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Dont escape all kinds of characters
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7 changes: 7 additions & 0 deletions docs/bib/bib2md.py
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from pathlib import Path

import pybtex.backends.markdown as fmt
from pybtex.database import parse_string
from pybtex.richtext import Tag, Text
from pybtex.style.formatting.unsrt import Style as UnsrtStyle
from pybtex.style.formatting.unsrt import field, sentence

fmt.SPECIAL_CHARS.remove("[")
fmt.SPECIAL_CHARS.remove("]")
fmt.SPECIAL_CHARS.remove("(")
fmt.SPECIAL_CHARS.remove(")")
fmt.SPECIAL_CHARS.remove("-")

HERE = Path(__file__).parent


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120 changes: 60 additions & 60 deletions docs/references.md
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Patrick N\. Raanes\.
*Improvements to Ensemble Methods for Data Assimilation in the Geosciences*\.
PhD thesis, University of Oxford, January 2016\.
\\url https://ora\.ox\.ac\.uk/objects/uuid:9f9961f0\-6906\-4147\-a8a9\-ca9f2d0e4a12\.
\\url https://ora\.ox\.ac\.uk/objects/uuid:9f9961f0-6906-4147-a8a9-ca9f2d0e4a12\.

### `bocquet2010a`

Marc Bocquet, Carlos A\. Pires, and Lin Wu\.
`"Beyond Gaussian statistical modeling in geophysical data assimilation"`\.
*Monthly Weather Review*, 138\(8\):2997–3023, 2010\.
*Monthly Weather Review*, 138(8):2997–3023, 2010\.

### `bocquet2015`

Marc Bocquet, Patrick N\. Raanes, and Alexis Hannart\.
`"Expanding the validity of the ensemble Kalman filter without the intrinsic need for inflation"`\.
*Nonlinear Processes in Geophysics*, 22\(6\):645–662, 2015\.
*Nonlinear Processes in Geophysics*, 22(6):645–662, 2015\.

### `sakov2008a`

Pavel Sakov and Peter R\. Oke\.
`"Implications of the form of the ensemble transformation in the ensemble square root filters"`\.
*Monthly Weather Review*, 136\(3\):1042–1053, 2008\.
*Monthly Weather Review*, 136(3):1042–1053, 2008\.

### `wiljes2016`

Jana de Wiljes, Walter Acevedo, and Sebastian Reich\.
`"Second\-order accurate ensemble transform particle filters"`\.
`"Second-order accurate ensemble transform particle filters"`\.
*arXiv preprint arXiv:1608\.08179*, 2016\.

### `bocquet2011`

Marc Bocquet\.
`"Ensemble Kalman filtering without the intrinsic need for inflation"`\.
*Nonlinear Processes in Geophysics*, 18\(5\):735–750, 2011\.
*Nonlinear Processes in Geophysics*, 18(5):735–750, 2011\.

### `hoteit2015a`

I\. Hoteit, D\.\-T\. Pham, M\. E\. Gharamti, and X\. Luo\.
I\. Hoteit, D\.-T\. Pham, M\. E\. Gharamti, and X\. Luo\.
`"Mitigating observation perturbation sampling errors in the stochastic EnKF"`\.
*Monthly Weather Review*, 143\(7\):2918–2936, 2015\.
*Monthly Weather Review*, 143(7):2918–2936, 2015\.

### `bocquet2013`

Marc Bocquet and Pavel Sakov\.
`"Joint state and parameter estimation with an iterative ensemble Kalman smoother"`\.
*Nonlinear Processes in Geophysics*, 20\(5\):803–818, 2013\.
*Nonlinear Processes in Geophysics*, 20(5):803–818, 2013\.

### `hunt2007`

Brian R\. Hunt, Eric J\. Kostelich, and Istvan Szunyogh\.
`"Efficient data assimilation for spatiotemporal chaos: a local ensemble transform Kalman filter"`\.
*Physica D: Nonlinear Phenomena*, 230\(1\):112–126, 2007\.
*Physica D: Nonlinear Phenomena*, 230(1):112–126, 2007\.

### `karspeck2007`

Alicia R\. Karspeck and Jeffrey L\. Anderson\.
`"Experimental implementation of an ensemble adjustment filter for an intermediate ENSO model"`\.
*Journal of Climate*, 20\(18\):4638–4658, 2007\.
*Journal of Climate*, 20(18):4638–4658, 2007\.

