Module:Medical cases data

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This module is rated as alpha. It is ready for third-party input, and may be used on a few pages to see if problems arise, but should be watched. Suggestions for new features or changes in their input and output mechanisms are welcome.

This module inserts charts and maps of medical cases related to a pandemic, broken down by subregions.

`caseTable`

Inserts a table of cases and deaths by region.

Usage: {{#invoke:Medical cases data|caseTable|config=Configuration}}

{{#invoke:Medical cases data|caseTable
|config=San Francisco Bay Area
}}

COVID-19 pandemic medical cases in the San Francisco Bay Area by county
Counties	Cases^[a]	Recov.^[b]	Deaths	Pop. (2019)	C/1M	Ref.
9	1,937,165		11,216	7,739,378	250,300	Ref.
Santa Clara	527,681	?	3,222	1,927,852	273,714	d c^[1]
Alameda^[c]	400,532	?	2,484	1,671,329	239,649	d c^[2]
Contra Costa	302,824	300,666	1,601	1,153,526	262,520	d c^[3]
San Francisco	203,788	?	1,373	881,549	231,170	d c^[4]
San Mateo	184,001	?	946	766,573	240,031	d c^[5]
Sonoma	119,749	118,903	668	494,336	242,242	d c^[6]
Solano	118,904	118,073	441	447,643	265,622	d c^[7]
Marin	44,650	7,030	274	258,826	172,510	d c^[8]
Napa	35,036	27,672	207	137,744	254,356	d c^[9]
^ Cumulative cases reported by each county's health department. Cases reported are those of county residents, including those who tested positive elsewhere in California. ^ Counties differ in what they consider to be a recovery. ^ Including cases in the City of Berkeley, which are reported by the Berkeley Public Health Division.

`map`

Inserts an interactive map of cases and deaths by region.

Usage: {{#invoke:Medical cases data|map|config=Configuration|frameWidth=Frame width in pixels|frameHeight=Frame height in pixels|caption=Caption as wikitext}}

{{#invoke:Medical cases data|map
|config=San Francisco Bay Area
|frameHeight=300
}}

COVID-19 pandemic medical cases in the San Francisco Bay Area by county

Configuration

Run this Wikidata Query Service query to obtain a list of localized outbreaks to add to the regions property in the table.

return {
	caption = "Cases by county", -- Table or map caption as wikitext
	outbreakItem = "Q94050008", -- QID of the Wikidata item representing the 
	regionTerm = "Counties", -- Term for each region, used as the first column's header
	regionNamePattern = "(.+) County", -- Naming pattern for regions, applied to each region's item's label to display a short name in first column; see [[mw:Extension:Scribunto/Lua reference manual#Patterns]]
	populationDate = "2020-01-01", -- Date of the population figures used to calculate per-capita infection rates
	regions = {
		-- Add a table for each region's outbreak
		{
			-- QID of the outbreak
			entity = "Q94259368",
			-- If there is tabular data for the outbreak, specify any column names that differ from the defaults
			columns = {cases = "AC_CumulCases", deaths = "AC_CumulDeaths"},
			-- Optional footnote for the region as wikitext
			note = "Including cases in the City of Berkeley, which are reported by the Berkeley Public Health Division.",
		},
	},
	columnNotes = {
		cases = "Cumulative cases reported by each county's health department.", -- (Optional) Footnote for the "Cases" column as wikitext
		recoveries = "Counties differ in what they consider to be a recovery.", -- (Optional) Footnote for the "Recoveries" column as wikitext
		deaths = "Includes suspected cases.", -- (Optional) Footnote for the "Deaths" column as wikitext
	}
}

Available configurations

The above documentation is transcluded from Module:Medical cases data/doc.
Editors can experiment in this module's sandbox and testcases pages.
Subpages of this module.

