Matlab M-Files

Most of the plots and statistical analysis done for this report were created using Matlab software, created by Mathworks (http://www.mathworks.com). Plots were converted to tagged PDF format using Adobe (http://www.adobe.com) Acrobat. The Matlab m-files provide partial documentation of the techniques used to create the analyses and plots in this report. This code was designed to run on Matlab 6.0 with NetCDF installed. Users are encouraged to visit the Web site http://woodshole.
http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/ for more information about the NetCDF format.

Although these programs have been used by the USGS, no warranty, expressed or implied, is made by the USGS or the United States Government as to the accuracy and functioning of the programs and related program material nor shall the fact of distribution constitute any such warranty, and no responsibility is assumed by the USGS in connection therewith.

adcp_contour: Creates the contour plots of current from the profiling current meters at sites B and C (see "Time Series Plots").

adjust_image: Create the time series photograph movie (see "Time Series Photographs).

attn_temp_curr: Creates the time series plots of beam attenuation, temperature, and current from sites B and C (see "Time Series Plots").

contour_agc: Creates the contour plots of echo intensity from sites B and C (see "Time Series Plots").

contour_temp: Creates the contour plots of temperature from sites A, B, and C (see "Time Series Plots").

create_thumbnail_page: Creates the thumbnails Web page (see "Time Series Photographs).

ctd_plots: Creates plots of temperature, salinity, beam attenuation, and sigma t from the CTD data (see "Hydrographic Data").

ctd_plots_profile: Creates profile plots of temperature, salinity, beam attenuation, and sigma t from the CTD data (see "Hydrographic Data").

ctd_bvfq: Creates plots of Brunt-Vaisala frequency from the CTD data (see "Hydrographic Data").

ctd_bvfq_profile: Creates profile plots of Brunt-Vaisala frequency from the CTD data (see "Hydrographic Data").

curr_statistics: Creates the tables of statistics of current (see "Statistics").

density_grad: Creates plots of the density (sigma-t) and density difference between depths (see "Time Series Plots").

get_pressure_diffs: Creates plots of the difference in pressure between ebb and flood tide (see "Time Series Plots").

hm_temp_movies: Creates movies of the internal waves passing by the horizontal mooring at site B (see "HM Temperatures).

mbay_iwave_ctd: Loads the CTD data into Matlab and corrects the latitude and longitude of stations with incorrect values (see "Hydrographic Data").

mbiwe_pres: Creates the time series plots of pressure from sites B and C (see "Time Series Plots").

mbiwe_pres_lp: Creates the time series plots of low-passed pressure from sites MBLT-A, B, and C (see "Time Series Plots").

mbiwe_weather: Creates the time series plots of wind and wave data from NOAA Buoy 44013 (see "Time Series Plots").

pres_table: Creates a table of the times of low water prior to internal wave events (see "Hydrographic Data").

principal_axes: Calculates the principal axes of current (see "Scatter Plots").

recombine_adcp: Merges the corrected ADCP data from times with internal waves with the data from periods of time with no internal waves (see "ADCP Errors").

sal_statistics: Creates the tables of statistics of salinity (see "Statistics").

scatter_plots: Creates the scatter plots of current (see "Scatter Plots").

temp_statistics: Creates the tables of statistics of temperature (see "Statistics").

whisk_adcp: Creates the whisker plots of current from the profiling current meters at sites B and C (see "Time Series Plots").

whisk_pcm: Creates the whisker plots of current from the point current meters at sites B and C (see "Time Series Plots").

whisk_surface: Creates the whisker plots of current from 20 m at sites LT-A, D/LT-B, B, and C (see "Time Series Plots").

whisk_surface: Creates the whisker plots of near-bottom current from at sites LT-A, D/LT-B, B, and C (see "Time Series Plots").