{"id":2613,"date":"2020-07-17T10:39:39","date_gmt":"2020-07-16T22:39:39","guid":{"rendered":"http:\/\/blogs.lincoln.ac.nz\/gis\/?p=2613"},"modified":"2023-05-07T03:17:41","modified_gmt":"2023-05-07T03:17:41","slug":"mapping-covid-19-vulnerability","status":"publish","type":"post","link":"https:\/\/blogs.lincoln.ac.nz\/gis\/mapping-covid-19-vulnerability\/","title":{"rendered":"Mapping Covid-19 Vulnerability"},"content":{"rendered":"<p><em>This post covers the mapping of South Island communities and their vulnerability to Covid-19 reinfection as part of an ERST202 class project.<\/em><\/p>\n<p>While semester 1 feels like a long time ago now, the threats from Covid-19 are still remarkably present.\u00a0 Recent incidents around returning Kiwis and their efforts to break out of quarantine illustrate just how vulnerable our borders are to reinfection and a dreaded &#8220;second wave&#8221;.\u00a0 The team of 5 million did an awesome job of taking NZ cases down to zero, but it&#8217;s easy to see that even one case in the wrong place at the wrong time could take us right back to level 4.\u00a0 There are certainly some spatial components to people being at threat, and there are also some spatial components behind what might make some areas more vulnerable than others, in the event that community transmission rears its ugly head.\u00a0 Things like the number of older people, or the medical resources in an area.\u00a0 At the end of last semester, the good folk of ERST202 took on mapping some of these factors for several South Island communities as part of a class project.<\/p>\n<p>This is not a new idea.\u00a0 The US Centres for Disease Control (CDC) have developed a <a href=\"https:\/\/svi.cdc.gov\/factsheet.html\" target=\"_blank\" rel=\"noopener noreferrer\">Social Vulnerability Index<\/a> (SVI) with an <a href=\"https:\/\/svi.cdc.gov\/map.aspx\" target=\"_blank\" rel=\"noopener noreferrer\">interactive map <\/a>that visualises how vulnerable different areas are to a range of events (you may need to run this in FireFox or Edge [<em>never thought I&#8217;d recommend someone using Edge..<\/em>.]).<\/p>\n<p><a href=\"https:\/\/d-blogs.lincoln.ac.nz\/gis\/wp-content\/uploads\/sites\/3\/2020\/07\/SVIMap.jpg\"><img loading=\"lazy\" decoding=\"async\" class=\"alignnone size-full wp-image-2623\" src=\"https:\/\/d-blogs.lincoln.ac.nz\/gis\/wp-content\/uploads\/sites\/3\/2020\/07\/SVIMap.jpg\" alt=\"\" width=\"1006\" height=\"713\" srcset=\"https:\/\/blogs.lincoln.ac.nz\/gis\/wp-content\/uploads\/sites\/3\/2020\/07\/SVIMap.jpg 1006w, https:\/\/blogs.lincoln.ac.nz\/gis\/wp-content\/uploads\/sites\/3\/2020\/07\/SVIMap-300x213.jpg 300w, https:\/\/blogs.lincoln.ac.nz\/gis\/wp-content\/uploads\/sites\/3\/2020\/07\/SVIMap-768x544.jpg 768w\" sizes=\"auto, (max-width: 1006px) 100vw, 1006px\" \/><\/a><\/p>\n<p>The colour codings allow you to tell quickly how at risk a particular area (US counties in this image) is compared to others, given the legend.<\/p>\n<p>Underneath the bonnet of this map is a fairly complex set of demographic factors (15 in all across four themes) that contribute to this:<\/p>\n<figure id=\"attachment_2624\" aria-describedby=\"caption-attachment-2624\" style=\"width: 431px\" class=\"wp-caption alignnone\"><a href=\"https:\/\/svi.cdc.gov\/Documents\/Publications\/SVI_Community_Materials\/atriskguidance.pdf\" target=\"_blank\" rel=\"https:\/\/svi.cdc.gov\/Documents\/Publications\/SVI_Community_Materials\/atriskguidance.pdf noopener noreferrer\"><img loading=\"lazy\" decoding=\"async\" class=\"wp-image-2624 size-full\" src=\"https:\/\/d-blogs.lincoln.ac.nz\/gis\/wp-content\/uploads\/sites\/3\/2020\/07\/SVIFactors.jpg\" alt=\"\" width=\"431\" height=\"360\" srcset=\"https:\/\/blogs.lincoln.ac.nz\/gis\/wp-content\/uploads\/sites\/3\/2020\/07\/SVIFactors.jpg 431w, https:\/\/blogs.lincoln.ac.nz\/gis\/wp-content\/uploads\/sites\/3\/2020\/07\/SVIFactors-300x251.jpg 300w\" sizes=\"auto, (max-width: 431px) 100vw, 431px\" \/><\/a><figcaption id=\"caption-attachment-2624\" class=\"wp-caption-text\"><em>https:\/\/svi.cdc.gov\/Documents\/Publications\/SVI_Community_Materials\/atriskguidance.pdf<\/em><\/figcaption><\/figure>\n<p>There are some challenges to doing something like this, not least of which is how do you set up these factors so that they are comparable in a logical and defensible way.\u00a0 (We hit on some similar issues <a href=\"http:\/\/blogs.lincoln.ac.nz\/gis\/where-the-wild-sub-clover-grows\/\" target=\"_blank\" rel=\"noopener noreferrer\">here<\/a>.)