Scripts_Novi_Bracco_MLCoralReefs.zip
Creators: name: Novi, Lyuba
Publisher: name: figshare
Year: 2022
Subjects: Uncategorized

description: -------------------------- Supplement to: --------------------------- "Machine Learning prediction of connectivity, biodiversity and resilience in the Coral Triangle". Lyuba Novi and Annalisa Bracco. --------------------------------------------------------------------------------- <br> -This folder contains the scripts used to plot the figures in the manuscripts. (except Fig.2 because it's only a schematic) <br> -Data from third parties are needed (see cited work and data in the manuscript). Third-parties data (freely downloadable) you need to run these scripts are: <br> 1. Coral Reefs Location Database: <br> ============================================== you need to have a Py.mat to put in /Fig1/Coral_reefs_Loacation_Database/ <br> Py.mat is a readable matlab workspace you must create using data from the Coral Reefs Location database: <br> % "UNEP-WCMC, WorldFish Centre, WRI, TNC (2021). Global distribution of warm-water coral reefs, compiled from multiple sources including the Millennium Coral Reef Mapping Project. Version 4.1. Includes contributions from IMaRS-USF and IRD (2005), IMaRS-USF (2005) and Spalding et al. (2001). Cambridge (UK): UN Environment World Conservation Monitoring Centre. Data DOI: https://doi.org/10.34892/t2wk-5t34." <br> % and must have the following structure: % Name: data, Size: 1x1, Class: struct <br> % struct with fields: X, Y, Time:[ ], Name: 'polygon', Units: '' % X is longitude Y is latitude. % ============================================== <br> 2. “Coral Spawning Database”: Spawning Sample locations data (from CSD “SpawningObservationBySite” entry): -------------------------------------------------------------------------------- % The coral spawning data are from the “Coral Spawning Database” (Baird, Andrew et al.,2020) available at https://doi.org/10.25405/data.ncl.13082333.v1 % You must have a file named 'All_spawning_observations_from_CSD.xlsx' located in /Fig1/ and it must contain data from the sheet named “SpawningObservationBySite” of the CSD (https://doi.org/10.25405/data.ncl.13082333.v1), and must be formatted as follows: %First Column: latitude, Second column: longitude, Third col: day, Fourth col: month, Fifth col: year % where day,month,year are included from the "Date" column of the CSD sheet mentioned above. % For Example: % -14.279444 -170.700833 27 10 1988 % -14.279444 -170.700833 9 11 1995 % .. etc <br> <br> 3. NetCDF reanalysis SST and SSH data from GLOBAL_REANALYSIS_001_030,from the Global Ocean Physics Reanalysis GLORYS12V1 1/12° product. MERCATOR GLORYS12V1 (global-reanalysis-001-030-monthly), E.U. Copernicus Marine Service Information (CMEMS), processed as written in manuscript. <br> - See within scripts for further comments on input structures requirements. <br> <br> 4. Composites of monthly maximum bleaching alert area (baa) from the NOAA Coral Reef Watch's (CRW) Version 3.1 heat stress monitoring products 42 at daily frequency and 0.05°degree447 resolution, processed as written in manuscript. <br> - See within scripts for further comments on input structures requirements. <br> <br> ------------------------------------------------ - Data and materials availability: ------------------------------------------------ δ-MAPS software (java version) can be found at https://github.com/FabriFalasca/delta-MAPS . The analyzed data (SST and SSH) are the GLOBAL_REANALYSIS_001_030, from the Global Ocean Physics Reanalysis GLORYS12V1 1/12° product. MERCATOR GLORYS12V1 (global-reanalysis-001-030-monthly), E.U. Copernicus Marine Service Information (CMEMS). The coral spawning data are from the “Coral Spawning Database” available at https://doi.org/10.25405/data.ncl.13082333.v1 . Composites of monthly maximum bleaching alert area are from the NOAA Coral Reef Watch's (CRW) Version 3.1 heat stress monitoring products at daily frequency and 0.05 o degree resolution, available at https://coralreefwatch.noaa.gov/product/5km/ . <br> <br> ----------------------------------------------------------- FINAL NOTES on other dependencies: ----------------------------------------------------------- * You will need to have the following two in the folder /utils/ setfigsize.m setproperty.m <br> * How the dMAPS input data (obtained from GLOBAL_REANALYSIS_001_030 GLORYS12V1 as written in manuscript) are called in these scripts: <br> - Neutral_years_SST_one-fourth_res_8yrs_BOXsm_detrended_whole.nc - Nina_years_SST_one-fourth_res_8yrs_BOXsm_detrended_whole.nc - Nino_years_SST_one-fourth_res_8yrs_BOXsm_detrended_whole.nc <br> * How the file containing the grid information is called in these scripts: Nino_years_SST_one-fourth_res_8yrs_BOXsm_deseas_detr.nc <br> (the grid information can also be retrieved by the netcdf used as input in dMAPS, and again relying on the freely-available reanalysis cited above and used in this work.) <br> * All the additional data stated above are not included in this folder (they are publicy available, under other DOIs) <br> ------------------------------------------------------- References for the third parties data: ------------------------------------------------------- - "UNEP-WCMC, WorldFish Centre, WRI, TNC (2021). Global distribution of warm-water coral reefs, compiled from multiple sources including the Millennium Coral Reef Mapping Project. Version 4.1. Includes contributions from IMaRS-USF and IRD (2005), IMaRS-USF (2005) and Spalding et al. (2001). Cambridge (UK): UN Environment World Conservation Monitoring Centre. Data DOI: https://doi.org/10.34892/t2wk-5t34." <br> - "Baird, Andrew et al. Coral Spawning Database. 10552719 Bytes (2020) doi:10.25405/DATA.NCL.13082333.V1." <br> - "GLOBAL_REANALYSIS_001_030. Global Ocean Physics Reanalysis GLORYS12V1 1/12° product. MERCATOR GLORYS12V1 (global-reanalysis-001-030-monthly). E.U. Copernicus Marine Service Information (CMEMS)." <br> - "NOAA Coral Reef Watch program, 20180813, NOAA Coral Reef Watch Version 3.1 Daily Global 5km Satellite Coral Bleaching Heat Stress Monitoring Product Suite: NOAA Coral Reef Watch program, College Park, Maryland, USA. https://coralreefwatch.noaa.gov/product/5km/. " <br> <br>