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v6 version of fluscore #2

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c2fd0f8
Update README.md
jingjtang Oct 15, 2019
9fd42a5
2018-2019 version
jingjtang Oct 15, 2019
43e7008
Changed options; added Delphi logo & revision info
jingjtang Oct 15, 2019
ae3bcf1
Add files via upload
jingjtang Oct 15, 2019
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10 changes: 10 additions & 0 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,16 @@ The site is live at http://delphi.midas.cs.cmu.edu/misc/fluscores/

# Legacy Changelog
````
=== v6: 2019-10-14 ===
+ Support 2017-2018, 2018-2019 national/regional scores
+ Support states & hospitalization scores
+ Delphi logo and revision information
by Jingjing Tang

=== v5: 2017-07-22 ===
+ Sidebar added for legend and scaling
by Tanay Vakharia

=== v4: 2016-11-04 ===
* backport of v3 changes from javascript to coffeescript

Expand Down
165 changes: 122 additions & 43 deletions site/fs_data.coffee
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Original file line number Diff line number Diff line change
@@ -1,25 +1,61 @@
(exports ? window).FS_Data = class FS_Data

@regions = ((if i == 0 then 'Nat' else "Reg#{i}") for i in [0..10])
@regions_2015 = ((if i == 0 then 'us' else "region#{i}") for i in [0..10])
@hhsRegions = ((if i == 0 then 'nat' else "hhs#{i}") for i in [0..10])
@targets_seasonal = ['onset', 'peakweek', 'peak']
@targets_seasonal_2015 = ['onset', 'pkwk', 'pkper']
@targets_local = ['1_week', '2_week', '3_week', '4_week']
@targets_local_2015 = ['1wk', '2wk', '3wk', '4wk']
@targets = @targets_seasonal.concat(@targets_local)
@targets_2015 = @targets_seasonal_2015.concat(@targets_local_2015)
#@regions = ((if i == 0 then 'Nat' else "Reg#{i}") for i in [0..10])
#@regions_2015 = ((if i == 0 then 'us' else "region#{i}") for i in [0..10])
#@hhsRegions = ((if i == 0 then 'nat' else "hhs#{i}") for i in [0..10])

#@targets_seasonal = ['onset', 'peakweek', 'peak']
#@targets_seasonal_2015 = ['onset', 'pkwk', 'pkper']
#@targets_local = ['1_week', '2_week', '3_week', '4_week']
#@targets_local_2015 = ['1wk', '2wk', '3wk', '4wk']
@errors = ['LS', 'AE']
@error_labels = ['log score', 'absolute error']
@error_labels = ['CDC log score', 'absolute error']
@wILI = null

@init = (season) ->
@init = (season, competition) ->
if @wILI != null
return
if season == 2014
@epiweeks = (('' + if i <= 13 then 201440 + i else 201500 + i - 13) for i in [1..32])
else if season in [2015, 20150]
@epiweeks = (('' + if i <= 12 then 201540 + i else 201600 + i - 12) for i in [2..30])
@targets_local = ['1_week', '2_week', '3_week', '4_week']
if competition == 'National'
@regions = ((if i == 0 then 'Nat' else "Reg#{i}") for i in [0..10])
@targets_seasonal = ['onset', 'peakweek', 'peak']
else if competition == 'State'
@regions =(['Alabama', 'Alaska', 'Arizona', 'Arkansas', 'California','Colorado', 'Connecticut', 'Delaware', 'District of Columbia','Georgia', 'Hawaii', 'Idaho', 'Illinois', 'Indiana', 'Iowa','Kansas', 'Kentucky', 'Louisiana', 'Maine', 'Maryland', 'Massachusetts', 'Michigan', 'Minnesota', 'Mississippi','Missouri', 'Montana', 'Nebraska', 'Nevada', 'New Hampshire','New Jersey', 'New Mexico', 'New York', 'New York City','North Carolina', 'North Dakota', 'Ohio', 'Oklahoma', 'Oregon','Pennsylvania', 'Puerto Rico', 'Rhode Island', 'South Carolina','South Dakota', 'Tennessee', 'Texas', 'Utah', 'Vermont','Virgin Islands', 'Virginia', 'Washington', 'West Virginia','Wisconsin', 'Wyoming'])
@targets_seasonal = ['peakweek', 'peak']
else
@regions = ['0-4 yr', '18-49 yr', '5-17 yr', '50-64 yr', '65+ yr', 'Overall']
@targets_seasonal = ['peakweek', 'peak']
else if season in [2015, 20150, 2016, 20160, 2017, 20170]
if competition == 'National'
@regions = ((if i == 0 then 'us' else "region#{i}") for i in [0..10])
@targets_seasonal = ['onset', 'pkwk', 'pkper']
else if competition == 'State'
@regions = (['Alabama', 'Alaska', 'Arizona', 'Arkansas', 'California','Colorado', 'Connecticut', 'Delaware', 'District of Columbia','Georgia', 'Hawaii', 'Idaho', 'Illinois', 'Indiana', 'Iowa','Kansas', 'Kentucky', 'Louisiana', 'Maine', 'Maryland','Massachusetts', 'Michigan', 'Minnesota', 'Mississippi','Missouri', 'Montana', 'Nebraska', 'Nevada', 'New Hampshire','New Jersey', 'New Mexico', 'New York', 'New York City','North Carolina', 'North Dakota', 'Ohio', 'Oklahoma', 'Oregon','Pennsylvania', 'Puerto Rico', 'Rhode Island', 'South Carolina','South Dakota', 'Tennessee', 'Texas', 'Utah', 'Vermont','Virgin Islands', 'Virginia', 'Washington', 'West Virginia','Wisconsin', 'Wyoming'])
