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Ningaloo Reef is a large fringing reef on the northwest coast of Australia and consists of a series of reef-channel cells, exposed to tropical cyclones and Southern Ocean swells. A field data set of wave transformation on a shore-normal transect (\autoref{fig:JGR_Fig1c}) taken at Sandy Bay in June 2009 is described in \citep{Pomeroy2012}. The transect is composed of a steep fore reef, a shallow reef flat ($~1-2 m$ depth) that is separated from the shore by a slightly deeper lagoon ($~2-3 m$ average depth). Instrument C1 was deployed on the forereef slope, C3 and C4 were located on the reef flat, while C5 and C6 were located inside the lagoon behind the reef. The wave field exhibits a dramatic decay in the incident swell band on the fore reef section with a transfer of part of the energy to infragravity waves which are dissipated due to bottom friction over the reef flat and lagoon.

The XBeach model formulations have been extended with a friction dissipation term in the wave action equation (\citet{VanDongeren2013}, which also describes the following case). For this site, optimum friction coefficient values ($f_{w} = 0.6$, $c_{f} = 0.1$) were determined for a 1D version of the model based  on conditions at the peak of the swell event. These settings were subsequently used to simulate the entire swell event from June 14 12:00 hours to June 19 00:00 hours (109 hours in total) when wave conditions varied significantly. Good agreement was generally observed throughout the simulation and at all sites (\autoref{fig:JGR_1D_ALL}; Figure 5 in \citet{VanDongeren2013}). The model reproduced the spatial variability in wave heights across the reef, as well as temporal changes in the response to the varying offshore wave conditions and tidal variations. The short wave height predictions matched the data reasonably well (\autoref{fig:JGR_1D_ALL} a-e), except for a small positive bias of a few centimeters. The IG wave heights were slightly under predicted (negative bias) at C1, but were generally in very good agreement for sites on the reef (\autoref{fig:JGR_1D_ALL} f-j). The time series of the predicted mean water level residuals (the time-averaged difference between the observed water level on the reef and the observation at C1, $\overline{\Delta z_{s}} = \overline{z_{s} - z_{s,C1}}$, thus describing wave setup) followed the observed residuals reasonably well, albeit that the model over predicts the observations by about 0.1 m. (\autoref{fig:JGR_1D_ALL} l-o) Note that at C1 the observed and predicted water levels rather than the residuals are shown (\autoref{fig:JGR_1D_ALL} k). A summary of the model skill (bias and the RMS error) for the short wave heights, IG heights and mean water level is shown in \autoref{fig:JGR_Statistics} (Figure 6 in \citet{VanDongeren2013}).
 
${tools.image(os.path.join(input_path, 'Ningaloo_reef/'), 'JGR_Fig1c.png', 'Cross-shore profile of the bathymetry along the main measurement transect with instrument locations shown.', 'JGR_Fig1c')}
 
${tools.image('Ningaloo_reef/', 'JGR_1D_ALL.eps', 'Comparison between the 1D model results (blue) and measured data (red) for the duration of the $~5$ day swell event. (a,f,k) are for instrument C1, (b,g.l) C3, (c,h,m) C4, (d,i,n) C5 and (e,j,o) C6. The peak of the storm is indicated by the red vertical line. Note the large reduction in vertical scale between C1 and the reef sites C3-C6.', 'JGR_1D_ALL')}
 
${tools.image('Ningaloo_reef/', 'JGR_Statistics.eps', 'Bias and RMS error from the 1D swell duration ($~5$ day) model results compared with the measured data at each site, based on the short wave heights, IG wave heights, and mean water levels.', 'JGR_Statistics')}
