Matlab code for the oceanographic analysis related to environmental conditions during coral spawning for Ningaloo Reef.
Contributions from: Jessica Benthuysen Camille Grimaldi 15 June 2026
Code for: Rosser, N., J.A. Benthuysen, C. Castro-Sanguino, C. M. Grimaldi. Contrasting environmental regimes shape coral reproductive phenology across neighbouring reef environments.
MATLAB (.m) files used in Rosser et al. manuscript describing the oceanographic environment.
Contact: Jessica Benthuysen (J.Benthuysen@aims.gov.au)
\aims\common\Oceanography\00XXXX-2024-2026-Ningaloo_coral_spawning
- plot_Ningaloo_survey_map.m Plot the locations of survey locations, in situ and remotely sensed temperature data, and wave buoys. Inputs: Rosser_Bundegi_paper_coordinates-2024-08-21.mat GA250_Ningaloo.mat %Geosciences Australia 250 m resolution bathymetry AIMS_WA_Ningaloo-2025-10-23.mat %AIMS_WA; in situ temperature locations Ningaloo_AIMS_temperature_IMOS_L3S_L3SM_timeseries-1993-01-01-2024-07-31_2024-09-15.mat %Site, pixels used from IMOS L3S and L3SM-1d night corresponding to temperature sites Ningaloo_Rosser_coordinates_IMOS_L3SM_timeseries-2012-01-01-2024-08-31_2024-10-06.mat %Site, pixels used from IMOS L3SM-1d night corresponding to survey sites
Outputs: Australia_map_insert-2024-08-22 Ningaloo_map-2025-03-06 Ningaloo_map-survey_sites_AIMS_IMOS_temperature_WHACS-2026-01-09 Figures are combined in powerpoint and exported as: Figure1_Ningaloo_survey_site_map-WHA-2025-03-06 FigureS1_Ningaloo_survey_site_map-2026-01-09
- plot_quick_view_IMOS_SST.m Plot the IMOS SST imagery; called by calc_AIMS_temperature_Ningaloo.m No outputs exported.
- calc_AIMS_temperature_Ningaloo.m Combines AIMS in situ temperature measurements based on the data records; Calculates the daily day, night, daily-mean in situ temperatures and also the night-time in situ temperature closest to the time of the night-time IMOS SST imagery.
Inputs: data_files/AIMS_temperature/ BUNDEGI_BR.mat; BUNDFL1.mat; CORALFL1.mat; TANDFL1.mat; TANTABIDDI_3.mat
Outputs: AIMS_WA_Ningaloo-2025-10-23.mat
- calc_IMOS_L3S_L3SM_SST_Ningaloo_site_timeseries.m Stores IMOS SST site information corresponding to coral survey locations and in situ temperature locations and extracts the IMOS L3S-1d-night and L3SM-1d night time series and SSTAARS climatology.
Inputs: Rosser_Bundegi_paper_coordinates-2024-08-21.mat IMOS L3S-1d night, L3SM-1d night SSTAARS.nc; SSTAARS_daily_fit.nc AIMS_WA_Ningaloo-2025-10-23.mat
Outputs: Ningaloo_Rosser_coordinates_IMOS_L3S_L3SM_timeseries-2010-01-01_2025-06-30_2025-10-23.mat Ningaloo_AIMS_temperature_IMOS_L3S_L3SM_timeseries-2010-01-01_2025-06-30_2025-10-24.mat
Outputs (figures) unused in paper: Ningaloo_IMOS_L3S_L3SM-1d-night-2010-01-01_2025-06-30-2025-10-23 SSTAARS_landmask_vs_L3SM_SST_values AIMS_temp_L3SM_SST_locations Ningaloo_AIMS_IMOS_L3S_L3SM-1d-night-2010-01-01_2025-06-30-2025-10-24
- calc_AIMS_temperature_IMOS_L3S_L3SM_Ningaloo.m Calculates the daily night time, day time, and daily average in situ temperatures and also the night-time temperatures selected for comparison against the IMOS L3SM-1d night product. Output uses: 2000-0400 (night time, AWST) and 0800-1600 (day time, AWST), and daily is based on 12-hour UTC; These periods are selected for comparison with satellite remote sensing. The output includes night time estimates based on the time of the nightly IMOS L3SM-1d night.