### `todter2015a`

Julian Tödter and Bodo Ahrens\.
`"A second\-order exact ensemble square root filter for nonlinear data assimilation"`\.
*Monthly Weather Review*, 143\(4\):1347–1367, 2015\.
`"A second-order exact ensemble square root filter for nonlinear data assimilation"`\.
*Monthly Weather Review*, 143(4):1347–1367, 2015\.

### `chen2003`

Zhe Chen\.
`"Bayesian filtering: from Kalman filters to particle filters, and beyond"`\.
*Statistics*, 182\(1\):1–69, 2003\.
*Statistics*, 182(1):1–69, 2003\.

### `bocquet2012a`

Marc Bocquet and Pavel Sakov\.
`"Combining inflation\-free and iterative ensemble Kalman filters for strongly nonlinear systems"`\.
*Nonlinear Processes in Geophysics*, 19\(3\):383–399, 2012\.
`"Combining inflation-free and iterative ensemble Kalman filters for strongly nonlinear systems"`\.
*Nonlinear Processes in Geophysics*, 19(3):383–399, 2012\.

### `doucet2001sequential`

Expand All @@ -94,74 +94,74 @@ Springer, 2001\.

Marc Bocquet and Pavel Sakov\.
`"An iterative ensemble Kalman smoother"`\.
*Quarterly Journal of the Royal Meteorological Society*, 140\(682\):1521–1535, 2014\.
*Quarterly Journal of the Royal Meteorological Society*, 140(682):1521–1535, 2014\.

### `sakov2008b`

Pavel Sakov and Peter R\. Oke\.
`"A deterministic formulation of the ensemble Kalman filter: an alternative to ensemble square root filters"`\.
*Tellus A*, 60\(2\):361–371, 2008\.
*Tellus A*, 60(2):361–371, 2008\.

### `zupanski2005`

Milija Zupanski\.
`"Maximum likelihood ensemble filter: theoretical aspects"`\.
*Monthly Weather Review*, 133\(6\):1710–1726, 2005\.
*Monthly Weather Review*, 133(6):1710–1726, 2005\.

### `sakov2012a`

Pavel Sakov, Dean S\. Oliver, and Laurent Bertino\.
`"An iterative EnKF for strongly nonlinear systems\."`\.
*Monthly Weather Review*, 140\(6\):1988–2004, 2012\.
*Monthly Weather Review*, 140(6):1988–2004, 2012\.

### `evensen2009a`

G\. Evensen\.
`"The ensemble Kalman filter for combined state and parameter estimation"`\.
*Control Systems, IEEE*, 29\(3\):83–104, 2009\.
*Control Systems, IEEE*, 29(3):83–104, 2009\.

### `raanes2015a`

Patrick Nima Raanes\.
`"On the ensemble Rauch\-Tung\-Striebel smoother and its equivalence to the ensemble Kalman smoother"`\.
*Quarterly Journal of the Royal Meteorological Society*, 142\(696\):1259–1264, 2016\.
`"On the ensemble Rauch-Tung-Striebel smoother and its equivalence to the ensemble Kalman smoother"`\.
*Quarterly Journal of the Royal Meteorological Society*, 142(696):1259–1264, 2016\.

### `anderson2010`

Jeffrey L\. Anderson\.
`"A non\-Gaussian ensemble filter update for data assimilation\."`\.
*Monthly Weather Review*, 138\(11\):4186–4198, 2010\.
`"A non-Gaussian ensemble filter update for data assimilation\."`\.
*Monthly Weather Review*, 138(11):4186–4198, 2010\.

### `raanes2019`

Patrick Nima Raanes, Andreas Størksen Stordal, and Geir Evensen\.
`"Revising the stochastic iterative ensemble smoother"`\.
*Nonlinear Processes in Geophysics*, 26\(3\):325–338, 2019\.
*Nonlinear Processes in Geophysics*, 26(3):325–338, 2019\.

### `van2009`

Peter Jan van Leeuwen\.
`"Particle filtering in geophysical systems"`\.
*Monthly Weather Review*, 137\(12\):4089–4114, 2009\.
*Monthly Weather Review*, 137(12):4089–4114, 2009\.

### `raanes2019a`

Patrick N\. Raanes, Marc Bocquet, and Alberto Carrassi\.
`"Adaptive covariance inflation in the ensemble Kalman filter by Gaussian scale mixtures"`\.
*Quarterly Journal of the Royal Meteorological Society*, 145\(718\):53–75, 2019\.
*Quarterly Journal of the Royal Meteorological Society*, 145(718):53–75, 2019\.
[doi:10\.1002/qj\.3386](https://doi.org/10.1002/qj.3386)\.

