This README.txt file was generated on 23 JAN 2025 by Sam Kelly ------------------- GENERAL INFORMATION ------------------- These Matlab scripts and data files replicate the figures in Green et al. (2025). See the paper captions for detailed figure descriptions. Input data files can be generated using the Matlab scripts in the "analysis_scripts" folder. ------------------------------------ SCRIPT DESCRIPTION OF plot_fig1.m ------------------------------------ This script plots figure 1. Function dependencies: (1) LAT2KM.m (2) LON2KM.m (3) FIXXLIM.m Input files: (1) bathy.mat Output files: (1) fig1.png ------------------------------------ SCRIPT DESCRIPTION OF plot_fig2.m ------------------------------------ This script plots figure 2. Function dependencies: None Input files: (1) data/NICE_2017_metadata.mat (2) data/modes/WM.mat (3) data/processed/WM.mat Output files: (1) fig2.pdf ------------------------------------ SCRIPT DESCRIPTION OF plot_fig3.m ------------------------------------ This script plots figure 3. Function dependencies: None Input files: (1) data/NICE_2017_metadata.mat (2) data/WM_tau.mat Output files: (1) fig3.png ------------------------------------ SCRIPT DESCRIPTION OF plot_fig4.m ------------------------------------ This script plots figure 4. Function dependencies: (1) myrotary_spectra.m Input files: (1) data/NICE_2017_metadata.mat (2) data/WM_tau.mat Output files: (1) fig4.png ------------------------------------ SCRIPT DESCRIPTION OF plot_fig5.m ------------------------------------ This script plots figure 5. Function dependencies: (1) cmocean.m Input files: (1) data/NICE_2017_metadata.mat (2) data/processed/*.mat (3) data/processed/post_QC_T/*.mat Output files: (1) fig5.png ------------------------------------ SCRIPT DESCRIPTION OF plot_fig6.m ------------------------------------ This script plots figure 6. Function dependencies: (1) my1D_spectra.m Input files: (1) data/NICE_2017_metadata.mat (2) data/processed/*.mat (3) data/modes/*.mat Output files: (1) fig6.png ------------------------------------ SCRIPT DESCRIPTION OF plot_fig7.m ------------------------------------ This script plots figure 7. Function dependencies: None Input files: (1) data/NICE_2017_metadata.mat (2) data/processed/*.mat (3) data/modes/*.mat Output files: (1) fig7.png ------------------------------------ SCRIPT DESCRIPTION OF plot_fig8.m ------------------------------------ This script plots figure 8. Function dependencies: (1) cmocean.m Input files: (1) data/NICE_2017_metadata.mat (2) data/processed/WM.mat (3) data/processed/post_QC_T/WM.mat Output files: (1) fig8.png ------------------------------------ SCRIPT DESCRIPTION OF plot_fig9.m ------------------------------------ This script plots figure 9. Function dependencies: None Input files: (1) data/NICE_2017_metadata.mat (2) data/modes/highpassed/*.mat (3) data/modes/{all} Output files: (1) fig9.png ------------------------------------ SCRIPT DESCRIPTION OF plot_fig10.m ------------------------------------ This script plots figure 10. Function dependencies: None Input files: (1) data/NICE_2017_metadata.mat (2) data/modes/highpassed/*.mat (3) data/modes/*.mat (4) data/processed/*.mat Output files: (1) fig10.png ------------------------------------ SCRIPT DESCRIPTION OF plot_fig11.m ------------------------------------ This script plots figure 11. Function dependencies: none Input files: (1) data/NICE_2017_metadata.mat (2) data/modes/highpassed/*.mat Output files: (1) fig11.pdf ------------------------------------ SCRIPT DESCRIPTION OF plot_fig12_13_14.m ------------------------------------ This script plots figures 12, 13 and 14. Function dependencies: None Input files: (1) data/NICE_2017_metadata.mat (2) data/modes/highpassed/*.mat (3) data/modes/*.mat Output files: (1) fig12.png (2) fig13.png (3) fig14.png ------------------------------------ SCRIPT DESCRIPTION OF plot_fig15_16_17.m ------------------------------------ This script plots figures 15, 16, and 17. Function dependencies: None Input files: (1) data/NICE_2017_metadata.mat (2) data/modes/highpassed/*.mat (3) data/modes/*.mat (4) data/WM_tau.mat Output files: (1) fig15.png (2) fig16.png (3) fig17.png ------------------------------------ SCRIPT DESCRIPTION OF plot_fig19.m ------------------------------------ This script plots figure 19. Function dependencies: None Input files: (1) data/NICE_2017_metadata.mat (2) data/processed/post_QC_U/WM.mat (3) data/processed/post_QC_T/WM.mat Output files: (1) fig19.pdf ------------------------------------ FUNCTION DESCRIPTION OF cmocean.m ------------------------------------ Colormap developed by Kristen Thyng Thyng, K.M., C.A. Greene, R.D. Hetland, H.M. Zimmerle, and S.F. DiMarco. 