Heavens, D. Mortlock, G. Lavaux, *Lifting weak lensing degeneracies with a field-based likelihood*, + `Monthly Notices of the Royal Astronomical Society (2022) 509, 3194 `_; + `arXiv:2108.04825 `_ + (cosmological parameter inference) + * N. Porqueres, A. Heavens, D. Mortlock, G. Lavaux, T. L. Makinen, *Field-level inference of cosmic shear with intrinsic + alignments and baryons*, + `arXiv:2304.04785 `_ + (intrinsic alignments and baryons) + +* Cosmic velocity field: + + * S. S. Boruah, G. Lavaux, M. J. Hudson, *Bayesian reconstruction of dark matter distribution from peculiar velocities: + accounting for inhomogeneous Malmquist bias*, + `Monthly Notices of the Royal Astronomical Society (2022) 517, 4529 `_; + `arXiv:2111.15535 `_ + (linear model for the velocity field, inhomogeneous Malmquist bias, observational effects) + * J. Prideaux-Ghee, F. Leclercq, G. Lavaux, A. Heavens, J. Jasche, *Field-Based Physical Inference From Peculiar Velocity Tracers*, + `Monthly Notices of the Royal Astronomical Society (2023) 518, 4191 `_; + `arXiv:2204.00023 `_ + (LPT structure formation model in the data model) + +* Primordial non-Gaussianity: + + * A. Andrews, J. Jasche, G. Lavaux, F. Schmidt, *Bayesian field-level inference of primordial + non-Gaussianity using next-generation galaxy surveys*, + `Monthly Notices of the Royal Astronomical Society (2023) 520, 5746 `_; + `arXiv:2203.08838 `_ (local fNL sampling) + +* Photometric redshift inference: + + * E. Tsaprazi, J. Jasche, G. Lavaux, F. Leclercq, *Higher-order statistics of the large-scale structure from photometric redshifts*, + `arXiv:2301.03581 `_ + (photometric redshift sampling with a structure formation model) + +* Effective Field Theory (EFT) bias model and likelihood: + + * F. Schmidt, F. Elsner, J. Jasche, N. M. Nguyen, G. Lavaux, *A rigorous EFT-based forward model for large-scale structure*, + `Journal of Cosmology and Astroparticle Physics (2019) 01, 042 `_; + `arXiv:1808.02002 `_ (EFT likelihood) + * F. Schmidt, G. Cabass, J. Jasche, G. Lavaux, *Unbiased cosmology inference from biased tracers using the EFT likelihood*, + `Journal of Cosmology and Astroparticle Physics (2020) 11, 008 `_; + `arXiv:2004.06707 `_ (biased tracers with EFT bias model and likelihood) + Acknowledgements ----------------