Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

[DO NOT MERGE] clustering #113

Draft
wants to merge 1 commit into
base: develop
Choose a base branch
from
Draft

[DO NOT MERGE] clustering #113

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
150 changes: 149 additions & 1 deletion website/src/app/shared/components/visualization-page/shared/visualization-6-data-handler.ts
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -12,6 +12,7 @@ interface DataEntry {
CASE_NUMBER: string;
RANK: number;
AGE: number;
SEX: string;
PERIOD: number;
TIME_BEFORE_DEATH: number;

Expand Down Expand Up @@ -47,6 +48,7 @@ const fakeEntries: DataEntry[] = [
CASE_NUMBER: '',
RANK: 0,
AGE: 0,
SEX: '',
PERIOD: 0,
TIME_BEFORE_DEATH: 0,

Expand All @@ -73,6 +75,7 @@ const fakeEntries: DataEntry[] = [
CASE_NUMBER: '',
RANK: 0,
AGE: 0,
SEX: '',
PERIOD: 0,
TIME_BEFORE_DEATH: 120,

Expand Down Expand Up @@ -111,6 +114,7 @@ export class Visualization6DataHandler implements DataHandler {

private data?: DataEntry[];
private sortBy: SortField = 'HEALTH_RANK';
private clusterBy: keyof DataEntry = 'SEX';
private sortRanks: Record<string, Record<SortField, number>> = {};
private ranks?: number[];
private ranksLookup?: Set<number>;
Expand Down Expand Up @@ -153,6 +157,7 @@ export class Visualization6DataHandler implements DataHandler {

this.data = undefined;
this.sortBy = 'HEALTH_RANK';
this.clusterBy = 'SEX';
this.sortRanks = {};
this.ranks = undefined;
this.ranksLookup = undefined;
Expand Down Expand Up @@ -181,6 +186,9 @@ export class Visualization6DataHandler implements DataHandler {
private updateData(): void {
let { data = [] } = this;

data = this.clusterData(data);
this.sortRanks = this.compileSortRanks(data);

data = this.filterByRank(data);
data = this.filterByAge(data);
data = this.filterByEncounters(data);
Expand All @@ -201,10 +209,150 @@ export class Visualization6DataHandler implements DataHandler {
for (const { CASE_NUMBER, AGE_RANK, HEALTH_RANK, OVERDOSE_RANK, TIME_FIRST_OD, TIME_FIRST_RX, OD_DIFF, RX_DIFF, INCARCERATIONS_RANK, PRESCRIPTIONS_RANK } of data) {
sortRanks[CASE_NUMBER] ??= { AGE_RANK, HEALTH_RANK, OVERDOSE_RANK, TIME_FIRST_OD, TIME_FIRST_RX, OD_DIFF, RX_DIFF, INCARCERATIONS_RANK, PRESCRIPTIONS_RANK };
}

return sortRanks;
}

private clusterData(data: DataEntry[]): DataEntry[] {
const { clusterBy } = this;
const clusteredData: Record<number, DataEntry[]> = {};
let maxValue: number;
switch (this.clusterBy) {
case 'AGE':
maxValue = 100;
break;
case 'SEX':
maxValue = 1;
break;
default:
maxValue = Math.max(...data.map(o => o[clusterBy] as number), 0);
}

for (const entry of data) {
const value = entry[clusterBy];
let cluster = 0;
if (clusterBy === 'SEX') {
cluster = value === 'M' ? 0 : 1; // M=0, F=1
} else {
cluster = Math.floor(value as number/maxValue * 10);
}
if (clusteredData[cluster]) {
clusteredData[cluster].push(entry);
} else {
clusteredData[cluster] = [entry];
}
}

return this.createClusterCases(clusteredData);
}

private createClusterCases(clusteredData: Record<number, DataEntry[]>): DataEntry[] {
let result: DataEntry[] = [];
const keys = Object.keys(clusteredData);

for (const key of keys) {
const binNum = parseInt(key);
result = result.concat(this.createClusterCase(clusteredData[binNum], binNum));
}

return result;
}

private createClusterCase(dataCluster: DataEntry[], binNum: number): DataEntry[] {
const result: DataEntry[] = [];
const periodCases: Record<number, DataEntry[]> = {};

for (const entry of dataCluster) {
if (!periodCases[entry.PERIOD]) {
periodCases[entry.PERIOD] = [entry];
} else {
periodCases[entry.PERIOD].push(entry);
}
}

const keys = Object.keys(periodCases);
for (const key of keys) {
const k = parseInt(key);
result.push(this.createPeriodEntry(periodCases[k], binNum));
}

return result;
}

private createPeriodEntry(periodData: DataEntry[], binNum: number): DataEntry {
const length = periodData.length;
let representativeCase: DataEntry = {
CASE_NUMBER: binNum.toString(),
RANK: 0,
AGE: 0,
SEX: periodData[0].SEX,
PERIOD: periodData[0].PERIOD,
TIME_BEFORE_DEATH: 0,
ALL_TYPES: 0,
HEALTH_ENCOUNTERS: 0,
OPIOID_PRESCRIPTIONS: 0,
INCARCERATIONS: 0,
OVERDOSES: 0,
NUM_ENCOUNTERS_TOTAL: 0,
AGE_RANK: 0,
HEALTH_RANK: 0,
OVERDOSE_RANK: 0,
INCARCERATIONS_RANK: 0,
PRESCRIPTIONS_RANK: 0,
FINAL_RANK: 0,
TIME_FIRST_OD: 0,
TIME_FIRST_RX: 0,
OD_DIFF: 0,
RX_DIFF: 0
};