### `lei2011`

Jing Lei and Peter Bickel\.
`"A moment matching ensemble filter for nonlinear non\-Gaussian data assimilation"`\.
*Monthly Weather Review*, 139\(12\):3964–3973, 2011\.
`"A moment matching ensemble filter for nonlinear non-Gaussian data assimilation"`\.
*Monthly Weather Review*, 139(12):3964–3973, 2011\.

### `wikle2007`

C\. K\. Wikle and L\. M\. Berliner\.
`"A Bayesian tutorial for data assimilation"`\.
*Physica D: Nonlinear Phenomena*, 230\(1\-2\):1–16, 2007\.
*Physica D: Nonlinear Phenomena*, 230(1-2):1–16, 2007\.

### `doucet2009`

Expand All @@ -173,19 +173,19 @@ Arnaud Doucet and Adam M\. Johansen\.

Marc Bocquet\.
`"Localization and the iterative ensemble Kalman smoother"`\.
*Quarterly Journal of the Royal Meteorological Society*, 142\(695\):1075–1089, 2016\.
*Quarterly Journal of the Royal Meteorological Society*, 142(695):1075–1089, 2016\.

### `raanes2014`

Patrick N\. Raanes, Alberto Carrassi, and Laurent Bertino\.
`"Extending the square root method to account for model noise in the ensemble Kalman filter"`\.
*Monthly Weather Review*, 143\(10\):3857–3873, 2015\.
*Monthly Weather Review*, 143(10):3857–3873, 2015\.

### `lorenz1998`

Edward N\. Lorenz and Kerry A\. Emanuel\.
`"Optimal sites for supplementary weather observations: simulation with a small model"`\.
*Journal of the Atmospheric Sciences*, 55\(3\):399–414, 1998\.
*Journal of the Atmospheric Sciences*, 55(3):399–414, 1998\.

### `frei2013`

Expand All @@ -203,24 +203,24 @@ Marco Frei and Hans R Künsch\.

Takemasa Miyoshi\.
`"The Gaussian approach to adaptive covariance inflation and its implementation with the local ensemble transform Kalman filter"`\.
*Monthly Weather Review*, 139\(5\):1519–1535, 2011\.
*Monthly Weather Review*, 139(5):1519–1535, 2011\.

### `mandel2016hybrid`

J\. Mandel, E\. Bergou, S\. Gürol, S\. Gratton, and I\. Kasanický\.
`"Hybrid Levenberg\-Marquardt and weak\-constraint ensemble Kalman smoother method"`\.
*Nonlinear Processes in Geophysics*, 23\(2\):59–73, 2016\.
`"Hybrid Levenberg-Marquardt and weak-constraint ensemble Kalman smoother method"`\.
*Nonlinear Processes in Geophysics*, 23(2):59–73, 2016\.

### `anderson2009a`

Jeffrey L\. Anderson\.
`"Spatially and temporally varying adaptive covariance inflation for ensemble filters"`\.
*Tellus A*, 61\(1\):72–83, 2009\.
*Tellus A*, 61(1):72–83, 2009\.

### `bengtsson2003`

Thomas Bengtsson, Chris Snyder, and Doug Nychka\.
`"Toward a nonlinear ensemble filter for high\-dimensional systems"`\.
`"Toward a nonlinear ensemble filter for high-dimensional systems"`\.
*Journal of Geophysical Research: Atmospheres*, 2003\.

### `lorenz1996predictability`
Expand All @@ -233,83 +233,83 @@ In *Proc\. ECMWF Seminar on Predictability*, volume 1, 1–18\. Reading, UK, 199

Daniel S\. Wilks\.
`"Effects of stochastic parametrizations in the Lorenz'96 system"`\.
*Quarterly Journal of the Royal Meteorological Society*, 131\(606\):389–407, 2005\.
*Quarterly Journal of the Royal Meteorological Society*, 131(606):389–407, 2005\.

### `harty2021`

Travis Harty, Matthias Morzfeld, and Chris Snyder\.
`"Eigenvector\-spatial localisation"`\.
*Tellus A: Dynamic Meteorology and Oceanography*, 73\(1\):1–18, 2021\.
`"Eigenvector-spatial localisation"`\.
*Tellus A: Dynamic Meteorology and Oceanography*, 73(1):1–18, 2021\.