Inputs: AIMS_WA_Ningaloo-2025-10-23.mat Ningaloo_AIMS_temperature_IMOS_L3S_L3SM_timeseries-2010-01-01_2025-06-30_2025-10-24.mat
Outputs: AIMS_WA_Ningaloo-day-night-2025-10-25.mat
Outputs (figures) unused in paper:
Ningaloo_AIMS_day_night_temperature-comparison-2025-10-24
AIMS_Ningaloo_temperature_all-2025-10-25
Bundegi_Tantabiddi_comparison_IMOS_SST_cal_val_night-2025-10-25
Bundegi_Tantabiddi_comparison2_IMOS_SST_cal_val_night-2025-10-25
- plot_compare_AIMS_temperature_IMOS_L3S_L3SM_Ningaloo.m Compares AIMS in situ temperature measurements with the IMOS SST imagery.
Inputs: AIMS_WA_Ningaloo-day-night-2025-10-25.mat Ningaloo_AIMS_temperature_IMOS_L3S_L3SM_timeseries-2010-01-01_2025-06-30_2025-10-24.mat Ningaloo_Rosser_coordinates_IMOS_L3SM_timeseries-2010-01-01-2025-06-30_2025-10-23.mat
Outputs: Figure 4: Figure4_Ningaloo_SST_clim_survey_sites_Bundegi_Tantabiddi-2025-10-29 Figure S2: FigureS2_Ningaloo_AIMS_IMOS_night_temperature_bias-2025-10-25
- plot_IMOS_L3S_L3SM_SST_Ningaloo_trends.m Calculates the monthly SST anomalies from the IMOS night-time L3S-1d (2011, 2012)and L3SM-1d (2012-2024) and plots the timeseries for each month.
Inputs: RRAP_MDS-01/m_files/calc_sst_clim_reconstruct.m [time_range, SST no leap year] Ningaloo_Rosser_coordinates_IMOS_L3S_L3SM_timeseries-2010-01-01_2025-06-30_2025-10-23.mat
Outputs: Ningaloo_Rosser_coordinates_IMOS_L3S_L3SM_timeseries-trends-2010-01-01_2025-06-30_2025-10-29.mat Figure S4: FigureS4_Ningaloo_IMOS_L3S_L3SM-1d-ngt-SSTA_trends_November_to_April-2025-11-30
Outputs (figures) unused in paper: IMOS_L3SM1d_SSTAARS_Bundegi-2022-10-01-2023-05-01
- calc_Ningaloo_site_PCA.m Conducts the principal component analysis for climatological oceanographic and meteorological variables at Bundegi and Ninglaoo Reef coral survey sites.
Inputs: WHACS-Wind_Wave_param-2025-12-14.xlsx WHACS-map_coords-2025-12-12.xlsx Australia_GEBCO_2025_elevation.mat Ningaloo_Rosser_coordinates_IMOS_L3S_L3SM_timeseries-2010-01-01_2025-06-30_2025-10-23.mat (Site, struct array)
Outputs: Wind_Wave_param_WHACS_elevation_0m-2026-01-09.mat (W, structure array) Figure 3: Figure5_Survey_sites_PCA_WHACS_SST-comparison-2026-01-10
- calc_WHACS_seasonal_wind_wave_spatial_climatology.m Calculates the climatology for wind and wave variables from the Wave Hindcast for the Australian Climate Service (WHACS) dataset.
Inputs: WHACS subset for the Ningaloo region
Outputs: Figure 5: WHACS_SpatialClim_final.jpg
Note that Figure S3 compares the WHACS wind and wave data with in situ wind and wave measurements.