\u00a0 The CDC&#8217;s approach was to rank each area unit based on the number of people (or things) fitting each criterion.\u00a0 These were then divided by the largest number of people (or things) across the whole area so that each factor is rescaled to\u00a0a value between 0 and 1.\u00a0 Combining them all and rescaling them\u00a0 again reflects the influence of each factor and makes each area comparable.\u00a0 This also means that different numbers can occur depending on whether the analysis is nation-wide, or state-wide, or county-wide.<\/p>\n<p>For our class project, we adopted a similar approach though simplified things down to just four factors:<\/p>\n<ul>\n<li>Population Density \u2013 higher population density increases the likelihood of community transmission<\/li>\n<li>% of population over 65 years of age \u2013 older people are at higher risk of death from Covid-19 and associated complications<\/li>\n<li>Socio-economic status \u2013 people of lower socio-economic status have fewer resources to allow them to remain isolated from exposure<\/li>\n<li>Access to hospitals and clinics \u2013 as distance away from hospitals and clinics increases, health care opportunities decrease.<\/li>\n<\/ul>\n<p>We did our analysis at the <a href=\"http:\/\/archive.stats.govt.nz\/methods\/classifications-and-standards\/geographic-hierarchy.aspx#gsc.tab=0\" target=\"_blank\" rel=\"noopener noreferrer\">meshblock level<\/a> within different census area units.\u00a0 Two of these factors come from or can be derived from <a href=\"http:\/\/blogs.lincoln.ac.nz\/gis\/mapping-the-census\/\">census data<\/a> (population density and % of population over 65).\u00a0 For the socio-economic status, we used the <a href=\"https:\/\/www.otago.ac.nz\/wellington\/departments\/publichealth\/research\/hirp\/otago020194.html\" target=\"_blank\" rel=\"noopener noreferrer\">NZ Deprivation Index<\/a>, available as a<a href=\"https:\/\/koordinates.com\/from\/data.nationalmap.co.nz\/layer\/87297\/\" target=\"_blank\" rel=\"noopener noreferrer\"> spatial data layer<\/a>.\u00a0 The locations of hospitals came from a Ministry of Health spreadsheet with street addresses that were then\u00a0<a href=\"http:\/\/blogs.lincoln.ac.nz\/gis\/the-spatial-smoking-gun-part-1\/\" target=\"_blank\" rel=\"noopener noreferrer\">geocoded<\/a> to give us points on the map.\u00a0 Distances were calculated from the centre of each meshblock to the nearest public hospital.<\/p>\n<p>For this analysis, each student worked with a census area unit.\u00a0 Within that area unit they worked at the meshblock scale and added in data related to each of the four factors.\u00a0 I provided them with the maximum value across the whole study area which they could use to rescale the factors across their particular area unit.\u00a0 In the end, we could stitch together all the area units into one larger study area &#8211; the rescaling meant that\u00a0each meshblock\u00a0was easily comparable against all the others.<\/p>\n<p>To keep things consistent, in terms of symbology, everyone used a <a href=\"http:\/\/blogs.lincoln.ac.nz\/gis\/save-your-marriage-use-layer-files\/\" target=\"_blank\" rel=\"noopener noreferrer\">layer file<\/a> on their final vulnerability score.\u00a0 And here&#8217;s our final result:<\/p>\n<p><a href=\"https:\/\/d-blogs.lincoln.ac.nz\/gis\/wp-content\/uploads\/sites\/3\/2020\/07\/WEbApp.jpg\"><img loading=\"lazy\" decoding=\"async\" class=\"alignnone size-full wp-image-2625\" src=\"https:\/\/d-blogs.lincoln.ac.nz\/gis\/wp-content\/uploads\/sites\/3\/2020\/07\/WEbApp.jpg\" alt=\"\" width=\"1433\" height=\"787\" srcset=\"https:\/\/blogs.lincoln.ac.nz\/gis\/wp-content\/uploads\/sites\/3\/2020\/07\/WEbApp.jpg 1433w, https:\/\/blogs.lincoln.ac.nz\/gis\/wp-content\/uploads\/sites\/3\/2020\/07\/WEbApp-300x165.jpg 300w, https:\/\/blogs.lincoln.ac.nz\/gis\/wp-content\/uploads\/sites\/3\/2020\/07\/WEbApp-1024x562.jpg 1024w, https:\/\/blogs.lincoln.ac.nz\/gis\/wp-content\/uploads\/sites\/3\/2020\/07\/WEbApp-768x422.jpg 768w\" sizes=\"auto, (max-width: 1433px) 100vw, 1433px\" \/><\/a><\/p>\n<p>Values closer to 1 are more vulnerable than those closer to 0.\u00a0 Here&#8217;s the\u00a0<a href=\"https:\/\/lincolngis.maps.arcgis.com\/apps\/webappviewer\/index.html?id=a8e60085e4b24904918ae5a1459c23e4\" target=\"_blank\" rel=\"noopener noreferrer\">web app<\/a> if you&#8217;ve like to take a closer look.