Aquila-Consortium/borg_public
32
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Import doc from main

Browse Source
This commit is contained in:
Guilhem Lavaux 2023-06-27 08:12:18 +02:00
parent 56a50eead3
commit 5d6a692932
1 changed files with 170 additions and 68 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

238
docs/source/index.rst
View File

@ -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 <https://aquila-consortium.org/publications/>`_.
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 <http://dx.doi.org/10.1111/j.1365-2966.2010.16610.x>`_;
`arXiv:0911.2493 <http://arxiv.org/pdf/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 <http://dx.doi.org/10.1088/0004-637X/779/1/15>`_;
`arXiv:1306.1821 <http://arxiv.org/pdf/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 <http://dx.doi.org/10.1093/mnras/stu2479>`_;
`arXiv:1402.1763 <http://arxiv.org/pdf/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 <http://dx.doi.org/10.1051/0004-6361/201730909>`_;
`arXiv:1706.08971 <http://arxiv.org/pdf/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 <http://dx.doi.org/10.1111/j.1365-2966.2010.16897.x>`_;
`arXiv:0911.2496 <http://arxiv.org/pdf/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 <http://dx.doi.org/10.1111/j.1365-2966.2010.17313.x>`_;
`arXiv:0911.2498 <http://arxiv.org/pdf/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 <http://dx.doi.org/10.1111/j.1365-2966.2012.21423.x>`_;
`arXiv:1106.2757 <http://arxiv.org/pdf/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 <http://dx.doi.org/10.1093/mnras/stt449>`_;
`arXiv:1203.3639 <http://arxiv.org/pdf/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 <http://dx.doi.org/10.1088/1475-7516/2015/01/036>`_;
`arXiv:1409.6308 <http://arxiv.org/pdf/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 <http://dx.doi.org/10.1093/mnras/stv2499>`_;
`arXiv:1509.05040 <http://arxiv.org/pdf/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 <http://dx.doi.org/10.1051/0004-6361/201833710>`_;
`arXiv:1806.11117 <http://arxiv.org/pdf/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 <http://arxiv.org/pdf/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 <http://dx.doi.org/10.1088/1475-7516/2015/01/036>`_;
`arXiv:1409.6308 <http://arxiv.org/pdf/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 <http://dx.doi.org/10.1093/mnras/stv2499>`_;
`arXiv:1509.05040 <http://arxiv.org/pdf/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 <http://dx.doi.org/10.1051/0004-6361/201833710>`_;
`arXiv:1806.11117 <http://arxiv.org/pdf/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 <http://arxiv.org/pdf/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 <http://dx.doi.org/10.1051/0004-6361/201730909>`_;
`arXiv:1706.08971 <http://arxiv.org/pdf/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 <http://dx.doi.org/10.1051/0004-6361/201834844>`_;
`arXiv:1812.05113 <http://arxiv.org/pdf/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 <http://dx.doi.org/10.1051/0004-6361/201834117>`_;
`arXiv:1808.07496 <http://arxiv.org/pdf/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 <http://dx.doi.org/10.1051/0004-6361/201936245>`_;
`arXiv:1907.02973 <http://arxiv.org/pdf/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 <http://dx.doi.org/10.1051/0004-6361/202038482>`_;
`arXiv:2005.12928 <http://arxiv.org/pdf/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 <http://dx.doi.org/10.1093/mnras/stab204>`_;
`arXiv:2011.07722 <http://arxiv.org/pdf/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 <http://dx.doi.org/10.1093/mnras/stab3234>`_;
`arXiv:2108.04825 <http://arxiv.org/pdf/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 <http://arxiv.org/pdf/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 <http://dx.doi.org/10.1093/mnras/stac2985>`_;
`arXiv:2111.15535 <http://arxiv.org/pdf/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 <http://dx.doi.org/10.1093/mnras/stac3346>`_;
`arXiv:2204.00023 <http://arxiv.org/pdf/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 <http://dx.doi.org/10.1093/mnras/stad432>`_;
`arXiv:2203.08838 <http://arxiv.org/pdf/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 <http://arxiv.org/pdf/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 <http://dx.doi.org/10.1088/1475-7516/2019/01/042>`_;
`arXiv:1808.02002 <http://arxiv.org/pdf/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 <http://dx.doi.org/10.1088/1475-7516/2020/11/008>`_;
`arXiv:2004.06707 <http://arxiv.org/pdf/2004.06707>`_ (biased tracers with EFT bias model and likelihood)
Acknowledgements
----------------