@targets_seasonal = ['pkwk', 'pkper']
else
@regions = ['0-4 yr', '18-49 yr', '5-17 yr', '50-64 yr', '65+ yr', 'Overall']
@targets_seasonal = ['pkwk', 'pkper']
@targets_local = ['1wk', '2wk', '3wk', '4wk']
if season in [2015, 20150]
@epiweeks = (('' + if i <= 12 then 201540 + i else 201600 + i - 12) for i in [2..30])
else if season in [2016, 20160]
@epiweeks = (('' + if i <= 12 then 201640 + i else 201700 + i - 12) for i in [3..30])
else if season in [2017, 20170]
@epiweeks = (('' + if i <= 12 then 201740 + i else 201800 + i - 12) for i in [2..29])
else if season in [2018, 20180]
if competition == 'National'
@regions = ((if i == 0 then "US National" else "HHS Region #{i}") for i in [0..10])
@targets_seasonal = ['Season onset', 'Season peak week', 'Season peak percentage']
else if competition == 'State'
@regions = (['Alabama', 'Alaska', 'Arizona', 'Arkansas', 'California','Colorado', 'Connecticut', 'Delaware', 'District of Columbia','Georgia', 'Hawaii', 'Idaho', 'Illinois', 'Indiana', 'Iowa','Kansas', 'Kentucky', 'Louisiana', 'Maine', 'Maryland','Massachusetts', 'Michigan', 'Minnesota', 'Mississippi','Missouri', 'Montana', 'Nebraska', 'Nevada', 'New Hampshire','New Jersey', 'New Mexico', 'New York', 'New York City','North Carolina', 'North Dakota', 'Ohio', 'Oklahoma', 'Oregon','Pennsylvania', 'Puerto Rico', 'Rhode Island', 'South Carolina','South Dakota', 'Tennessee', 'Texas', 'Utah', 'Vermont','Virgin Islands', 'Virginia', 'Washington', 'West Virginia','Wisconsin', 'Wyoming'])
@targets_seasonal = ['Season peak week', 'Season peak percentage']
else
@regions = ['0-4 yr', '18-49 yr', '5-17 yr', '50-64 yr', '65+ yr', 'Overall']
@targets_seasonal = ['Season peak week', 'Season peak percentage']
@targets_local = ['1 wk ahead', '2 wk ahead', '3 wk ahead', '4 wk ahead']
@epiweeks = (('' + if i <= 12 then 201840 + i else 201900 + i - 12) for i in [2..30])
else
throw new Error('unsupported season: ' + season)
getCallback = (hhs, name) =>
Expand All @@ -32,13 +68,15 @@
for w in wili
[min, max] = [Math.min(min, w), Math.max(max, w)]
@wILI[name] = ((w - min) / (max - min) for w in wili)

@targets = @targets_seasonal.concat(@targets_local)
@wILI = { combine: [] }
weekRange = Epidata.range(@epiweeks[0], @epiweeks[@epiweeks.length - 1])
for [hhs, name] in _.zip(@hhsRegions, @regions)
@wILI[name] = []
Epidata.fluview(getCallback(hhs, name), hhs, weekRange)
#for [hhs, name] in _.zip(@hhsRegions, @regions)
#@wILI[name] = []
#Epidata.fluview(getCallback(hhs, name), hhs, weekRange)

@update = (data, season, error, target, region, epiweek) ->
@update = (data, season, error, target, region, group) ->
totals = null
if target == 'combine'
targets = @targets
Expand All @@ -49,9 +87,9 @@
else
targets = [target]
regions = if region == 'combine' then @regions else [region]
if season == 20150
targets = (@targets_2015[@targets.indexOf(t)] for t in targets)
regions = (@regions_2015[@regions.indexOf(r)] for r in regions)
if season in [20150, 20160, 20170, 20180]
targets = (@targets[@targets.indexOf(t)] for t in targets)
regions = (@regions[@regions.indexOf(r)] for r in regions)
nr = regions.length
nt = targets.length
teams = (t for t of data)
Expand Down Expand Up @@ -102,25 +140,26 @@
if files.length == 0
return onFailure('no files selected')
for file in files
if season in [2014, 2015] and !file.name.endsWith('.zip')
if season in [2014, 2015, 2016, 2017, 2018] and !file.name.endsWith('.zip')
return onFailure("#{file.name} is not a zip file")
else if season == 20150 and !file.name.endsWith('.csv')
else if season in [20150, 20160, 20170, 20180] and !file.name.endsWith('.csv')
return onFailure("#{file.name} is not a csv file")
# load files one after another
fileIndex = 0
data = {}
loadFunc = if season == 20150 then loadFull else loadSingle
callback = (name, fileData, error) ->
loadFunc = if season in [20150, 20160, 20170, 20180] then loadFull else loadSingle

callback = (name, fileData, error, season) ->
if error?
