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Merge remote-tracking branch 'origin/main'
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@KunaalAgarwal
KunaalAgarwal committed Aug 2, 2023
2 parents e7b35ba + 6647a3b commit 011187f
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Showing 2 changed files with 115 additions and 74 deletions.
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189 changes: 115 additions & 74 deletions sdk/plot/drugUtilization.js
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Original file line number Diff line number Diff line change
Expand Up @@ -2,14 +2,11 @@ import {getAllData, plot} from "./plot.js";
import {convertDatasetToDistributionId, getDatasetByKeyword, getDatasetByTitleName} from "../metastore.js";
import {getDatastoreQuerySql} from "../sql.js";

let drugUtilDatasets;
let drugUtilIds;
//pre import retrieval
const drugUtilDatasets = (await getDatasetByKeyword("drug utilization")).slice(22); //only need datasets from 2013 onwards
const drugUtilIds = await Promise.all(drugUtilDatasets.map(async dataset => await convertDatasetToDistributionId(dataset.identifier)));

async function rawDrugUtil(ndcs, filter = "ndc", dataVariables = ["year", "total_amount_reimbursed", "number_of_prescriptions", "suppression_used"]){
if (drugUtilIds === undefined || drugUtilDatasets === undefined){
drugUtilDatasets = (await getDatasetByKeyword("drug utilization")).slice(22);//only need datasets from 2013 onwards
drugUtilIds = await Promise.all(drugUtilDatasets.map(async dataset => await convertDatasetToDistributionId(dataset.identifier)));
}
const adjustedNdcsList = Array.isArray(ndcs) ? ndcs : [ndcs];
if (!dataVariables.includes("suppression_used")) {
dataVariables.push("suppression_used");
Expand Down Expand Up @@ -41,7 +38,7 @@ async function getDrugUtilDataPlot(ndcs, axis= {x: "year", y: "total_amount_reim
return acc;
}, {xData: [], yData: [], y2Data: []});
result.xData.sort()
return [{x: result.xData, y: result.yData, name: axis.y}, {x: result.xData, y: result.y2Data, yaxis:'y2', name: axis.y2}]
return [{x: result.xData, y: result.yData, name: ndcs[0] + axis.y}, {x: result.xData, y: result.y2Data, yaxis:'y2', name: ndcs[0] + axis.y2}]
}

async function plotDrugUtil(ndcs, layout, div, axis) {
Expand All @@ -53,8 +50,9 @@ async function plotDrugUtil(ndcs, layout, div, axis) {
return plot(data.flat(), layout, "line", div);
}


async function getDrugUtilDataBar(ndc, yAxis = "total_amount_reimbursed", year = '2022') {
const drugUtil = await getDatasetByTitleName(`State Drug Utilization Data ${year}`);
const drugUtil = await getDatasetByTitleName("State Drug Utilization Data " + year);
const drugUtilId = await convertDatasetToDistributionId(drugUtil.identifier);
const response = await getDatastoreQuerySql(`[SELECT state,${yAxis},suppression_used FROM ${drugUtilId}][WHERE ndc = "${ndc}"]`);
const filteredData = response.filter(x => x["suppression_used"] === "false");
Expand Down Expand Up @@ -82,85 +80,128 @@ async function plotDrugUtilBar(ndc, layout, div, yAxis){
return plot(data, layout, "bar", div);
}

async function removedOutliers(data) {
const yValues = data.y.slice();
yValues.sort((a, b) => a - b);

// Calculate the quartiles and IQR
const q1 = yValues[Math.floor(yValues.length * 0.25)];
const q3 = yValues[Math.ceil(yValues.length * 0.75)];
const iqr = q3 - q1;
const maxValue = q3 + iqr * 1.5;
const minValue = q1 - iqr * 1.5;

return {
x: data.x.filter((_, i) => data.y[i] >= minValue && data.y[i] <= maxValue),
y: data.y.filter((y) => y >= minValue && y <= maxValue)
}
// Remove outliers from getDrugUtilDataBar
async function removedOutliers(ndc, yAxis, year) {
let data = await getDrugUtilDataBar(ndc, yAxis, year);
let refinedData = data['x'].map((o,i) => {return {x: o, y: data['y'][i]}})
refinedData.sort( function(a, b) {return a.y - b.y;});
let yValues = refinedData.map(o => o.y);

let q1 = yValues[Math.floor((yValues.length / 4))];
let q3 = yValues[Math.ceil((yValues.length * (3 / 4)))];
let iqr = q3 - q1;
let maxValue = q3 + iqr*1.5;
let minValue = q1 - iqr*1.5;

let nonOutlierPos = yValues.map((o,i) => {if((yValues[i] <= maxValue) && (yValues[i] >= minValue)) {return i}});
let nonOutliers = refinedData.filter((o,i) => nonOutlierPos.includes(i));

let res = {};
res['x'] = nonOutliers.map(o => o.x);
res['y'] = nonOutliers.map(o => o.y);
return res;
}

