{"id":16742549,"url":"https://github.com/dcherian/eq_waves","last_synced_at":"2026-02-06T03:31:43.813Z","repository":{"id":4849299,"uuid":"6003695","full_name":"dcherian/eq_waves","owner":"dcherian","description":"Vertical structure of 7-day period inertial-gravity waves in the equatorial Pacific","archived":false,"fork":false,"pushed_at":"2017-07-25T19:52:55.000Z","size":20640,"stargazers_count":0,"open_issues_count":0,"forks_count":1,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-12-02T11:39:50.846Z","etag":null,"topics":["equatorial","oceanography","waves"],"latest_commit_sha":null,"homepage":"","language":"Matlab","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":"Gamevy/node-redis-pubsub-emitter","license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/dcherian.png","metadata":{"files":{"readme":"README.org","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2012-09-28T22:08:25.000Z","updated_at":"2017-09-26T06:19:25.000Z","dependencies_parsed_at":"2022-08-25T13:31:16.098Z","dependency_job_id":null,"html_url":"https://github.com/dcherian/eq_waves","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/dcherian/eq_waves","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dcherian%2Feq_waves","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dcherian%2Feq_waves/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dcherian%2Feq_waves/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dcherian%2Feq_waves/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/dcherian","download_url":"https://codeload.github.com/dcherian/eq_waves/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dcherian%2Feq_waves/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29148134,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-06T02:39:25.012Z","status":"ssl_error","status_checked_at":"2026-02-06T02:37:22.784Z","response_time":59,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.5:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["equatorial","oceanography","waves"],"created_at":"2024-10-13T01:24:07.243Z","updated_at":"2026-02-06T03:31:43.797Z","avatar_url":"https://github.com/dcherian.png","language":"Matlab","funding_links":[],"categories":[],"sub_categories":[],"readme":"#+OPTIONS: :links nil\n* Introduction\n\nThis repository contains code for what should become Cherian, Farrar \u0026 Durland (201x) - The upper-ocean vertical structure of 7-day period inertial-gravity waves in the equatorial Pacific.\n\n* Instructions\n\nTo reproduce all of the figures you will first need to\n- 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/~.\n- 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.\n- 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.\n- Run ~master.m~\n- Run ~figs_paper.m~\n\nThen ~images/~ will contain all figures used in the paper.\n\n* Contents\nThe code expects the following layout.\n#+BEGIN_src text\n  -- eq_waves\n  ----- data/\n  ---------- dynht/dyn*.cdf\n  ---------- temp/t*.cdf\n  ---------- ETOPO2v2g_f4.nc\n  ---------- woa13_decav_t00_01v2.nc\n  ---------- woa13_decav_s00_01v2.nc\n  ---------- woa_landsea_01.msk\n  ----- images/\n  ----- scripts/*.m\n  ----- README.org (this file)\n#+END_src\n\n*** Overall Scripts\n\n|--------------------+----------------------------------------------------------|\n| Script             | Description                                              |\n|--------------------+----------------------------------------------------------|\n| ~master.m~           | Recreate everything from scratch.                        |\n| ~figs_paper.m~       | Make figures used in paper.                              |\n| ~TestInference.m~    | Runs tests with fake data.                               |\n| ~InferOneLocation.m~ | Recreates everything but for just one specified location |\n| ~DefaultOptions.m~   | Conveniently creates default options structure           |\n|                    | with values used in paper                                |\n| ~PlotMode.m~         | Plots mode structure at one location.                    |\n| ~PlotModeMap.m~      | Plots mode structure at all locations as big map.        |\n|                    | Calls ~PlotMode~ to do actual plotting.                    |\n| ~ReadTaoTriton.m~    | Reads in data. Can do so at just one location if needed. |\n| ~TheoreticalModes.m~ | Calls ~vertmode~ with WOA data, calculates mode structures |\n|                    | and saves them in ~flat-bottom-modes.mat~                  |\n|--------------------+----------------------------------------------------------|\n\n*** Analysis Scripts\n\n|--------------------------+-----------------------------------------------------------------------|\n| Script                   | Description                                                           |\n|--------------------------+-----------------------------------------------------------------------|\n| ~InferModeShape.m~         | Does most of the heavy lifting                                        |\n| ~DoRegression.m~           | Calls ~dcregress~ for regression between provided variables.            |\n|                          | Also estimates error bounds.                                          |\n| ~EstimateNoiseSpectrum.m~  | Fits a power law to spectrum of provide input.                        |\n|                          | Returns amplitude α and spectral slope β such that spectrum, S = αe^{β} |\n| ~CalcSignificanceBounds.m~ | Calculates minimum regression slope that would indicate that          |\n|                          | a regression is not returning a null result.  Calls ~TestMC~ to         |\n|                          | do iterations between data and red noise time series.                 |\n| ~SaveNullBoundsForTao.m~   | Runs ~CalcSignificanceBounds~ at every available instrument depth       |\n|                          | and saves results to ~bounds.mat~ so they can be used by ~InferModeShape |\n| ~figs.m~                   | Code for various figures made during analysis.                        |\n|                          |                                                                       |\n|--------------------------+-----------------------------------------------------------------------|\n\n*** Utility Scripts\n|---------------------------------------+----------------------------------------------------------------|\n| Script                                | Description                                                    |\n|---------------------------------------+----------------------------------------------------------------|\n| ~TestMC.m~                              | Runs monte carlo iterations between provided input and         |\n|                                       | noise timeseries with provided properties.                     |\n|                                       | Called by ~CalcSignificanceBounds~ to do the hard work.       |\n| ~dcregress.m~                           | Does the actual regression                                     |\n| ~BandPass.m~                            | BandPass filters                                               |\n| ~FilterSeries.m~                        | Does the actual filtering                                      |\n| ~synthetic_timeseries_known_spectrum.m~ | Creates fake time series with specified spectral properties.   |\n|                                       | (code from Tom Farrar)                                          |\n| ~GappySpectrum.m~                       | Calculates spectrum of a gappy timeseries.                     |\n| ~findCommmonTimeRange.m~                | Finds common time range for dyn ht and temperature time Series |\n| ~getTitleString.m~                      | Creates a formatted title string for plots.                    |\n|---------------------------------------+----------------------------------------------------------------|\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdcherian%2Feq_waves","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fdcherian%2Feq_waves","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdcherian%2Feq_waves/lists"}