2016. True colors of oceanography: Guidelines for effective and accurate colormap selection. Oceanography 29(3):9?13, http://dx.doi.org/10.5670/oceanog.2016.66 https://www.mathworks.com/matlabcentral/fileexchange/57773-cmocean-perceptually-uniform-colormaps ------------------------------------ FUNCTION DESCRIPTION OF LAT2KM.m ------------------------------------ Input: None Output: The number of kilometers per degree of latitude. ------------------------------------ FUNCTION DESCRIPTION OF LON2KM.m ------------------------------------ Input: Latitude [deg] Output: The number of kilometers per degree of longitude. ------------------------------------ FUNCTION DESCRIPTION OF FIXXLIM.m ------------------------------------ Input: gca (Matlab handle, see Matlab documentation) right x-limit scale (i.e., the desired x/y aspect ratio of the figure) Output: The x-limits that have the desired aspect ratio (given the y-limits and the right x limit). ------------------------------------ FUNCTION DESCRIPTION OF my1D_spectra.m ------------------------------------ Calculate the one-sided spectra components of a horizontal velocity vector timeseries in cycles per second Input: (1) time (2) complex velocity time series (Z = u+iv) (3) Number of bands to average (M*2 = degrees of freedom) Output: (1) frequency (2) power spectra density (3) error ------------------------------------ FUNCTION DESCRIPTION OF myrotary_spectra.m ------------------------------------ Calculate the rotary spectra components of a horizontal velocity vector timeseries in cycles per second Input: (1) time (2) complex velocity time series (Z = u+iv) (3) Number of bands to average (M*2 = degrees of freedom) Output: (1) frequency (2) power spectra density for negative frequencies (3) power spectra density for positive frequencies (4) error ------------------------------------ DATA FILE DESCRIPTION OF bathy.mat ------------------------------------ Great Lakes Bathymetry (https://www.ncei.noaa.gov/products/great-lakes-bathymetry) in Matlab format Structure: bathy fields: x (1 x 9841) [m] distance east y (1 x 4201) [m] distance north lon (1 x 9841) [deg] longitude lat (1 x 4201) [deg] latitude H (9841 x 4201) [m] bottom depth ------------------------------------ DATA FILE DESCRIPTION OF NICE_2017_metadata.mat ------------------------------------ Metadata for mooring array Fields: z (201 x 1) [m] depth time (1 x 39586) [days] time mooring_list.name (1 x 10) list of mooring names Structure: T_chain.* fields: depth (1 x 1) [m] depth lon (1 x 1) [deg] longitude lat (1 x 1) [deg] latitude sensor (m x 3) [serial number, depth, flag] temperature sensor data (m=number of sensors on mooring) Note: several unused fields in data.mat that are not documented here. ------------------------------------ DATA FILE DESCRIPTION OF WM_tau.mat ------------------------------------ Wind observations from NOAA buoy 45006 near WM Fields: Uwind (1 x 139586) [m/s] complex wind speed (real = east, imaginary = north) tau (1 x 139586) [Pa] complex wind stress (real = east, imaginary = north) tau_high (1 x 139586) [Pa] complex wind stress high-passed (real = east, imaginary = north) ------------------------------------ DATA FILE DESCRIPTION OF /data/modes/*.mat ------------------------------------ Data files for each vertical modes 0-4 at each mooring fields: H (1 x 1) [m] water depth tstart (1 x 1) [day] start time for analysis tend (1 x 1) [day] end time for analysis N2_profile (201 x 1) [1/s^2] buoyancy frequency squared used to compute modes Cn (5 x 1) [m/s] eigenspeed HPHI (201 x 5) [] vertical mode shape for horizontal velocity VPHI (201 x 5) [] vertical mode shape for vertical velocity pn (139586 x 5) [Pa] modal pressure Un (139586 x 5) [m/s] modal velocity (complex: real=u*p, imaginary=v*p) Fn (139586 x 5) [W/m] energy flux (complex: real=u*p, imaginary=v*p) KEn (139586 x 5) [J/m^2] Kinetic energy PEn (139586 x 5) [J/m^2] Available potential energy Note: modes/lowpassed/*.mat and modes/highpassed/*.mat are identical, but have been filtered for low and high frequencies. Note: several unused fields in data.mat that are not documented here. ------------------------------------ DATA FILE DESCRIPTION OF /data/processed/*.mat ------------------------------------ Data files for uniformly gridded data at each mooring fields: U (201 x 139586) [m/s] velocity (complex: real=u*p, imaginary=v*p) pot_dens (201 x 139586) [kg/m^3] potential density (referenced to surface) zeta (201 x 139586) [m] isopycnal displacement ------------------------------------ DATA FILE DESCRIPTION OF /data/processed/post_QC_U/*.mat ------------------------------------ Data files for non-gridded velocity at each mooring fields: Uraw (m x n) [m/s] velocity (m=depth bins, n=time bins) depthrraw (m x 1) [m] depth mtimeraw (1 x n) [days] time ------------------------------------ DATA FILE DESCRIPTION OF /data/processed/post_QC_T/*.mat ------------------------------------ Data files for gridded temperature at each mooring fields: dens_situ (201 x 139586) [kg/m^3] in situ density T_theta (201 x 139586) [K] potential temperature (referenced to the surface) pot_situ (201 x 139586) [kg/m^3] potential density (referenced to the surface)