<\/p>\n<p>So now we can get a sense of, given our factors, how vulnerability varies across the study area.\u00a0 For instance, we can look more closely at each meshblock and see how its vulnerability scores rack up:<\/p>\n<p><a href=\"https:\/\/d-blogs.lincoln.ac.nz\/gis\/wp-content\/uploads\/sites\/3\/2020\/07\/HighVul.jpg\"><img loading=\"lazy\" decoding=\"async\" class=\"alignnone size-full wp-image-2626\" src=\"https:\/\/d-blogs.lincoln.ac.nz\/gis\/wp-content\/uploads\/sites\/3\/2020\/07\/HighVul.jpg\" alt=\"\" width=\"342\" height=\"275\" srcset=\"https:\/\/blogs.lincoln.ac.nz\/gis\/wp-content\/uploads\/sites\/3\/2020\/07\/HighVul.jpg 342w, https:\/\/blogs.lincoln.ac.nz\/gis\/wp-content\/uploads\/sites\/3\/2020\/07\/HighVul-300x241.jpg 300w\" sizes=\"auto, (max-width: 342px) 100vw, 342px\" \/><\/a><\/p>\n<p>This particular one has low population density and % of people over 65 (0 for both, in fact), but is high on the deprivation scale and far from the nearest hospital.<\/p>\n<p>But there are a few caveats:<\/p>\n<ul>\n<li>Each meshblock&#8217;s vulnerability is only comparable to other meshblocks in the study area and not to any outside the study area.\u00a0 If we did this on a national scale the numbers would most likely change;<\/li>\n<li>The demographic data are based on the 2013 census, as it was felt that the 2018 results were unreliable without some further study;<\/li>\n<li>Meshblocks are the finest scale we have access to for mapping census data &#8211; any value we map gets spread homogeneously across the area of the meshblock so we can&#8217;t easily take into account how, say, population might vary <em>within<\/em> a meshblock.\u00a0 This becomes more important as the meshblocks get larger;<\/li>\n<li>The hospital vulnerability used straight line distances from the meshblock centre to the nearest hospital.\u00a0 This is quite different from the actual distance that might need to be travelled on the state highway system to get to the nearest hospital.\u00a0 If we&#8217;d had more time, we would have used some <a href=\"http:\/\/blogs.lincoln.ac.nz\/gis\/a-smokin-script\/\" target=\"_blank\" rel=\"noopener noreferrer\">network analysis<\/a> to determine the actual road distances<\/li>\n<\/ul>\n<p>In the end, this is a very simple analysis compared to the SVI, but it does serve to demonstrate (I hope!) the usefulness of spatial indices to better prepare for eventualities.\u00a0 While things are (mostly) fine and dandy, Covid-wise, <em>right now<\/em>, we&#8217;ll have to remain vigilant if and when the borders begin to open up.\u00a0 A national scale vulnerability index like this could be a part of the planning and help government focus their efforts..<\/p>\n<p>C<\/p>\n","protected":false},"excerpt":{"rendered":"<p>This post covers the mapping of South Island communities and their vulnerability to Covid-19 reinfection as part of an ERST202 class project. While semester 1 feels like a long time ago now, the threats from Covid-19 are still remarkably present.\u00a0 Recent incidents around returning Kiwis and their efforts to break out of quarantine illustrate just [&hellip;]<\/p>\n","protected":false},"author":3,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[1],"tags":[],"class_list":["post-2613","post","type-post","status-publish","format-standard","hentry","category-uncategorized"],"_links":{"self":[{"href":"https:\/\/blogs.lincoln.ac.nz\/gis\/wp-json\/wp\/v2\/posts\/2613","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/blogs.lincoln.ac.nz\/gis\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/blogs.lincoln.ac.nz\/gis\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/blogs.lincoln.ac.nz\/gis\/wp-json\/wp\/v2\/users\/3"}],"replies":[{"embeddable":true,"href":"https:\/\/blogs.lincoln.ac.nz\/gis\/wp-json\/wp\/v2\/comments?post=2613"}],"version-history":[{"count":1,"href":"https:\/\/blogs.lincoln.ac.nz\/gis\/wp-json\/wp\/v2\/posts\/2613\/revisions"}],"predecessor-version":[{"id":4101,"href":"https:\/\/blogs.lincoln.ac.nz\/gis\/wp-json\/wp\/v2\/posts\/2613\/revisions\/4101"}],"wp:attachment":[{"href":"https:\/\/blogs.lincoln.ac.nz\/gis\/wp-json\/wp\/v2\/media?parent=2613"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/blogs.lincoln.ac.nz\/gis\/wp-json\/wp\/v2\/categories?post=2613"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/blogs.lincoln.ac.nz\/gis\/wp-json\/wp\/v2\/tags?post=2613"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}