# Generating and Plotting Figures for Tropical Cyclone Climatology Analysis and Reconstruction

These data files and MATLAB scripts reproduce the model data and figures as published in Bramante et al. (in press) Increased typhoon activity in the Pacific deep tropics driven by Little Ice Age circulation changes, Nature Geoscience

## Motivation
We are dedicated to practicing reproducible research, and these files are intended to allow other researchers to reproduce our analyses and produce modifications should they wish.

## File Summary

1. **calculate_storm_indexes_from_CMIP5.m** - Calculate the Genesis Potential Index and its components from monthly CMIP5 output data

2. **calculate_Pac_climate_modes_from_CMIP5.m** - Calculates time series of Pacific Meridional Mode, Pacific Decadal Oscillation, and the Cold Tongue Index from CMIP5 model output

3. **calculate_Hadley_from_CMIP5_spatial_streamfunction.m** - a MATLAB script that calculates the overturning circulation streamfunction of zonally averaged winds from CMIP5 model output

4. **calculate_Walker_from_CMIP5_spatial.m** - Calculate time series of vertical and meridional winds associated with Walker circulation for CMIP5 models 

5. **gpi_change_ensemble.m** - Calculates average of storm indices over multi-centennial time period for each model

6. **gpi_change_ensemble_data.mat** - Output of gpi_change_ensemble.m. Is plotted in LTD_plots_publication.m, Section 1, Figure 3, ED Figure 6

7. **gpi_correlation_maps.m** - Calculates Spearman rank or Pearson correlation coefficients between maps of storm indices and time series of Pacific climate modes

8. **pmm_correlation_GPI.m** - Output of gpi_correlation_maps.m. Is plotted in LTD_plots_publication.m, Section 4, Figure 5, ED Figure 7

9. **MCA_LIA_walker_cell.m** - Calculate meridional and vertical wind anomalies from output of calculate_Walker_from_CMIP5_spatial.m

10. **MCA-LIA_walker_cell_0-20N.mat** - Output from MCA_LIA_walker_cell.m plotted in LTD_plots_publication Section 6, Figure 4

11. **MCA_LIA_hadley_cell.m** - Calculate zonal and vertical wind and streamfunction anomalies from output of calculate_Hadley_from_CMIP5_spatial_streamfunction.m

12. **MCA-LIA_hadley_cell_100-180.mat** - Output from MCA_LIA_hadley_cell.m, plotted in LTD_plots_publication.m Section 5, ED Figure 8

13. **LTD_plots_publication.m** - reproduces most of the figures in Bramante et al. It requires all of the data files (.mat,.csv) included with these files.

14. **storm_selection_sensitivity_publication.m** - Performs and plots a sensitivity analysis of the statistical procedure used to select storm layers in grain size plots, ED Figures 4 and 5

15. **LTD3D1_grain_size.csv** - downcore grain size and age information used in storm_selection_sensitivity_publication.m to calculate and plot storm frequency in the Jaluit Atoll record: Figures 1,2; ED Figures 1-5

16. **blue_hole_bathymetry.csv** - Jaluit NW blue hole bathymetry profile plotted in LTD_plots_publication Sections 2-3, Figure 1, ED Figure 1

17. **blue_hole_CTD_cast.csv** - Jaluit NW blue hole CTD profiles plotted in LTD_plots_publication Sections 2-3, Figure 1, ED Figure 1

18. **LTD3D1_MCMCAges_108.csv** - CSV file containing Monte Carlo realizations of LTD3 age model using Bacon. Plotted in LTD_plots_publication.m Section 7, ED Figure 3 and storm_selection_sensitivity.m ED Figures 4-5 

19. **gpi_change_ensemble_monte_carlo_300y.mat** - Bootstrap sampling of 300-year averages of Vertical Wind Shear and Potential Intensity plotted in LTD_plots_publication.m, Section 6, Figure 4

20. **eof.m** - Perform Empirical Orthogonal Function analysis on spatio-temporal data from one variable

21. **mca.m** - Perform Maximum Covariance analysis between two spatio-temporal data sets with the same temporal sampling

22. **compile_GCM_netcdf.m** - Compiles all CMIP5 GCM data for a given variable from a given folder from NetCDF files that are often split up in time, sorts them in temporal order, and samples them spatially using geographic coordinates

23. **Bramante et al - WDC Paleo data.xlsx** - A copy of all LTD3D1 core data deposited with the NOAA National Centers for Environmental Information World Data Center for Paleoclimatology database

