Most of the plots and statistical analysis included
with this report were created using Matlab software created by Mathworks (www.mathworks.com).
Plots were further aesthetically modified and converted to tagged
PDF version using Adobe (www.adobe.com)
Illustrator and Acrobat.
DISCLAIMER: Matlab mfiles provided here were not
created as turn key programs. They were designed to run on Matlab
6.0 with NetCDF installed. Users are encouraged to
look at (crusty.er.usgs.gov/~cdenham/)
for more information on the NetCDF format. Mfiles
are provided here merely to give the user a better understanding
of techniques used, and are not supported by their creator or by
USGS. Additional subroutines may be found at:
1) crusty.er.usgs.gov/~cdenham/snackbar/snackbar.html
2) seamat.whoi.edu/
Plotting Tools Used for
this Report:
ADCP_Plotmaker:
Plots the lowpassed wind stress for a chosen station along with
an image plot of the available lowpassed ADCP data
in directional component form.
ADCP_Rot_Plotmaker:
Plots the lowpassed wind stress for a chosen valley station along
with an image plot of the available lowpassed ADCP
data in directional component form, rotated along the valley axis.
ADCP_Rot_Valley:
Creates image plots of the along valley axis component of available
lowpassed ADCP data for the valley stations.
ADCP_ScatterPlot_NY:
For a given station, creates a four paneled plot containing scatter
plots of eastward and northward current component and principal
axes ellipse for hourlyaveraged and lowpassed ADCP
current data from 5 meters below the surface and from the deepest
depth bin available.
ADCP_Whisk_All_Plotmaker:
Given a specific depth, or 'B' for the bottommost bin, this program
creates whisker plots of the lowpassed ADCP data from
each station closest to the given depth.
ADCP_Whisk_Plotmaker:
Given a specific station, this program creates whisker plots of
the lowpassed wind stress and ADCP data from that
station at particular depths (5, 15, and bottom for the shelf station;
5, 15, 30, 45, and bottom for the valley stations).
ADCP_Whisk_Rot_Val_Plotmaker:
Given a specific depth, or 'B' for the bottommost bin, this program
creates whisker plots of the lowpassed ADCP data rotated
to along and across valley axis from each of the valley stations
(A, B, C, & F) at approximately the selected depth.
ADCP_Whisk_Shelf_Plotmaker:
Given a specific depth, or 'B' for the bottommost bin, this program
creates whisker plots of the lowpassed ADCP data from
each of the shelf stations (D & E) closest to the selected depth
ADCP_Whisk_Valley_Plotmaker:
Given a specific depth, or 'B' for the bottommost bin, this program
creates whisker plots of the lowpassed ADCP data from
each of the valley stations (A, B, C, & F) closest to the selected
depth
All_Sal_Temp_Plotmaker:
Program which creates four separate plots, one each of deep and
shallow salinity and deep and shallow temperature from each of the
stations.
animateNY:
Program that creates the individual frames (saved as PPM
files) which can be combined to create the animation of the New
York data in this data report.
contourEnCTD:
Program that creates contour plots of the temperature, salinity,
fluorescence, and beam attenuation data from the Endeavor cruise
casts as a function of depth and distance along the canyon.
contourOcCTD:
Program that creates contour plots of the temperature, salinity,
fluorescence, and beam attenuation data from the Oceanus cruise
casts as a function of depth and distance along the canyon.
Curr_Scat_Plot:
For a given station, creates a multipaneled plot containing scatter
plots of eastward and northward current component and principal
axes ellipse for hourlyaveraged and lowpassed BASS/MAVS
current data from the available depths.
Curr_Sp_Dir_Plotmaker:
Program which sorts current data for a given station and a given
depth into current speed and direction bins and plots those bins.
locsCTD:
Program which creates a map of the New York coast line and bathymetry
in the area of the New York Bight along with the cast locations
from the Endeavor and Oceanus cruises.
Mean_Flow_Ell_BASS:
Program to plot the low passed wind stress and mean flow (by month)
for shelf (plot one) and valley (plot two) stations from the BASS
data.
Mean_Flow_Ellipse_Plot:
Program to plot the low passed wind stress and mean flow (by month)
for each station at specific depths from ADCP data.
NYCurr_Whisk:
Program to plot ADCP current data as whiskers off of
the xaxis. Had to be specifically tailored to site/data type because
of axes range and labeling restrictions.