^ “Respiratory virus data”, “COVID cases and deaths dashboard”, “COVID-19 hospitalizations by date”, “COVID-19 Hospitalizations Dashboard”, “Count of deaths with COVID-19 by date”, “Deaths with COVID-19 by age group”, Santa Clara County Public Health. November 29, 2024.
^ Alameda County Data Sharing Initiative, Alameda County Public Health Department. November 23, 2024.
^ Contra Costa Health Services. May 22, 2023.
^ “ARCHIVED: COVID-19 Cases by Geography Over Time”, “COVID-19 Deaths Over Time”, “COVID-19 Hospitalizations”, DataSF, San Francisco Department of Public Health. November 19, 2024.
^ San Mateo County Health. April 27, 2023.
^ Case and Testing Data, Hospitalizations and Deaths, County of Sonoma. November 29, 2024.
^ Solano County Public Health. March 2, 2023.
^ “COVID-19 Case Disposition”, “COVID-19 Cumulative Demographics”, “Total Cases and Recovered by Date Reported among Marin County Community Residents”, “Total Hospitalizations and Deaths by Event Date among Marin County Community Residents”, Marin Health & Human Services. February 14, 2023.
^ “COVID-19 in Napa County”, “Landing Page”, “Situation Update Archive”, Napa County Health & Human Services Agency. May 14, 2023.

-- Usage: =p._caseTable({config="San Francisco Bay Area"})

local p = {}
local lang = mw.getContentLanguage()
local tabularData = require("Module:Tabular data")
local wd = require("Module:wd")
local mapFrame = require("Module:Mapframe")

local propertyIDsByDisposition = {
	-- tests = "P8011",
	cases = "P1603",
	-- hospitalizations = "P8049",
	recoveries = "P8010",
	deaths = "P1120",
}

local function round(x)
	return (math.modf(x + (x < 0 and -0.5 or 0.5)))
end

function p.pointInTime(statement)
	local qualifiers = statement.qualifiers and statement.qualifiers.P585
	local time = qualifiers and qualifiers[1].datavalue.value.time
	return time and tonumber(lang:formatDate("U", time))
end

-- =tonumber(p.mostRecentStatement("Q83873577", "P1120").mainsnak.datavalue.value.amount)
function p.mostRecentStatement(entityID, propertyID, startDate, endDate)
	local startTime = startDate and tonumber(lang:formatDate("U", startDate)) or -math.huge
	local endTime = endDate and tonumber(lang:formatDate("U", endDate)) or math.huge
	
	local statements = mw.wikibase.getBestStatements(entityID, propertyID)
	local latestTime = -math.huge
	local latestStatement
	for i, statement in ipairs(statements) do
		local time = p.pointInTime(statement)
		if time and time > startTime and time < endTime and time > latestTime then
			latestTime = time
			latestStatement = statement
		end
	end
	return latestStatement
end

function p.statementReference(statement)
	local reference = statement.references and statement.references[1]
	local referenceSnak = reference and reference.snaks.P248 and reference.snaks.P248[1]
	local declarationQID = referenceSnak and referenceSnak.datavalue.value.id
	if not declarationQID then
		return nil
	end
	local name = mw.wikibase.formatValue(referenceSnak)
	local url = mw.wikibase.getBestStatements(declarationQID, "P856")[1].mainsnak.datavalue.value
	return {
		name = declarationQID,
		wikitext = url and mw.ustring.format("[%s %s]", url, name) or name,
	}
end

function p._regionData(regionConfigs, populationDate, ignoredSources)
	local regions = {}
	for i, regionConfig in ipairs(regionConfigs) do
		local outbreakEntity = regionConfig.entity
		local locationEntity = mw.wikibase.getBestStatements(outbreakEntity, "P276")[1].mainsnak.datavalue.value.id
		local dataTableStatement = mw.wikibase.getBestStatements(outbreakEntity, "P8204")[1]
		local dataTableName
		local dataTable
		if dataTableStatement then
			local qualifiers = dataTableStatement and dataTableStatement.qualifiers
			local source = qualifiers and qualifiers.P1433 and qualifiers.P1433[1].datavalue.value.id
			local ignored = false
			for i, ignoredSource in ipairs(ignoredSources or {}) do
				if source == ignoredSource then
					ignored = true
					break
				end
			end
			if not ignored then
				dataTableName = dataTableStatement.mainsnak.datavalue.value
				dataTable = mw.ext.data.get((dataTableName:gsub("^Data:", "")))
			end
		end
		
		local region = {
			outbreakEntity = outbreakEntity,
			locationEntity = locationEntity,
			name = mw.wikibase.getLabel(locationEntity),
			link = mw.wikibase.getSitelink(locationEntity),
			population = tonumber(wd._property({
				"raw",
				locationEntity,
				"P1082",
				P585 = populationDate,
			})),
			dataTableName = dataTableName,
			note = regionConfig.note,
			sources = {},
		}
		