## Dependencies not included for lack of permission to distribute:

1. Kerry Emanuel's Matlab code for calculation potential intensity (Accessible as of September 1, 2020 at ftp://texmex.mit.edu/pub/emanuel/TCMAX/)

2. IBTrACS best track dataset (West Pacific, WMO Agencies only)

## Suggested implementation
Implementing these files requires MATLAB with the Mapping Toolbox.

Files 1-4 sample data directly from NetCDF GCM output. GCM data are not included here, so these files demonstrate the calculations performed.
Files 5,7-9,11 calculate temporal averages from the data files produced by Files 1-4
Files 13-14 plot the data that are both produced by Files 5,7-9,11 and are included in this repository
Files 15-18 are data files described below
Files 20-21 Matlab function files for conducting certain spatio-temporal analysis
File 22 is a Matlab function file used for sampling GCM NetCDF output using a third party NetCDF toolbox for MATLAB
File 23 is a copy of the fully documented LTD3D1 grain size and age constraint data deposited with NOAA

## CSV file descriptions and metadata

1. blue_hole_bathymetry.csv
    * Transect of depth soundings made with an Edgetech 3100 Chirp sub-bottom sonar system with a 4–24 kHz fish 
    * Date of collection: November 9, 2015
    * Location: Jaluit Atoll northwest blue hole, Republic of the Marshall Islands (6.2561 N, 169.411 E)
    * Columns
        * Distance from rim (m) - Distance from the start of the transect at the rim of the blue hole, in meters
        * Depth (m) - Depth of the bottom (first major reflector) relative to the water surface at the time of acquisition

2. blue_hole_CTD_cast.csv
    * Conductivity, Temperature, and Depth (CTD) profile from the surface of the blue hole to its bottom, Performed with a YSI Castaway CTD
    * Date of collection: November 10, 2015
    * Location: Jaluit Atoll northwest blue hole, Republic of the Marshall Islands (6.2561 N, 169.411 E)
    * Columns
        * Pressure (dBar) - water pressure in decibars at which measurement was taken
        * Depth (m) - water depth in meters relative to water surface at time of acquisition, calculated from Pressure
        * Temperature (C) - water temperature, in Celsius
        * Conductivity (us/cm) - water conductivity in microSiemens per centimeter
        * Specific conductance (us/cm) - water specific conductance in microSiemens per centimeter
        * Salinity (PSU) - water salinity in Practical Salinity Units calculated from water conductivity and specific conductance
        * Sound velocity (m/s) - velocity of sound in the water in meters per second, calculated from pressure, temperature, and salinity
        * Density (kg/m3) - density of the seawater and its constituents in kilograms per cubic meter, calculated from pressure, temperature, and salinity

3. LTD3D1_grain_size.csv
    * Depth profile of grain size fractions in a sediment core retrieved using a Rossfelder P-3 vibracoring system to push an aluminum barrel into unconsolidated sand
    * Date of collection: November 10, 2015
    * Location: Jaluit Atoll northwest blue hole, Republic of the Marshall Islands (6.2561 N, 169.411 E)
    * Columns
        * Sample depth in core (cm) - depth from the core top, in centimeters, of the midpoint of each subsample of the core (taken at 1 cm intervals)
        * Age (cal yr BP) - median calibrated age from Bacon age model (see paper for details) of each subsample
        * Fraction > 63 um - fraction of sediment by bulk dry weight that is larger than 63 micrometers in diameter. Sediment separated by wet sieving.
        * Fraction > 250 um - fraction of sediment by bulk dry weight that is larger than 250 micrometers in diameter. Sediment separated by dry sieving.
        * Fraction > 2000 um - fraction of sediment by bulk dry weight that is larger than 2000 micrometers in diameter. Sediment separated by dry sieving. Many samples have 0 fraction because they contained no sediment of the requisite size.

4. LTD3D1_MCMCAges_108.csv
    * Collection of 7668 Monte Carlo realizations of downcore age from the Bacon age model
    * Each value is an age in cal. yr BP
    * Each row is a different Monte Carlo iteration, and each column represents a depth interval in the core
    * The depth intervals are labeled 'V#', where the # is the bottom depth of each subsample in centimeters. To convert to equivalent depth in LTD3D1_grain_size.csv, subtract 0.5

## Permissions
These files should have been released upon publication of the underlying paper. Please cite that paper in any publications resulting from use of the files in this project.