31:T552,### Drug costs and mortality hypothesis: Increasing drug prices are associated with nonadherence leading to higher mortality. Exposure: Drug costs Outcome: Diabetes death covered medicaid, expansion of medicaid by state. Check if coverage varies by state. Check rates of obesity. More descriptive. --- # Drug and mortality data sources (private, IBM and public, CDC Wonder ### IBM Redbook database: The purpose of RED BOOK is to allow comprehensive access to current and accurate drug pricing and description information. https://www.nlm.nih.gov/research/umls/rxnorm/sourcereleasedocs/mmx.html#:~:text=The%20purpose%20of%20RED%20BOOK,drug%20pricing%20and%20description%20information.&text=RED%20BOOK%20covers%20FDA%2Dapproved,counter%20drugs%2C%20and%20nondrug%20products. ### IBM MarketScan Commercial Database and pricing data from SSR Health, LLC: Pharmacy claims for patients under employer insurance. https://pubmed.ncbi.nlm.nih.gov/33295971/ ### CDC drug overdose data by drug type: https://www.cdc.gov/nchs/nvss/vsrr/drug-overdose-data.htm ### death categories, CDC Wonder: https://wonder.cdc.gov/wonder/help/mcd-provisional.html#ICD-10%20Changes ![image.png](${await FileAttachment("image.png").url()}) --- ### National Vital Statistics System multiple-cause-of-death database ![image@1.png](${await FileAttachment("image@1.png").url()}) ---32:T565,cdcData = (await fetchp("https://wonder.cdc.gov/controller/datarequest/D76", { // fetch with proxy method: 'POST', // body: { // "request_xml": // //xmlParameters by year and race // // { // // "b_parameters" : { // // "B_1": "D76.V1-level1", // // "B_2": "D76.V8", // // "B_3": "*None*", // // "B_4": "*None*", // // "B_5": "*None*" // // }, // // "m_parameters" : { // // "M_1": "D76.M1", // Deaths, must be included // // "M_2": "D76.M2", //Population, must be included // // "M_3": "D76.M3", //Crude rate, must be included // // "M_31": "D76.M31", //Standard error (crude rate) // // "M_32": "D76.M32" , // 95% confidence interval (crude rate) // // "M_41": "D76.M41", // Standard error (age-adjusted rate) // // "M_42": "D76.M42" // 95% confidence interval (age-adjusted rate) // // } // // } // xmlParameters // , // "accept_datause_restrictions": "true", // } }) //.then(response => response.text()).then(response => console.log(response)) .then(response => response.text()))//.split("\n")//.then(xml => xmlToObject(xml)))//.replace(/\t/g,'')//.replace(/\r/g,'') 33:T536,//createParameterList = function (parameterList){ // python hekper function // def createParameterList(parameterList): // """Helper function to create a parameter list from a dictionary object""" // parameterString = "" // for key in parameterList: // parameterString += "\n" // parameterString += "" + key + "\n" // if isinstance(parameterList[key], list): // for value in parameterList[key]: // parameterString += "" + value + "\n" // else: // parameterString += "" + parameterList[key] + "\n" // parameterString += "\n" // return parameterString // let parameterString = "" // for (let key in parameterList){ // parameterString += "\n" // parameterString += "" + key + "\n" // if (instanceOf(parameterList[key], list)){ // for (let value in parameterList[key]){ // parameterString += "" + value + "\n" // } // } else{ // parameterString += "" + parameterList[key] + "\n" // } // parameterString += "\n" // } // return parameterString // }34:T2cfb,xmlParameters = ` B_1 D76.V1-level1 B_2 D76.V8 B_3 *None* B_4 *None* B_5 *None* F_D76.V1 2009 2010 2011 2012 2013 F_D76.V10 *All* F_D76.V2 C00-D48 F_D76.V27 *All* F_D76.V9 *All* I_D76.V1 2009 (2009) 2010 (2010) 2011 (2011) 2012 (2012) 2013 (2013) I_D76.V10 *All* (The United States) I_D76.V2 C00-D48 (Neoplasms) I_D76.V27 *All* (The United States) I_D76.V9 *All* (The United States) M_1 D76.M1 M_2 D76.M2 M_3 D76.M3 M_41 D76.M41 M_42 D76.M42 O_V10_fmode freg O_V1_fmode freg O_V27_fmode freg O_V2_fmode freg O_V9_fmode freg O_aar aar_std O_aar_pop 0000 O_age D76.V5 O_javascript on O_location D76.V9 O_precision 1 O_rate_per 100000 O_show_totals true O_timeout 300 O_title Example1 O_ucd D76.V2 O_urban D76.V19 VM_D76.M6_D76.V10 VM_D76.M6_D76.V17 *All* VM_D76.M6_D76.V1_S *All* VM_D76.M6_D76.V7 *All* VM_D76.M6_D76.V8 *All* V_D76.V1 V_D76.V10 V_D76.V11 *All* V_D76.V12 *All* V_D76.V17 *All* V_D76.V19 *All* V_D76.V2 V_D76.V20 *All* V_D76.V21 *All* V_D76.V22 *All* V_D76.V23 *All* V_D76.V24 *All* V_D76.V25 *All* V_D76.V27 V_D76.V4 *All* V_D76.V5 1 1-4 