		local columns = regionConfig.columns
		local latestTableDate = dataTable and tabularData._cell({
			data = dataTable,
			output_row = -1,
			output_column = columns and (columns.date or columns.P585_date) or "date",
		})
		local latestTableTime = latestTableDate and tonumber(lang:formatDate("U", latestTableDate))
		local usesDataTable = false
		
		local casesStatement = p.mostRecentStatement(outbreakEntity, propertyIDsByDisposition.cases)
		local casesTime = casesStatement and p.pointInTime(casesStatement)
		if casesTime and (not latestTableTime or casesTime > latestTableTime) then
			region.cases = tonumber(casesStatement.mainsnak.datavalue.value.amount)
			local reference = p.statementReference(casesStatement)
			if reference then
				region.sources[reference.name] = reference.wikitext
			end
		elseif latestTableTime then
			region.cases = dataTable and (tabularData._cell({
				data = dataTable,
				output_row = -1,
				output_column = columns and columns.cases or "totalConfirmedCases",
			}) or tabularData._lookup({
				data = dataTable,
				search_pattern = "%d",
				search_column = columns and columns.cases or "totalConfirmedCases",
				occurrence = -1,
				output_column = columns and columns.cases or "totalConfirmedCases",
			})) + (columns and columns.cases2 and tabularData._cell({
				data = dataTable,
				output_row = -1,
				output_column = columns.cases2,
			}) or 0)
			usesDataTable = true
		end
		region.arrivalDate = dataTable and tabularData._lookup({
			data = dataTable,
			search_pattern = "[1-9]",
			search_column = columns and columns.cases or "totalConfirmedCases",
			occurrence = 1,
			output_column = columns and (columns.date or columns.P585_date) or "date",
		})
		
		local deathsStatement = p.mostRecentStatement(outbreakEntity, propertyIDsByDisposition.deaths)
		local deathsTime = deathsStatement and p.pointInTime(deathsStatement)
		if deathsTime and (not latestTableTime or deathsTime > latestTableTime) then
			region.deaths = tonumber(deathsStatement.mainsnak.datavalue.value.amount)
			local reference = p.statementReference(deathsStatement)
			if reference then
				region.sources[reference.name] = reference.wikitext
			end
		elseif latestTableTime then
			region.deaths = dataTable and (tabularData._cell({
				data = dataTable,
				output_row = -1,
				output_column = columns and columns.deaths or "deaths",
			}) or tabularData._lookup({
				data = dataTable,
				search_pattern = "%d",
				search_column = columns and columns.deaths or "deaths",
				occurrence = -1,
				output_column = columns and columns.deaths or "deaths",
			}))
			usesDataTable = true
		end
		
		local recoveriesStatement = p.mostRecentStatement(outbreakEntity, propertyIDsByDisposition.recoveries)
		local recoveriesTime = recoveriesStatement and p.pointInTime(recoveriesStatement)
		if recoveriesTime and (not latestTableTime or recoveriesTime > latestTableTime) then
			region.recoveries = tonumber(recoveriesStatement.mainsnak.datavalue.value.amount)
			local reference = p.statementReference(recoveriesStatement)
			if reference then
				region.sources[reference.name] = reference.wikitext
			end
		elseif latestTableTime then
			region.recoveries = columns and columns.recoveries and dataTable and (tabularData._cell({
				data = dataTable,
				output_row = -1,
				output_column = columns.recoveries,
			}) or tabularData._lookup({
				data = dataTable,
				search_pattern = "%d",
				search_column = columns.recoveries,
				occurrence = -1,
				output_column = columns.recoveries,
			}))
			usesDataTable = true
		end
		
		local viewLinks = {
			mw.ustring.format("[[d:%s|d]]", region.outbreakEntity),
		}
		if dataTableName then
			table.insert(viewLinks, mw.ustring.format("[[c:%s|c]]", dataTableName))
		end
		region.viewLink = table.concat(viewLinks, "&nbsp;")
		
		if usesDataTable then
			local formattedDate = latestTableTime
			local reference = mw.ustring.format("%s. %s.", dataTable.sources:gsub("<br */?>.*", ""), lang:formatDate("F j, Y", latestTableDate))
			region.sources[dataTableName] = reference
		end
		
