Introduction

This repository contains code for what should become Cherian, Farrar & Durland (201x) - The upper-ocean vertical structure of 7-day period inertial-gravity waves in the equatorial Pacific.

Instructions

To reproduce all of the figures you will first need to

• Download the TAO/TRITON data from http://www.pmel.noaa.gov/tao/drupal/disdel/. The code expects one netcdf file per site stored in data/dynht/ and data/temp/.
• Download the World Ocean Atlas data from https://www.nodc.noaa.gov/OC5/woa13/. You’ll need woa_landsea_01.msk, woa13_decav_t00_01v2.nc and woa13_decav_s00_01v2.nc saved to the data/ folder.
• Download ETOPO 2v2g data from https://ngdc.noaa.gov/mgg/global/relief/ETOPO2/ETOPO2v2-2006/ETOPO2v2g/netCDF/. You’ll need ETOPO2v2g_f4.nc saved to the data/ folder.
• Run master.m
• Run figs_paper.m

Then images/ will contain all figures used in the paper.

Contents

The code expects the following layout.

-- eq_waves
----- data/
---------- dynht/dyn*.cdf
---------- temp/t*.cdf
---------- ETOPO2v2g_f4.nc
---------- woa13_decav_t00_01v2.nc
---------- woa13_decav_s00_01v2.nc
---------- woa_landsea_01.msk
----- images/
----- scripts/*.m
----- README.org (this file)

Overall Scripts

Script	Description
master.m	Recreate everything from scratch.
figs_paper.m	Make figures used in paper.
TestInference.m	Runs tests with fake data.
InferOneLocation.m	Recreates everything but for just one specified location
DefaultOptions.m	Conveniently creates default options structure
	with values used in paper
PlotMode.m	Plots mode structure at one location.
PlotModeMap.m	Plots mode structure at all locations as big map.
	Calls PlotMode to do actual plotting.
ReadTaoTriton.m	Reads in data. Can do so at just one location if needed.
TheoreticalModes.m	Calls vertmode with WOA data, calculates mode structures
	and saves them in flat-bottom-modes.mat

Analysis Scripts

Script	Description
InferModeShape.m	Does most of the heavy lifting
DoRegression.m	Calls dcregress for regression between provided variables.
	Also estimates error bounds.
EstimateNoiseSpectrum.m	Fits a power law to spectrum of provide input.
	Returns amplitude α and spectral slope β such that spectrum, S = αeβ
CalcSignificanceBounds.m	Calculates minimum regression slope that would indicate that
	a regression is not returning a null result. Calls TestMC to
	do iterations between data and red noise time series.
SaveNullBoundsForTao.m	Runs CalcSignificanceBounds at every available instrument depth
	and saves results to bounds.mat so they can be used by ~InferModeShape
figs.m	Code for various figures made during analysis.

Utility Scripts

Script	Description
TestMC.m	Runs monte carlo iterations between provided input and
	noise timeseries with provided properties.
	Called by CalcSignificanceBounds to do the hard work.
dcregress.m	Does the actual regression
BandPass.m	BandPass filters
FilterSeries.m	Does the actual filtering
synthetic_timeseries_known_spectrum.m	Creates fake time series with specified spectral properties.
	(code from Tom Farrar)
GappySpectrum.m	Calculates spectrum of a gappy timeseries.
findCommmonTimeRange.m	Finds common time range for dyn ht and temperature time Series
getTitleString.m	Creates a formatted title string for plots.