function mapdrawYawsEndemic
%This file draws a map of the World, coloring countries based on their
%current status of Yaws endemicity. 


%--------
%Last Modified: 12.21.2021
%Written on Matlab R2021a Update 2 (9.10.0.1669831) 
%with Mapping Toolbox
   
%This file requires the borders.m package from 
%(https://www.mathworks.com/matlabcentral/fileexchange/50390-borders)

%Data Sources:
    %GHOendemicity.csv from https://www.who.int/data/gho/data/indicators/indicator-details/GHO/status-of-yaws-endemicity
        %CSV file contain a a table of the current status of Yaws endemicity by country
        %Options for current status include:
            %No previous history of yaws
            %Previously endemic (current status unknown)
            %Currently endemic
            %Interrupted transmission
        %Data reported from 2018
    %ssd_admbnda_adm0_imwg_nbs_20180817.shp from https://data.humdata.org/dataset/south-sudan-administrative-boundaries
        %Shapefile of South Sudan
    %sdn_admbnda_adm0_cbs_nic_ssa_20200831.shp from https://data.humdata.org/dataset/sudan-administrative-boundaries-levels-0-2
        %Shapefile of Sudan
        
    %Shapefiles of South Sudan and Sudan are used because the borders
    %package does not recognize them as two separate countries, however the
    %data from the WHO lists the two countries seperately, therefore the
    %must be plotted seperately. 
    
    %The borders package lists some countries names differently than
    %reported by the WHO, some examples are:
        %Myanmar (WHO) = Burma (borders)
        %Eswatini (WHO) = Swaziland (borders)
        %Republic of Korea (WHO) = Korea, Republic of (borders)
        %United States of America (WHO) = United States (borders)
    %Cleaning of the CSV file to reflect the names recognized by the
    %borders package was done prior to reading the data into MATLAB. 
    
    
    tic %timing function to test efficiency
    
    % Set the file for textual output and write the date and time we run the code
    % After multiple run, the last output is at the bottom of this text file
    diary 'mapdrawYaws_code_output.txt'
    disp_Diary('--------------- New run  ----------------')
    disp_Diary(datetime)
    
    %% Step 1: File Uploads and Data Cleaning

    %Import the options of the csv file
    opts=detectImportOptions('GHOendemicity.csv');
    %Defines what row variable names are found in
    opts.VariableNamesLine = 2;
    %Defines line that the data begins on
    opts.DataLine = 3;
    %Reads the table
    YawsEndemicCountryData = readtable('GHOendemicity.csv',opts, 'ReadVariableNames', true);
       
    %Loads the list of places that are recognized by the borders
    %package
    bd = load('borderdata.mat');

    %Gives a list of all of the countries that reported data
    CountryNames = YawsEndemicCountryData(:,1);

    %% Step 2: Use borders.m package to draw the map

    % Start a new figure
    figure

    %prints all of the country borders, with grey fill
    bordersm('countries','black','facecolor', [0.5,0.5,0.5])
    framem('off'); %Remove Frame
    mlabel off; % Get the numbers off (latitute)
    plabel off; % Get the numbers off (longitute)

    %goes through each country in the data and colors based on yaws status
    for countryIndex = 1:size(CountryNames,1)
        disp_Diary(CountryNames{countryIndex,1});
        disp_Diary(YawsEndemicCountryData{countryIndex,2});

        %This line ensures that only countries that are
        %recognized by the borders package are filled in 
        %Specifically excludes South Sudan and Sudan 
        if contains(YawsEndemicCountryData{countryIndex,1}, bd.places) && not(strcmp(YawsEndemicCountryData{countryIndex,1},'South Sudan')) && not(strcmp(YawsEndemicCountryData{countryIndex,1},'Sudan'))
            %Defines a color for each country based on yaws status,
            %default color is white. 
            Color = [1,1,1];
            if strcmp('No previous history of yaws',YawsEndemicCountryData{countryIndex,2})
                Color = [1,1,1]; %No history is White
            elseif strcmp('Previously endemic (current status unknown)',YawsEndemicCountryData{countryIndex,2})
                Color = [0.678, 0.847, 0.902]; %Previously is Light Blue
            elseif strcmp('Currently endemic',YawsEndemicCountryData{countryIndex,2})
                Color = [1, 0, 0]; %Currently is Red
            elseif strcmp('Interrupted transmission',YawsEndemicCountryData{countryIndex,2})
                Color = [0, 0, 1]; %Transmission interupted is Green
            else
                disp_Diary(CountryNames{countryIndex,1});
            end
        
            %fills in the given country with color described above. 
            bordersm(CountryNames{countryIndex,1}, 'facecolor', Color)
            
        elseif not(strcmp(YawsEndemicCountryData{countryIndex,1},'South Sudan')) && not(strcmp(YawsEndemicCountryData{countryIndex,1},'Sudan'))
            disp(CountryNames{countryIndex,1});
        end
    end
    
    %Defines legend based on specified example colors 
    h(5) = bordersm('Western Sahara', 'facecolor', [0.5,0.5,0.5]);
    h(1) = geoshow('sdn_admbnda_adm0_cbs_nic_ssa_20200831.shp', 'FaceColor', [1,1,1],'LineWidth',0.5);%Sudan
    h(2) = geoshow('ssd_admbnda_adm0_imwg_nbs_20180817.shp', 'FaceColor', [0.678, 0.847, 0.902],'LineWidth',0.5);%South Sudan
    h(4) = bordersm('India', 'facecolor', [0, 0, 1]);
    h(3) = bordersm('Ghana', 'facecolor', [1, 0, 0]);
    lgd = legend([h(1),h(2),h(3),h(4),h(5)],'No History','Previously Endemic, Currently Unknown','Currently Endemic', 'Interrupted Transmission', 'No data');
    lgd.NumColumns = 2
    lgd.Location = 'SouthOutside'
            
    % Save the figure
    SaveFigure('YawsMap')
    
    toc
    
    %% Additional Functions

function SaveFigure(filename)
        % Saves a current graphics file to file named filename.pdf
        
        % Get the handle
        h=gcf;
        set(h,'Units','Inches');
        pos = get(h,'Position');
        
        % Cut all the white margins
        set(h,'PaperPositionMode','Auto','PaperUnits','Inches','PaperSize',[pos(3), pos(4)])
    
        % Actually save
        print(h,['Figures/' filename, '.pdf'],'-dpdf','-r0')  
        
        % This outputs on the screen what figure was saved into what file
        disp_Diary(['Saved a figure ' num2str(get(gcf,'Number')) ' into a file ' ...
            filename '.pdf'])
end
    
function disp_Diary(string)
        % Displays text on the screen and also logs it in the diary
        diary on
        disp(string)
        diary off
end

end