		table.insert(regions, region)
	end
	return regions
end

local function addNumericCell(row, contents)
	if contents then
		row
			:tag("td")
			:attr("align", "right")
			:attr("data-sort-value", contents)
			:wikitext(lang:formatNum(contents))
	else
		row
			:tag("td")
			:addClass("unknown")
			:addClass("table-unknown")
			:attr("align", "center")
			:css({
				background = "#ececec",
				color = "#2c2c2c",
				["font-size"] = "smaller",
				["vertical-align"] = "middle",
			})
			:attr("data-sort-value", "0")
			:wikitext("?")
	end
	return row
end

-- Usage: =p._caseTable({config="San Francisco Bay Area"})
function p._caseTable(args)
	local frame = mw.getCurrentFrame()
	local config = args.config and mw.loadData("Module:Medical cases data/" .. args.config)
	local populationDate = config and config.populationDate or args.populationDate
	local regions = p._regionData(
		config and config.regions,
		populationDate,
		config and config.ignoredSources)
	table.sort(regions, function (left, right)
		local leftCases = left.cases or 0
		local rightCases = right.cases or 0
		return leftCases == rightCases and left.name < right.name or leftCases > rightCases
	end)
	
	local totals = {
		regions = #regions,
		cases = 0,
		deaths = 0,
		recoveries = 0,
		population = 0,
	}
	for i, region in ipairs(regions) do
		totals.cases = totals.cases + (region.cases or 0)
		totals.deaths = totals.deaths + (region.deaths or 0)
		totals.recoveries = totals.recoveries and region.recoveries and (totals.recoveries + region.recoveries)
		totals.population = totals.population + (region.population or 0)
	end
	
	local htmlTable = mw.html.create("table")
		:addClass("wikitable")
		:addClass("sortable")
		:addClass("plainrowheaders")
		:attr("align", "right")
		:css({
			["font-size"] = "85%",
		})
	htmlTable
		:tag("caption")
		:wikitext(config and config.caption or args.caption)
	
	local headerRow = htmlTable
		:tag("tr")
	local totalRow = htmlTable
		:tag("tr")
	
	local columnNotes = config and config.columnNotes
	headerRow
		:tag("th")
		:attr("scope", "col")
		:attr("data-sort-type", "text")
		:wikitext(config and config.regionTerm or args.regionTerm or "Regions")
		:wikitext(columnNotes and columnNotes.regions and frame:expandTemplate {
			title = "efn",
			args = {
				columnNotes.regions
			}
		})
	totalRow
		:tag("th")
		:attr("align", "right")
		:wikitext(lang:formatNum(totals.regions))
	headerRow
		:tag("th")
		:attr("scope", "col")
		:attr("data-sort-type", "number")
		:wikitext("Cases")
		:wikitext(columnNotes and columnNotes.cases and frame:expandTemplate {
			title = "efn",
			args = {
				columnNotes.cases
			}
		})
	totalRow
		:tag("th")
		:attr("align", "right")
		:attr("data-sort-type", "number")
		:wikitext(lang:formatNum(totals.cases))
	local recoveriesHeader = headerRow
		:tag("th")
		:attr("scope", "col")
		:attr("data-sort-type", "number")
	recoveriesHeader
		:tag("abbr")
		:attr("title", "Recoveries")
		:wikitext("Recov.")
	recoveriesHeader
		:wikitext(columnNotes and columnNotes.recoveries and frame:expandTemplate {
			title = "efn",
			args = {
				columnNotes.recoveries
			}
		})
	totalRow
		:tag("th")
		:attr("align", "right")
		:wikitext(totals.recoveries and lang:formatNum(totals.recoveries))
	headerRow
		:tag("th")
		:attr("scope", "col")
		:attr("data-sort-type", "number")
		:wikitext("Deaths")
		:wikitext(columnNotes and columnNotes.deaths and frame:expandTemplate {
			title = "efn",
			args = {
				columnNotes.deaths
			}
		})
	totalRow
		:tag("th")
		:attr("align", "right")
		:attr("data-sort-type", "number")
		:wikitext(lang:formatNum(totals.deaths))
	local populationHeader = headerRow
			:tag("th")
			:attr("scope", "col")
			:attr("data-sort-type", "number")
	populationHeader
		:tag("abbr")
		:attr("title", "Population")
		:wikitext("Pop.")
	if populationDate then
		populationHeader
			:wikitext(mw.ustring.format(" (%d)", lang:formatDate("Y", populationDate)))
	end
	populationHeader
		:wikitext(columnNotes and columnNotes.population and frame:expandTemplate {
			title = "efn",
			args = {
				columnNotes.population
			}
		})
	totalRow
		:tag("th")
		:attr("align", "right")
		:attr("data-sort-type", "number")
		:wikitext(lang:formatNum(totals.population))
	headerRow
		:tag("th")
		:attr("scope", "col")
		:attr("data-sort-type", "number")
			:tag("abbr")
			:attr("title", "Cases per 1 million inhabitants")
			:wikitext("C/1M")
		:wikitext(columnNotes and columnNotes.casesPerMillion and frame:expandTemplate {
			title = "efn",
			args = {
				columnNotes.casesPerMillion
			}
		})
	totalRow
		:tag("th")
		:attr("align", "right")
		:attr("data-sort-type", "number")
		:wikitext(lang:formatNum(round(totals.cases / totals.population * 1e6)))
	headerRow
		:tag("th")
		:attr("scope", "col")
		:attr("rowspan", 2)
		:addClass("unsortable")
			:tag("abbr")
			:attr("title", "Reference")
			:wikitext("Ref.")
	