async function plotDrugUtilMap(ndc, outliers = true, div, yAxis, year) {
let data = await getDrugUtilDataBar(ndc, yAxis, year);
if (outliers) { data = await removedOutliers(data) }
const allStates = new Set(['AK', 'AL', 'AR', 'AZ', 'CA', 'CO', 'CT', 'DE', 'FL', 'GA', 'GU', 'HI', 'IA', 'ID',
'IL', 'IN', 'KS', 'KY', 'LA', 'MA', 'MD', 'ME', 'MI', 'MN', 'MO', 'MS', 'MT', 'NC', 'ND', 'NE',
'NH', 'NJ', 'NM', 'NV', 'NY', 'OH', 'OK', 'OR', 'PA', 'RI', 'SC', 'SD', 'TN', 'TX', 'UT', 'VA', 'VT', 'WA', 'WI', 'WV', 'WY']);

for (const state of allStates) {
if (!data.x.includes(state)) {
data.x.push(state);
data.y.push(-1);
}
async function choroplethMap(outliers = 'true', ndc = '00536105556', yAxis, year) {
let data;
if(outliers === 'true') {
data = await getDrugUtilDataBar(ndc, yAxis, year)
} else {
data = await removedOutliers(ndc, yAxis, year);
}

// Add missing states
let refinedData = {x: data['x'], y: data['y']};
let allStates = ['AK', 'AL', 'AR', 'AZ', 'CA', 'CO', 'CT', 'DE', 'FL', 'GA', 'GU', 'HI', 'IA', 'ID', 'IL', 'IN', 'KS', 'KY', 'LA', 'MA', 'MD', 'ME', 'MI', 'MN', 'MO', 'MS', 'MT', 'NC', 'ND', 'NE', 'NH', 'NJ', 'NM', 'NV', 'NY', 'OH', 'OK', 'OR', 'PA', 'RI', 'SC', 'SD', 'TN', 'TX', 'UT', 'VA', 'VT', 'WA', 'WI', 'WV', 'WY'];
allStates.forEach(s => {
if(!(data['x'].includes(s))) {
refinedData['x'].push(s);
refinedData['y'].push(-1);
}
})

var choroplethData = [{
type: 'choropleth',
locationmode: 'USA-states',
locations: data['x'],
z: data['y'],
//text: data['x'],
zmin: 0,
zmax: Math.max.apply(Math, data['y']),
colorscale: [
[0, 'rgb(211, 211, 211)'],
[0.001, 'rgb(242,240,247)'],
[0.01, 'rgb(242,240,247)'], [0.2, 'rgb(218,218,235)'],
[0.4, 'rgb(188,189,220)'], [0.6, 'rgb(158,154,200)'],
[0.8, 'rgb(117,107,177)'], [1, 'rgb(84,39,143)']
],
colorbar: {
title: 'Total Amount Reimbursed',
x: 1,
y: 0.6
},
marker: {
line:{
color: 'rgb(255,255,255)',
width: 2
}
}

let choroplethData = [{
type: 'choropleth',
locationmode: 'USA-states',
locations: data.x,
z: data.y,
zmin: 0,
zmax: Math.max(...data.y),
colorscale: [
[0, 'rgb(211, 211, 211)'],
[0.001, 'rgb(242,240,247)'],
[0.01, 'rgb(242,240,247)'], [0.2, 'rgb(218,218,235)'],
[0.4, 'rgb(188,189,220)'], [0.6, 'rgb(158,154,200)'],
[0.8, 'rgb(117,107,177)'], [1, 'rgb(84,39,143)']
],
colorbar: {
title: 'Total Amount Reimbursed',
x: 1,
y: 0.6
},
marker: {
line: {
color: 'rgb(255,255,255)',
width: 2
}
}
}];

let layout = {
title: '2022 US Total Amount Reimbursed by State',
geo: {
scope: 'usa',
showlakes: true,
lakecolor: 'rgb(255,255,255)'
},
width: 800,
height: 600

var layout = {
title: '2022 US Total Amount Reimbursed by State',
geo:{
scope: 'usa',
showlakes: true,
lakecolor: 'rgb(255,255,255)'
},
width: 1000, height: 600
};
return plot(choroplethData, layout, "choropleth", div);

const div = DOM.element("div");
Plotly.newPlot(div, choroplethData, layout);
return div;
}

async function getDrugUtilDataXX(ndc, yAxis) {
let range = 2022-2014+1;
let allYears = [...Array(range).keys()].map(o => 2014+o);
let res;
res = Promise.all(allYears.map(async (year,i) => {
let data = await sdk.getDrugUtilDataBar(ndc, yAxis, year);
return {year: year, xx: data['y'][data['x'].indexOf('XX')]};
})).then(refinedData => refinedData.filter(o => o.xx !== undefined));
return res
}

async function plotDrugUtilDataXX(ndc, yAxis) { //
let res = {};
let data = await getDrugUtilDataXX(ndc, yAxis);
res['x'] = data.map(o => o.year);
res['y'] = data.map(o => o.xx)
let layout = ({
title: {
text: "Total Amount Reimbursed for Aggregated States (XX)" ,
},
yaxis: {
title: {
text: 'Total Amount Reimbursed',
}
},
width: 1150
})
return sdk.plot([res], layout);
}

export {
//data retrieval
getDrugUtilData,
getDrugUtilDataBar,
plotDrugUtilMap,
removedOutliers,
choroplethMap,
getDrugUtilDataXX,
//plotting
plotDrugUtil,
plotDrugUtilBar
plotDrugUtilBar,
plotDrugUtilDataXX
}

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