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I am achieving a hover state per continent through:

var continentId =""
function getID(continentId){
    jQuery.each(mapObject.mapData.paths, function(i, val) {
            if (val.continent == continentId){
                continentCodes[i] = "#3e9d01";
                mapObject.series.regions[0].setValues(continentCodes);
            }
    });
}

function removeGetID(continentId){
    jQuery.each(mapObject.mapData.paths, function(i, val) {
            if (val.continent == continentId){
                continentCodes[i] = "#128da7";
                mapObject.series.regions[0].setValues(continentCodes);
            }
    });
}

//LIST COUNTRIES & CONTINENTS TEMP
jQuery('.continentLink').hover(function(e) {
    continentId = this.id;
    getID(continentId);
}, function(){
    removeGetID(continentId);
});

Is there any way to shorten this so that I don't have to have multiple each statements? I'm really trying to learn to write efficient code.

Here's the full code if it helps: JSFIDDLE

jQuery(function(){
//JSON MARKERS
var markers = [{latLng: [-34.033333300000000000, 23.066666700000040000], name: 'Knysna', info:'its got a lake...'},
    {latLng: [-33.924868500000000000, 18.424055299999963000], name: 'Cape Town', info:'its nice...'}];
//JSON MARKERS  

//JSON STYLING
var markerStyle = {initial: {fill: '#F8E23B',stroke: '#383f47'}};
var regionStyling = {initial: {fill: '#128da7'},hover: {fill: "#A0D1DC"}};
//JSON STYLING

//GLOBAL VARIABLES
var countryList = "", continentList = "";
var resultsDup = {};
var continentCodes = {};
//GLOBAL VARIABLES

//INIT MAP PLUGIN
jQuery('#world-map').vectorMap({
    map: 'world_mill_en',
    normalizeFunction: 'polynomial',
    markerStyle:markerStyle,
    regionStyle:regionStyling,
    backgroundColor: '#383f47',
    series: {regions: [{values: {},attribute: 'fill'}]},
    markers: markers,
    onRegionClick:function (event, code){
        jQuery('#world-map').vectorMap('set', 'focus', code);
    },
    onMarkerClick: function(events, index){
        jQuery('#infobox').html(markers[index].name);
    }
});
//INIT MAP PLUGIN

var mapObject  = jQuery('#world-map').vectorMap('get', 'mapObject');

//LIST COUNTRIES & CONTINENTS
jQuery.each(mapObject.mapData.paths, function(i, val) {

    countryList += '<li><a id='+i+' class="countryLink">'+val.name+'</a></li>';

    //remove duplicate continents
    var resultsList = val.continent;
    if (resultsDup[resultsList]) {
        jQuery(this).remove();
    }else{
        resultsDup[resultsList] = true;
        continentList += '<li><a id='+val.continent+' class="continentLink">'+val.continent+'</a></li>';
    }
    //remove duplicate continents


});
//display countries
jQuery('#countryList').html(countryList);

//display continents
jQuery('#continentList').html(continentList);

var continentId =""
function getID(continentId){
    jQuery.each(mapObject.mapData.paths, function(i, val) {
            if (val.continent == continentId){
                continentCodes[i] = "#3e9d01";
                mapObject.series.regions[0].setValues(continentCodes);
            }
    });
}

function removeGetID(continentId){
    jQuery.each(mapObject.mapData.paths, function(i, val) {
            if (val.continent == continentId){
                continentCodes[i] = "#128da7";
                mapObject.series.regions[0].setValues(continentCodes);
            }
    });
}

//LIST COUNTRIES & CONTINENTS TEMP
jQuery('.continentLink').hover(function(e) {
    continentId = this.id;
    getID(continentId);
}, function(){
    removeGetID(continentId);
});

//Zoom to Country Function
jQuery('.countryLink').click(function(e) {
    jQuery('#world-map').vectorMap('set', 'focus', this.id);
});

//Continent Hover function

});
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You are looking to remove the copy pasted code, to make it more DRY.

Beyond that, it seems that really whether you getID or removeGetID, you set a number of ID's and then update mapObject. Furthermore, it seems that you do not need to update mapObject within the loop, which is slow.

I would counter-propose

var helpfullyNamedConstant1 = '#3e9d01';
var helpfullyNamedConstant2 = '#128da7';

function setContinentCodes(continentId, continentCodesValue ){
    jQuery.each(mapObject.mapData.paths, function(i, val) {
            if (val.continent == continentId){
                continentCodes[i] = continentCodesValue ;
            }
    });
    mapObject.series.regions[0].setValues(continentCodes);
}

jQuery('.continentLink').hover(function(e) {
    setContinentCodes(this.id, helpfullyNamedConstant1);
}, function(){
    setContinentCodes(this.id, helpfullyNamedConstant2);
});
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