	local regionNamePattern = config and config.regionNamePattern or args.regionNamePattern
	for i, region in ipairs(regions) do
		local row = htmlTable:tag("tr")
		local name = region.name
		if regionNamePattern then
			name = mw.ustring.match(region.name, regionNamePattern) or name
		end
		row
			:tag("th")
			:attr("scope", "row")
			:wikitext(mw.ustring.format("[[%s|%s]]", region.link, name))
			:wikitext(region.note and frame:expandTemplate {
				title = "efn",
				args = {
					region.note,
				}
			})
		addNumericCell(row, region.cases)
		addNumericCell(row, region.recoveries)
		addNumericCell(row, region.deaths)
		addNumericCell(row, region.population)
		addNumericCell(row, region.cases and region.population and round(region.cases / region.population * 1e6))
		local refCell = row
			:tag("td")
			:attr("align", "center")
			:wikitext(region.viewLink)
		for name, wikitext in pairs(region.sources) do
			refCell:wikitext(frame:callParserFunction {
				name = "#tag:ref",
				args = {
					name = name,
					wikitext,
				},
			})
		end
	end
	
	local footerRow = htmlTable
		:tag("tr")
		:addClass("sortbottom")
	footerRow
		:tag("td")
		:attr("colspan", 7)
		:attr("align", "left")
		:css({
			width = 0,
		})
		:wikitext(frame:expandTemplate {
			title = "notelist",
		})
	
	return htmlTable
end

function p.caseTable(frame)
	return p._caseTable(frame.args)
end

function p._statistics(args)
	local frame = mw.getCurrentFrame()
	local config = args.config and mw.loadData("Module:Medical cases data/" .. args.config)
	local populationDate = config and config.populationDate or args.populationDate
	local regions = p._regionData(
		config and config.regions,
		populationDate,
		config and config.ignoredSources)
	
	local stats = {
		regions = #regions,
		cases = 0,
		deaths = 0,
		recoveries = 0,
		recoveriesRegions = 0,
		population = 0,
	}
	for i, region in ipairs(regions) do
		stats.cases = stats.cases + (region.cases or 0)
		stats.deaths = stats.deaths + (region.deaths or 0)
		if region.recoveries then
			stats.recoveries = stats.recoveries + region.recoveries
			stats.recoveriesRegions = stats.recoveriesRegions + 1
		end
		stats.population = stats.population + (region.population or 0)
		if not stats.arrivalDate or region.arrivalDate < stats.arrivalDate then
			stats.arrivalDate = region.arrivalDate
		end
	end
	return stats
end

function p.statistics(frame)
	return p._statistics(frame.args)[mw.text.trim(frame.args[1])]
end

local function fillColor(casesPerCapita)
	-- [[c:Template:COVID-19 Prevalence in US by county]]
	local percent = casesPerCapita * 100
	if percent >= 10.00 then return "#510000" end
	if percent >=  3.00 then return "#99000d" end
	if percent >=  1.00 then return "#cb181d" end
	if percent >=  0.30 then return "#fb6a4a" end
	if percent >=  0.10 then return "#fc9272" end
	if percent >=  0.03 then return "#fcbba1" end
	if percent >=  0.00 then return "#fee5d9" end
	return "#cccccc"
end