periodData.forEach(value => {
representativeCase.RANK += value.RANK;
representativeCase.AGE += value.AGE;
representativeCase.TIME_BEFORE_DEATH += value.TIME_BEFORE_DEATH;
representativeCase.ALL_TYPES += value.ALL_TYPES;
representativeCase.HEALTH_ENCOUNTERS += value.HEALTH_ENCOUNTERS;
representativeCase.OPIOID_PRESCRIPTIONS += value.OPIOID_PRESCRIPTIONS;
representativeCase.INCARCERATIONS += value.INCARCERATIONS;
representativeCase.OVERDOSES += value.OVERDOSES;
representativeCase.NUM_ENCOUNTERS_TOTAL += value.NUM_ENCOUNTERS_TOTAL;
representativeCase.AGE_RANK += value.AGE_RANK;
representativeCase.HEALTH_RANK += value.HEALTH_RANK;
representativeCase.OVERDOSE_RANK += value.OVERDOSE_RANK;
representativeCase.INCARCERATIONS_RANK += value.INCARCERATIONS_RANK;
representativeCase.PRESCRIPTIONS_RANK += value.PRESCRIPTIONS_RANK;
representativeCase.FINAL_RANK += value.FINAL_RANK;
representativeCase.TIME_FIRST_OD += value.TIME_FIRST_OD;
representativeCase.TIME_FIRST_RX += value.TIME_FIRST_RX;
representativeCase.OD_DIFF += value.OD_DIFF;
representativeCase.RX_DIFF += value.RX_DIFF;
});

representativeCase = {
...representativeCase,
RANK: representativeCase.RANK/length,
AGE: representativeCase.AGE/length,
TIME_BEFORE_DEATH: representativeCase.TIME_BEFORE_DEATH/length,
ALL_TYPES: representativeCase.ALL_TYPES/length,
HEALTH_ENCOUNTERS: representativeCase.HEALTH_ENCOUNTERS/length,
OPIOID_PRESCRIPTIONS: representativeCase.OPIOID_PRESCRIPTIONS/length,
INCARCERATIONS: representativeCase.INCARCERATIONS/length,
OVERDOSES: representativeCase.OVERDOSES/length,
NUM_ENCOUNTERS_TOTAL: representativeCase.NUM_ENCOUNTERS_TOTAL/length,
AGE_RANK: representativeCase.AGE_RANK/length,
HEALTH_RANK: representativeCase.HEALTH_RANK/length,
OVERDOSE_RANK: representativeCase.OVERDOSE_RANK/length,
INCARCERATIONS_RANK: representativeCase.INCARCERATIONS_RANK/length,
PRESCRIPTIONS_RANK: representativeCase.PRESCRIPTIONS_RANK/length,
FINAL_RANK: representativeCase.FINAL_RANK/length,
TIME_FIRST_OD: representativeCase.TIME_FIRST_OD/length,
TIME_FIRST_RX: representativeCase.TIME_FIRST_RX/length,
OD_DIFF: representativeCase.OD_DIFF/length,
RX_DIFF: representativeCase.RX_DIFF/length
};

return representativeCase;
}

private filterByRank(data: DataEntry[]): DataEntry[] {
const { ranks } = this;
if (ranks === undefined) {
Expand Down
4 changes: 4 additions & 0 deletions website/src/app/shared/components/visualization-page/visualization-page.component.scss
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -45,6 +45,10 @@
z-index: 2;
left: 50%;
top: 50%;

&.smooth-hide {
z-index: 0;
}
}

.visualization {
Expand Down
2 changes: 1 addition & 1 deletion website/src/assets/pages/vis6-maps-of-health/data.sql
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -156,4 +156,4 @@ WITH
SELECT *
FROM FINAL
GROUP BY CASE_NUMBER, PERIOD
ORDER BY RANK ASC, PERIOD ASC
ORDER BY RANK ASC, PERIOD ASC
68 changes: 38 additions & 30 deletions website/src/assets/pages/vis6-maps-of-health/vis3.vl.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -319,6 +319,10 @@
"field": "RX_DIFF_VALUE",
"type": "quantitative",
"title": "Days from 1st prescription to death"
},
{
"field": "HEALTH_ENCOUNTERS",
"type": "quantitative"
}
]
}
Expand Down Expand Up @@ -532,42 +536,46 @@
]
},
{
"mark": "text",
"data": {
"name": "sortable"
},
"view": {
"strokeWidth": 0,
"strokeOpacity": 0
},
"params": [
"vconcat": [
{
"name": "sort_by__raw",
"select": {
"type": "point",
"toggle": false
"mark": "text",
"data": {
"name": "sortable"
},
"bind": "legend",
"value": [
"view": {
"strokeWidth": 0,
"strokeOpacity": 0
},
"params": [
{
"LABEL": "Health encounters"
"name": "sort_by__raw",
"select": {
"type": "point",
"toggle": false
},
"bind": "legend",
"value": [
{
"LABEL": "Health encounters"
}
]
}
],
"encoding": {
"opacity": {
"field": "LABEL",
"title": "Sort By",
"type": "ordinal",
"legend": {
"orient": "right",
"legendX": 0,
"legendY": 0,
"symbolSize": 0
}
}
]
}
],
"encoding": {
"opacity": {
"field": "LABEL",
"title": "Sort By",
"type": "ordinal",
"legend": {
"orient": "right",
"legendX": 0,
"legendY": 0,
"symbolSize": 0
}
}
}
]
}
],
"config": {
Expand Down
Loading