// A function to handle "secondary" checkboxes
function secondaryCheckboxes(qID, primaryPosition, secondaryCount) {
  // Identify the elements
  var thisQuestion = $('#question'+qID);
  $('div.question-item', thisQuestion).parent().addClass('answer-row');
  var primaryRow = $('div.question-item:eq('+(primaryPosition-1)+')', thisQuestion).closest('.answer-row');
  var primaryInput = $('input.checkbox', primaryRow);
  var secondaryRows = primaryRow.nextAll('div.answer-row:lt('+(secondaryCount)+')');
  var secondaryInputs = $('input.checkbox', secondaryRows);
 
  // Indent the secondaries
  secondaryRows.css({ 'margin-left':'2.5em' });
 
  // Initial states of the secondary answers
  if (primaryInput.prop('checked') == false ) {
    secondaryRows.hide(); 
  } 
 
  // A listener on the primary answer to show or hide secondary answers 
  primaryInput.click(function (event) { 
 
    // Hide/show the secondary answers accordingly
    if (!$(this).is(':checked')) {
      secondaryRows.hide();        
      secondaryInputs.prop('checked', false);
      secondaryInputs.each(function(i) {
        checkconditions(this.value, this.name, this.type);
      });
    }
    else {
      secondaryRows.show(); 
    }
  });
}

// A function to handle "secondary" checkboxes
function secondaryCheckboxes(qID, primaryPosition, secondaryCount) {
  // Identify the elements
  var thisQuestion = $('#question'+qID);
  var primaryRow = $('li.question-item:eq('+(primaryPosition-1)+')', thisQuestion).closest('li.question-item');
  var primaryInput = $('input:checkbox', primaryRow);
  var secondaryRows = primaryRow.nextAll('li.question-item:lt('+(secondaryCount)+')');
  var secondaryInputs = $('input:checkbox', secondaryRows);
 
  // Indent the secondaries
  secondaryRows.css({ 'margin-left':'2.5em' });
 
  // Initial states of the secondary answers
  if (primaryInput.prop('checked') == false ) {
    secondaryRows.hide(); 
  } 
 
  // A listener on the primary answer to show or hide secondary answers 
  primaryInput.on('change', function (event) { 
 
    // Hide/show the secondary answers accordingly
    if (!$(this).is(':checked')) {
      secondaryRows.hide();        
      secondaryInputs.prop('checked', false).trigger('change');
    }
    else {
      secondaryRows.show(); 
    }
  });
}

.js .answer-container .ls-hidden {
    display: none !important;
}

// A function to handle "child" checkboxes
function dependantCheckboxes(qID, primaryCodes, secondaryCodes, tertiaryCodes) {
  // Identify the elements annd assign classes/attributes
  var thisQuestion = $('#question'+qID);
  thisQuestion.addClass('with-dependants');
  $.each(primaryCodes, function(i, val) {
    var thisItem = $('li[id$="X'+qID+val+'"]');
    $(thisItem).addClass('level-1 parent-item').attr('data-code', val).attr('data-level', '1');
  });  
  $.each(secondaryCodes, function(i, val) {
    var thisItem = $('li[id$="X'+qID+val+'"]');
    var thisParent1 = $(thisItem).prevAll('li[data-level="1"]:eq(0)');
    $(thisItem).addClass('level-2 parent-item child-item').attr('data-code', val).attr('data-level', '2').attr('data-parent-1', $(thisParent1).attr('data-code'));
  });  
  $.each(tertiaryCodes, function(i, val) {
    var thisItem = $('li[id$="X'+qID+val+'"]');
    var thisParent1 = $(thisItem).prevAll('li[data-level="1"]:eq(0)');
    var thisParent2 = $(thisItem).prevAll('li[data-level="2"]:eq(0)');
    $(thisItem).addClass('level-3 child-item').attr('data-code', val).attr('data-level', '3').attr('data-parent-1', $(thisParent1).attr('data-code')).attr('data-parent-2', $(thisParent2).attr('data-code'));
  });  
 
  // A function to handle the states of child items
  function handleChildren(el) { 
    var thisitem = $(el).closest('li');
    var thisCode = $(thisitem).attr('data-code');
    var thisLevel = $(thisitem).attr('data-level');
    var thisChildren = $('li[data-level="'+(Number(thisLevel)+1)+'"][data-parent-'+thisLevel+'="'+thisCode+'"]', thisQuestion);
 
    // Hide/show the secondary answers accordingly
    if (!$(el).is(':checked')) {
      $(thisChildren).fadeOut(300, function(e) {      
        $('input:checkbox', thisChildren).prop('checked', false).trigger('change');
      });  
    }
    else {
      $(thisChildren).fadeIn(300); 
    }
  }
 
  // Initial states of the secondary answers 
  $('.parent-item input:checkbox', thisQuestion).each(function(i) { 
    handleChildren($(this));
  });
 
  // A listener on the primary answer to show or hide secondary answers 
  $('.parent-item input:checkbox', thisQuestion).on('change', function(e) { 
    handleChildren($(this));
  });
}

.with-dependants .child-item {
  display: none;
}
 
.with-dependants li.level-2 {
  margin-left: 2.5em;
}
 
.with-dependants li.level-3 {
  margin-left: 5em;
}

<script type="text/javascript" charset="utf-8">
 
  $(document).on('ready pjax:scriptcomplete',function(){
    dependantCheckboxes(
      {QID}, 
      ['SQ1', 'SQ2'], // First-level sub-question codes 
      ['SQ11', 'SQ12', 'SQ21', 'SQ22'], // Second-level sub-question codes
      ['SQ111', 'SQ112', 'SQ121', 'SQ122', 'SQ211', 'SQ212', 'SQ213', 'SQ221', 'SQ222'] // Third-level sub-question codes
    );
    });  
</script>