-- Usage: =p._map({config="San Francisco Bay Area"})
function p._map(args)
	local frame = mw.getCurrentFrame()
	local config = args.config and mw.loadData("Module:Medical cases data/" .. args.config)
	local populationDate = config and config.populationDate or args.populationDate
	local regions = p._regionData(
		config and config.regions,
		populationDate,
		config and config.ignoredSources)
	
	local params = {
		frame = "yes",
		["frame-width"] = args.frameWidth or (config and config.frameWidth),
		["frame-height"] = args.frameHeight or (config and config.frameHeight),
		text = args.caption or (config and config.caption),
	}
	for i, region in ipairs(regions) do
		i = i == 1 and "" or i
		params["type" .. i] = "shape"
		params["id" .. i] = region.locationEntity
		params["title" .. i] = region.name
		params["stroke-color" .. i] = "#ffffff"
		params["stroke-width" .. i] = 1
		params["fill" .. i] = fillColor(region.cases / region.population)
		
		local details = {
			mw.ustring.format("%s cases (%s/1M)", lang:formatNum(region.cases),
				lang:formatNum(round(region.cases / region.population * 1e6))),
			mw.ustring.format("%s deaths", lang:formatNum(region.deaths)),
		}
		if region.recoveries then
			table.insert(details, mw.ustring.format("%s recoveries", lang:formatNum(region.recoveries)))
		end
		params["description" .. i] = table.concat(details, "<br>")
	end
	
	return frame:preprocess(mapFrame._main(params))
end

function p.map(frame)
	return p._map(frame.args)
end

return p

[1] Cumulative cases reported by each county's health department. Cases reported are those of county residents, including those who tested positive elsewhere in California.

[2] Counties differ in what they consider to be a recovery.

[4] Including cases in the City of Berkeley, which are reported by the Berkeley Public Health Division.

[Data:COVID-19_cases_in_Santa_Clara_County,_California.tab-3] “Respiratory virus data”, “COVID cases and deaths dashboard”, “COVID-19 hospitalizations by date”, “COVID-19 Hospitalizations Dashboard”, “Count of deaths with COVID-19 by date”, “Deaths with COVID-19 by age group”, Santa Clara County Public Health. November 29, 2024.

[Data:COVID-19_cases_in_Alameda_County,_California.tab-5] Alameda County Data Sharing Initiative, Alameda County Public Health Department. November 23, 2024.

[Data:COVID-19_cases_in_Contra_Costa_County,_California.tab-6] Contra Costa Health Services. May 22, 2023.

[Data:COVID-19_cases_in_San_Francisco.tab-7] “ARCHIVED: COVID-19 Cases by Geography Over Time”, “COVID-19 Deaths Over Time”, “COVID-19 Hospitalizations”, DataSF, San Francisco Department of Public Health. November 19, 2024.

[Data:COVID-19_cases_in_San_Mateo_County,_California.tab-8] San Mateo County Health. April 27, 2023.

[Data:COVID-19_cases_in_Sonoma_County,_California.tab-9] Case and Testing Data, Hospitalizations and Deaths, County of Sonoma. November 29, 2024.

[Data:COVID-19_cases_in_Solano_County,_California.tab-10] Solano County Public Health. March 2, 2023.

[Data:COVID-19_cases_in_Marin_County,_California.tab-11] “COVID-19 Case Disposition”, “COVID-19 Cumulative Demographics”, “Total Cases and Recovered by Date Reported among Marin County Community Residents”, “Total Hospitalizations and Deaths by Event Date among Marin County Community Residents”, Marin Health & Human Services. February 14, 2023.

[Data:COVID-19_cases_in_Napa_County,_California.tab-12] “COVID-19 in Napa County”, “Landing Page”, “Situation Update Archive”, Napa County Health & Human Services Agency. May 14, 2023.

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