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Resolves #1466 #1534

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merged 13 commits into from
Sep 24, 2020
Merged

Resolves #1466 #1534

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a0bbe47
added incident case data parsing
Sep 16, 2020
dfc1ead
Merge pull request #5 from reichlab/master
mzorn-58 Sep 22, 2020
70a7ac3
Merge pull request #6 from reichlab/master
mzorn-58 Sep 22, 2020
87a4e68
Weekly report and update rmd
mzorn-58 Sep 22, 2020
88a03fa
added loading of generated incident cases JSON
Sep 23, 2020
3fddb0d
[skip ci] Github Actions build: 206
invalid-email-address Sep 23, 2020
39f1177
Merge pull request #1532 from mzorn-58/master
hannanabdul55 Sep 23, 2020
3736403
added incident case data parsing
Sep 16, 2020
f9e93b9
added loading of generated incident cases JSON
Sep 23, 2020
f36d955
changed default target to Incident Deaths
Sep 23, 2020
2cc490b
added semicolon
Sep 23, 2020
5068d41
fixed merge conflict
Sep 23, 2020
d042ba4
fix merge conflict leftover
Sep 23, 2020
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4,198 changes: 4,198 additions & 0 deletions code/reports/2020-09-22-weekly-report.html
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808 changes: 404 additions & 404 deletions code/reports/weekly-report.Rmd
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920 changes: 920 additions & 0 deletions data-truth/zoltar-truth.csv
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7 changes: 6 additions & 1 deletion visualization/scripts/convert_forecasts.py
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Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,7 @@ def reformat_forecasts(file_path, target, root, data):
if "US" in locations_in_file:
df.loc[df["location"] == 'US', "location_name"] = "US National"

# Only visualize wk ahead forecasts
# Only visualize 4 wk ahead forecasts
if target == 'Cumulative Deaths':
targets = ['1 wk ahead cum death',
'2 wk ahead cum death',
Expand All @@ -39,6 +39,11 @@ def reformat_forecasts(file_path, target, root, data):
'2 wk ahead inc death',
'3 wk ahead inc death',
'4 wk ahead inc death']
elif target == 'Incident Cases':
targets = ['1 wk ahead inc case',
'2 wk ahead inc case',
'3 wk ahead inc case',
'4 wk ahead inc case']
df = df[df["target"].isin(targets)]

# Only visualize certain states
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3 changes: 2 additions & 1 deletion visualization/scripts/modules/meta.js
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Expand Up @@ -28,7 +28,8 @@ const targets = [

const targets_cats = [
'Cumulative Deaths',
'Incident Deaths'
'Incident Deaths',
'Incident Cases'
]

module.exports.regions = regions
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19 changes: 19 additions & 0 deletions visualization/vis-master/covid-csv-tools/dist/csv.js
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6 changes: 6 additions & 0 deletions visualization/vis-master/covid-csv-tools/dist/meta.js
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Expand Up @@ -68,6 +68,12 @@ exports.targetFullNameCum = {
'3-ahead': '3 wk ahead cum death',
'4-ahead': '4 wk ahead cum death'
};
exports.targetFullNameIncCase = {
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Is this variable used anywhere?

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@ydhuang28 ydhuang28 Sep 23, 2020 •
edited
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Yep, it's used here to pick out the incident case data from the filtered CSV files. For some reason GitHub doesn't expand the diff automatically...

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Maybe because it has csv in the filename?

'1-ahead': '1 wk ahead inc case',
'2-ahead': '2 wk ahead inc case',
'3-ahead': '3 wk ahead inc case',
'4-ahead': '4 wk ahead inc case'
};
/**
* Target type for each target. Note that there can be only two
* target types, 'percent' and 'week'.
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2 changes: 1 addition & 1 deletion visualization/vis-master/scripts/parse.js
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Expand Up @@ -21,7 +21,7 @@ const HISTORY_IN_FILE = './scripts/assets/history.json'
const HISTORY_OUT_FILE = './src/assets/data/history.json'
const METADATA_OUT_FILE = './src/assets/data/metadata.json'
//const SEASONS = utils.getSubDirectories(DATA_DIR)
SEASONS = ["Incident Deaths", "Cumulative Deaths"]
SEASONS = ["Incident Deaths", "Cumulative Deaths", "Incident Cases"]

console.log(' Generating data files for flusight')
console.log(' ----------------------------------\n')
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2 changes: 1 addition & 1 deletion visualization/vis-master/src/components/Panels/Choropleth.vue
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Expand Up @@ -299,7 +299,7 @@ export default {
require.ensure(["../../store/data"], () => {
this.importLatestChunk(require("../../store/data"));

this.updateSelectedSeason(this.seasons.length - 1);
this.updateSelectedSeason(0); // first loaded season is Incident Deaths

// Setup map
this.initChoropleth(
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1 change: 1 addition & 0 deletions visualization/vis-master/src/store/actions.js
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Expand Up @@ -22,6 +22,7 @@ export const importLatestChunk = (context, dataChunk) => {
addScoresData(context, dataChunk.latestScoresData)
addDistData(context, dataChunk.latestDistData)
initMetadata(context, dataChunk.metadata)
addSeasonData(context, dataChunk.incCaseSeasonData)
//initHistory(context, dataChunk.history)
}

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3 changes: 3 additions & 0 deletions visualization/vis-master/src/store/data.js
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Expand Up @@ -6,6 +6,8 @@ import latestSeasonData from '!json!../assets/data/season-latest.json'
import latestScoresData from '!json!../assets/data/scores-latest.json'
import latestDistData from '!json!../assets/data/distributions/season-latest-nat.json'

import incCaseSeasonData from '!json!../assets/data/season-Incident Cases.json'

const seasonDataCtx = require.context(
'file-loader!../assets/data/',
false,
Expand Down Expand Up @@ -55,6 +57,7 @@ export {
latestSeasonData,
latestScoresData,
latestDistData,
incCaseSeasonData,
//history,
metadata
}