### `rainwater2013`

Sabrina Rainwater and Brian Hunt\.
`"Mixed\-resolution ensemble data assimilation"`\.
*Monthly weather review*, 141\(9\):3007–3021, 2013\.
`"Mixed-resolution ensemble data assimilation"`\.
*Monthly weather review*, 141(9):3007–3021, 2013\.

### `counillon2009a`

François Counillon, Pavel Sakov, and Laurent Bertino\.
`"Application of a hybrid \`enkf\-oi\` to ocean forecasting"`\.
*Ocean Science*, 5\(4\):389–401, 2009\.
`"Application of a hybrid \`enkf-oi\` to ocean forecasting"`\.
*Ocean Science*, 5(4):389–401, 2009\.

### `pajonk2012a`

Oliver Pajonk, Bojana V\. Rosić, Alexander Litvinenko, and Hermann G\. Matthies\.
`"A deterministic filter for non\-Gaussian Bayesian estimation—applications to dynamical system estimation with noisy measurements"`\.
*Physica D: Nonlinear Phenomena*, 241\(7\):775–788, 2012\.
`"A deterministic filter for non-Gaussian Bayesian estimation—applications to dynamical system estimation with noisy measurements"`\.
*Physica D: Nonlinear Phenomena*, 241(7):775–788, 2012\.

### `lorenz2005`

Edward N\. Lorenz\.
`"A look at some details of the growth of initial uncertainties"`\.
*Tellus A: Dynamic Meteorology and Oceanography*, 57\(1\):1–11, 2005\.
*Tellus A: Dynamic Meteorology and Oceanography*, 57(1):1–11, 2005\.

### `bocquet2019a`

Marc Bocquet and Alban Farchi\.
`"On the consistency of the local ensemble square root kalman filter perturbation update"`\.
*Tellus A: Dynamic Meteorology and Oceanography*, 71\(1\):1613142, 2019\.
*Tellus A: Dynamic Meteorology and Oceanography*, 71(1):1613142, 2019\.

### `lorenz1984`

Edward N\. Lorenz\.
`"Irregularity: a fundamental property of the atmosphere"`\.
*Tellus A*, 36\(2\):98–110, 1984\.
*Tellus A*, 36(2):98–110, 1984\.

### `vano2006`

J\. A\. Vano, J\. C\. Wildenberg, M\. B\. Anderson, J\. K\. Noel, and J\. C\. Sprott\.
`"Chaos in low\-dimensional Lotka–Volterra models of competition"`\.
*Nonlinearity*, 19\(10\):2391, 2006\.
`"Chaos in low-dimensional Lotka–Volterra models of competition"`\.
*Nonlinearity*, 19(10):2391, 2006\.

### `emerick2012`

Alexandre A\. Emerick and Albert C\. Reynolds\.
`"History matching time\-lapse seismic data using the ensemble Kalman filter with multiple data assimilations"`\.
*Computational Geosciences*, 16\(3\):639–659, 2012\.
`"History matching time-lapse seismic data using the ensemble Kalman filter with multiple data assimilations"`\.
*Computational Geosciences*, 16(3):639–659, 2012\.

### `pinheiro2019a`

Flavia R\. Pinheiro, Peter J\. van Leeuwen, and Gernot Geppert\.
`"Efficient nonlinear data assimilation using synchronization in a particle filter"`\.
*Quarterly Journal of the Royal Meteorological Society*, 145\(723\):2510–2523, 2019\.
*Quarterly Journal of the Royal Meteorological Society*, 145(723):2510–2523, 2019\.

### `vissio2020`

Gabriele Vissio and Valerio Lucarini\.
`"Mechanics and thermodynamics of a new minimal model of the atmosphere"`\.
*The European Physical Journal Plus*, 135\(10\):1–21, 2020\.
*The European Physical Journal Plus*, 135(10):1–21, 2020\.

### `grudzien2020a`

Colin Grudzien, Marc Bocquet, and Alberto Carrassi\.
`"On the numerical integration of the lorenz\-96 model, with scalar additive noise, for benchmark twin experiments"`\.
*Geoscientific Model Development*, 13\(4\):1903–1924, 2020\.
`"On the numerical integration of the lorenz-96 model, with scalar additive noise, for benchmark twin experiments"`\.
*Geoscientific Model Development*, 13(4):1903–1924, 2020\.

### `lorenz2005a`

Edward\. N\. Lorenz\.
`"Designing chaotic models"`\.
*Journal of the Atmospheric Sciences*, 62\(5\):1574–1587, 2005\.
*Journal of the Atmospheric Sciences*, 62(5):1574–1587, 2005\.

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