docs: update joss paper to include plots

joss-paper/2dps.png:Zone.Identifier

@@ -0,0 +1,4 @@
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+ZoneId=3
+ReferrerUrl=https://21cmsense.readthedocs.io/en/latest/tutorials/understanding_21cmsense.html
+HostUrl=https://21cmsense.readthedocs.io/en/latest/_images/tutorials_understanding_21cmsense_75_0.png

joss-paper/paper.bib

@@ -299,3 +299,41 @@ @ARTICLE{Schosser2024
  adsurl = {https://ui.adsabs.harvard.edu/abs/2024arXiv240104174S},
  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
 }
+
+@ARTICLE{Liu2020,
+ author = {{Liu}, Adrian and {Shaw}, J. Richard},
+ title = "{Data Analysis for Precision 21 cm Cosmology}",
+ journal = {\pasp},
+ keywords = {dark ages, reionization, first stars, methods: statistical, techniques: interferometric, Astrophysics - Instrumentation and Methods for Astrophysics, Astrophysics - Cosmology and Nongalactic Astrophysics},
+ year = 2020,
+ month = jun,
+ volume = {132},
+ number = {1012},
+ eid = {062001},
+ pages = {062001},
+ doi = {10.1088/1538-3873/ab5bfd},
+archivePrefix = {arXiv},
+ eprint = {1907.08211},
+ primaryClass = {astro-ph.IM},
+ adsurl = {https://ui.adsabs.harvard.edu/abs/2020PASP..132f2001L},
+ adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+@ARTICLE{jwst,
+ author = {{Castellano}, Marco and {Fontana}, Adriano and {Treu}, Tommaso and {Santini}, Paola and {Merlin}, Emiliano and {Leethochawalit}, Nicha and {Trenti}, Michele and {Vanzella}, Eros and {Mestric}, Uros and {Bonchi}, Andrea and {Belfiori}, Davide and {Nonino}, Mario and {Paris}, Diego and {Polenta}, Gianluca and {Roberts-Borsani}, Guido and {Boyett}, Kristan and {Brada{\v{c}}}, Maru{\v{s}}a and {Calabr{\`o}}, Antonello and {Glazebrook}, Karl and {Grillo}, Claudio and {Mascia}, Sara and {Mason}, Charlotte and {Mercurio}, Amata and {Morishita}, Takahiro and {Nanayakkara}, Themiya and {Pentericci}, Laura and {Rosati}, Piero and {Vulcani}, Benedetta and {Wang}, Xin and {Yang}, Lilan},
+ title = "{Early Results from GLASS-JWST. III. Galaxy Candidates at z 9-15}",
+ journal = {\apjl},
+ keywords = {Reionization, 1383, Astrophysics - Astrophysics of Galaxies},
+ year = 2022,
+ month = oct,
+ volume = {938},
+ number = {2},
+ eid = {L15},
+ pages = {L15},
+ doi = {10.3847/2041-8213/ac94d0},
+archivePrefix = {arXiv},
+ eprint = {2207.09436},
+ primaryClass = {astro-ph.GA},
+ adsurl = {https://ui.adsabs.harvard.edu/abs/2022ApJ...938L..15C},
+ adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}

joss-paper/paper.md

@@ -31,9 +31,16 @@ bibliography: paper.bib
 # Summary
 
 The 21cm line of neutral hydrogen is a powerful probe of the high-redshift
-universe, and is the subject of a number of current and upcoming
+universe (Cosmic Dawn and the Epoch of Reionization), with an unprecedented potential to
+inform us about key processes of early galaxy formation, the first stars and even
+cosmology and structure formation [@Liu2020], via intensity mapping.
+It is the subject of a number of current and upcoming
 low-frequency radio experiments, including the MWA [@mwa], LOFAR [@lofar], HERA [@hera]
-and the SKA [@Pritchard2015].
+and the SKA [@Pritchard2015], which complement the detailed information concerning the
+brightest sources in these early epochs from powerful optical and near-infrared telescopes
+such as the JWST [@jwst].
+
+
 21cmSense is a Python package that provides a modular framework for calculating the
 sensitivity of these experiments, in order to enhance the process of their design.
 This paper presents version v2.0.0 of 21cmSense, which has been re-written from the ground up
@@ -48,14 +55,14 @@ key assumptions to accelerate the calculation:
 
 1. Each baseline (pair of antennas) in the interferometer intrinsically measures a dense
  blob of 2D spatial Fourier modes of the sky intensity distribution, centred at a
- particular Fourier coordinate *(u,v)* given by the displacement vector between the
- antennas forming the baseline, and covering an area in this *(u,v)*-space that is given
+ particular Fourier coordinate $(u,v)$ given by the displacement vector between the
+ antennas forming the baseline, and covering an area in this $(u,v)$-space that is given
  by the Fourier-transform of the primary beam of the instrument.
  The Fourier-space representation of the sky is thus
- built up by collecting many baselines that cover the so-called "*(u,v)*-plane".
+ built up by collecting many baselines that cover the so-called "$(u,v)$-plane".
  ``21cmSense`` approximates this process of synthesising many baselines by
- nearest-grid-point interpolation onto a regular grid in the *(u,v)*-plane.
- Furthermore, importantly the *(u,v)*-grid is chosen to have cells that are comparable
+ nearest-grid-point interpolation onto a regular grid in the $(u,v)$-plane.
+ Furthermore, importantly the $(u,v)$-grid is chosen to have cells that are comparable
  to the instrument's Fourier-space beam size, so that a particular baseline essentially
  measures a single cell in the grid, and no more.
  This maximizes resolution while keeping the covariance between cells small.
@@ -86,7 +93,17 @@ Some of the key new features introduced in this version of 21cmSense include:
 7. Built-in profiles for several major experiments: MWA, HERA and SKA-1. These can be
  used as-is, or as a starting point for defining a custom instrument.
 
+An example of the predicted sensitivity of the HERA experiment after a year's observation
+at $z=8.5$ is shown in Figure \ref{sense}, corresponding to the sampling of the $(u,v)$-grid
+shown in Figure \ref{uvsampling}. The sensivity here is a signal-to-noise,
+assuming a signal magnitude computed using a semi-numerical model from the 21cmFAST
+code [@21cmfast], using parameters from [@Munoz22].
+This figure also demonstrates that the new
+21cmSense is capable of producing sensitivity predictions in the cylindrically-averaged
+2D power spectrum space, which is helpful for upcoming experiments.
 
+![Sampling of the $(u,v)$-plane for the HERA experiment during a full year of observations.]{label="uvsampling"}(uv-sampling.png)
+![Predicted sensitivity of 1000 hours (one year) of HERA observations, as a function of perpendicular and line-of-sight fourier scale. The sensitivity is represented as the signal-to-noise on each $k$-mode, assuming a particular astrophysical model.]{label="sense"}(2dps.png)
 
 # Statement of need
 

joss-paper/uv-sampling.png:Zone.Identifier

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