OBS_ATTN_Plotmaker:
Given a specific station (other than F, at which there was no OBS
or ATTN instrumentation), this program plots optical
backscatter and beam attenuation from available depths.
P_CS_OBS_Plotmaker:
Given a specific station, this program plots the st. deviation of
pressure, and the current speed and optical backscatter from the
available depths.
plotEnCTD:
Program which takes the CTD data from the Endeavor
cruise and creates plots of certain data variables for each cast.
plotMeteorNY:
Program which creates time series plots of several environmental
variables from the Ambrose Light station.
plotMeteorStatsNY:
Program which plots meteorological statistics from various buoys.
plotOcCTD:
Program which takes the CTD data from the Oceanus cruise
and creates plots of certain data variables for each cast.
plotOpt2Sed:
Program which plots beam attenuation and optical backscatter vs.
sediment concentration for Oceanus and Endeavor CTD
data.
PlotStatsNY:
Program which plots the statistics of current and temperature calculated
with Stats_Curr_Temp.m
PressurePlot.m:
Given a specific station, this program plots the lowpassed wind
stress, the hourly averaged pressure, and the lowpassed pressure.
Sal_Plotmaker:
Given a specific station, this program plots the salinity data from
the surface, two intermediate depths (if available), and the bottom.
Temp_Plotmaker:
Given a specific station, this program plots the temperature data
from the surface, two intermediate depths (if available), and the
bottom.
whiskWindNY:
Program to plot wind stress data as whiskers off of the xaxis.
Had to be specifically tailored to site/data type because of axes
range and labeling restrictions.
Statistics Calculation Tools:
Ellipse_Calc:
Program which calculates the ellipse parameters for a given station
at a given depth and outputs onscreen in matlab.
meteorStatsNY:
Program to calculate various meteorological statistics for a given
buoy.
nanmax: Program
to calculate the maximum of a set of values ignoring the matlab
fill value of "NaN".
nanmean: Program
to calculate the mean of a set of values ignoring the matlab fill
value of "NaN".
nanmin: Program
to calculate the minimum of a set of values ignoring the matlab
fill value of "NaN".
nanstd: Program
to calculate the standard deviation of a set of values ignoring
the matlab fill value of "NaN".
nansum: Program
to calculate the sum of a set of values ignoring the matlab fill
value of "NaN".
nanvar: Program
to calculate the variance of a set of values ignoring the matlab
fill value of "NaN".
Stats_Curr_Temp:
Program which calculates the mean, maximum, minimum, and standard
deviation values of current and temperature, by month and for the
entire data set, at a given station and depth. Calls PlotStatsNY
to plot these results.
Stats_Current:
Program which calculates a variety of statistics for currents from
several ADCP depths and all available VMCM/BASS
data and outputs it to the screen. For the data report, this information
was recorded in a table.
Stats_Ellipse:
Program which calculates the ellipse parameters for all available
VMCM/BASS data from a given station and
from several ADCP depths and outputs it to the screen.
For the data report, this information was recorded in a table.
Other Tools Used:
angleXtoCompass:
Program to convert polar coordinate angles (measured counterclockwise
from xaxis) to compass angles (measured clockwise from north)
binsort: Program
which sorts a given variable into bins defined by two vectors.
gregaxd_fooled:
Program modified from gregaxd which can handle labeling the time
axis when it has been scaled by some factor.
gregaxdNM:
Modification of gregaxd which does not include month labels.
NY_Tides:
Computes a tidal analysis on the pressure data available from a
given New York station.
NY_Tides_Curr:
Computes a tidal analysis on the current data available from a particular
depth at a given New York station.
pcaben: Program
which calculates ellipse parameters for currents.
ridfill: Program
which replaces fill values with zeroes.
ridfill_nan:
Program which replaces fill values with "NaN's" (Not A
Number  matlab's fill value)
singleJD:
This program converts julian dates from a two vector format to a
single vector format.
transformNY:
Given an angle of rotation for the valley, this program rotates
current data to along and across valley axis.
UVtoSpDir: This
program converts u and v (eastward and northward) velocity components
into speed and direction (direction is standard polar coordinate,
measured counterclockwise from xaxis)
value2Index:
Given a list of values and a target value, this program finds the
index of the value in the list closest to the target value.
varify: Program
which excludes empty data points from a data set.