return onFailure(error)
data[name] = fileData
if fileIndex < files.length
loadFunc(files[fileIndex++], callback)
loadFunc(files[fileIndex++], callback, season)
else
return onSuccess((t for t of data), data)
loadFunc(files[fileIndex++], callback)
loadFunc(files[fileIndex++], callback, season)

loadSingle = (file, callback) ->
loadSingle = (file, callback, season) ->
reader = new FileReader()
reader.onload = (event) ->
zip = new JSZip(event.target.result)
Expand All @@ -135,7 +174,7 @@
unpackValues(data[region], values, FS_Data.targets_local)
catch ex
error = ex.message ? '' + ex
callback(file.name, data, error)
callback(file.name, data, error, season)
reader.readAsArrayBuffer(file)

unpackValues = (data, values, targets) ->
Expand All @@ -162,39 +201,79 @@
fix = (n) -> if Number.isNaN(n) then -10 else n
return (fix(parseFloat(f)) for f in fields)

loadFull = (file, callback) ->
loadFull = (file, callback, season) ->
reader = new FileReader()
reader.onload = (event) ->
data = {}
error = null
csv = event.target.result
try
for region in FS_Data.regions_2015
for region in FS_Data.regions
data[region] = {}
for target in FS_Data.targets_2015
values = parseFullCSV(csv, region, target)
for target in FS_Data.targets
if season in [20150, 20160, 20170]
results = []
else if season == 20180
results = (0 for [0...FS_Data.epiweeks.length])
values = parseFullCSV(csv, region, target, results, season)
unpackValues(data[region], values, [target])
catch ex
error = ex.message ? '' + ex
callback(file.name, data, error)
callback(file.name, data, error, season)
reader.readAsText(file)

parseFullCSV = (csv, l, t) ->

parseFullCSV = (csv, l, t, results, season) ->
fix = (n) -> if Number.isNaN(n) then -10 else n
results = []
AEresults = []
headers = csv.split('\n')[0].split(',')
cw_no = -100
for j in [0...headers.length]
headers[j] = '"' + headers[j] + '"'
if headers[j].includes('location')
loc_no = j
else if headers[j].includes('target')
tg_no = j
else if headers[j].includes('score')
ls_no = j
else if headers[j].includes('competition_week')
cw_no = j

#loc_no = headers.indexOf('location')
#tg_no = headers.indexOf('target')
#ls_no = headers.indexOf('score')

#if 'competition_week' in headers
#cw_no = headers.indexOf('competitionweek')
#else
#cw_no = 5

for row in csv.split('\n').slice(1)
row = row.split(',')
if row.length == 0
continue
location = row[1]
target = row[2]
ls = row[7]
if location == l and target == t
results.push(fix(parseFloat(ls)))
if row.length == 9
ae = row[8]
AEresults.push(fix(parseFloat(ae)))
location = '"' + row[loc_no] + '"'
target = row[tg_no]
ls = row[ls_no]


if season in [20150, 20160, 20170]
if location.includes(l) and target.includes(t)
results.push(fix(parseFloat(ls)))
#if row.length >= 9
#ae = row[8]
#AEresults.push(fix(parseFloat(ae)))
else if season in [20180]

#Problem with competition week hasn't been solved
#Potential problem with inclues function (don't know why it happens occationally)
competitionweek = row[cw_no]
#competitionweek = row[-100]
#if location == l and target == t
if location.includes(l) and target.includes(t)
#results.push(fix(parseFloat(ls)))
results[competitionweek-1] = fix(parseFloat(ls))
# No AEresults for 2018
if AEresults.length == 0
# pad the abs err scores with 0s. to change when AE scores are available
for i in [0...results.length]
Expand Down
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