5-14 15-24 25-34 35-44 45-54 55-64 65-74 75-84 85+ V_D76.V51 *All* V_D76.V52 *All* V_D76.V6 00 V_D76.V7 *All* V_D76.V8 *All* V_D76.V9 action-Send Send finder-stage-D76.V1 codeset finder-stage-D76.V10 codeset finder-stage-D76.V2 codeset finder-stage-D76.V27 codeset finder-stage-D76.V9 codeset stage request ` //var data = // "\nB_1\nD76.V1-level1\n\n" // "" + key + "\n" //{ // // group by year and race // "b_parameters" : { // "B_1": "D76.V1-level1", // "B_2": "D76.V8", // "B_3": "*None*", // "B_4": "*None*", // "B_5": "*None*"} // , // // include deaths, population, and crude rate // "m_parameters" : { // "M_1": "D76.M1", // Deaths, must be included // "M_2": "D76.M2", // Population, must be included // "M_3": "D76.M3", // Crude rate, must be included // "M_31": "D76.M31", // Standard error (crude rate) // "M_32": "D76.M32", // 95% confidence interval (crude rate) // "M_41": "D76.M41", // Standard error (age-adjusted rate) // "M_42": "D76.M42" // 95% confidence interval (age-adjusted rate) // }, // // include all years, months, census regions, hhs regions, states. Only include ICD-10 K00-K92 for disease of the digestive system // "f_parameters" : { // "F_D76.V1": ["*All*"], // year/month // "F_D76.V10": ["*All*"], // Census Regions - dont change // "F_D76.V2": ["K00-K92"], // ICD-10 Codes // "F_D76.V27": ["*All*"], // HHS Regions - dont change // "F_D76.V9": ["*All*"] // State County - dont change // }, // // include all dates, census regions, hhs regions, and states. // "i_parameters" : { // "I_D76.V1": "*All* (All Dates)", // year/month // "I_D76.V10": "*All* (The United States)", // Census Regions - dont change // "I_D76.V2": "K00-K92 (Diseases of the digestive system)", // ICD-10 Codes // "I_D76.V27": "*All* (The United States)", // HHS Regions - dont change // "I_D76.V9": "*All* (The United States)" // State County - dont change // }, // // For this example, we want to include ten-year age groups for ages 15-44. // // For all other categories, include all values // "v_parameters" : { // "V_D76.V1": "", // Year/Month // "V_D76.V10": "", // Census Regions // "V_D76.V11": "*All*", // 2006 Urbanization // "V_D76.V12": "*All*", // ICD-10 130 Cause List (Infants) // "V_D76.V17": "*All*", // Hispanic Origin // "V_D76.V19": "*All*", // 2013 Urbanization // "V_D76.V2": "", // ICD-10 Codes // "V_D76.V20": "*All*", // Autopsy // "V_D76.V21": "*All*", // Place of Death // "V_D76.V22": "*All*", // Injury Intent // "V_D76.V23": "*All*", // Injury Mechanism and All Other Leading Causes // "V_D76.V24": "*All*", // Weekday // "V_D76.V25": "*All*", // Drug/Alcohol Induced Causes // "V_D76.V27": "", // HHS Regions // "V_D76.V4": "*All*", // ICD-10 113 Cause List // "V_D76.V5": ["15-24", "25-34", "35-44"], // Ten-Year Age Groups // "V_D76.V51": "*All*", // Five-Year Age Groups // "V_D76.V52": "*All*", // Single-Year Ages // "V_D76.V6": "00", // Infant Age Groups // "V_D76.V7": "*All*", // Gender // "V_D76.V8": "*All*", // Race // "V_D76.V9": "" // State/County // }, // //For this example, include age-adjusted rates, use ten-year age groups (D76.V5), use state location by default, // //show rates per 100,000, use 2013 urbanization and use ICD-10 Codes (D76.V2) for cause of death category // "o_parameters" : { // "O_V10_fmode": "freg", // Use regular finder and ignore v parameter value // "O_V1_fmode": "freg", // Use regular finder and ignore v parameter value // "O_V27_fmode": "freg", // Use regular finder and ignore v parameter value // "O_V2_fmode": "freg", // Use regular finder and ignore v parameter value // "O_V9_fmode": "freg", // Use regular finder and ignore v parameter value // "O_aar": "aar_std", // age-adjusted rates // "O_aar_pop": "0000", // population selection for age-adjusted rates // "O_age": "D76.V5", // select age-group (e.g. ten-year, five-year, single-year, infant groups) // "O_javascript": "on", // Set to on by default // "O_location": "D76.V9", // select location variable to use (e.g. state/county, census, hhs regions) // "O_precision": "1", // decimal places // "O_rate_per": "100000", // rates calculated per X persons // "O_show_totals": "false", // Show totals for // "O_timeout": "300", // "O_title": "Digestive Disease Deaths, by Age Group", // title for data run // "O_ucd": "D76.V2", // select underlying cause of death category // "O_urban": "D76.V19" // select urbanization category // }, // // values for non-standard age adjusted rates (see mortality online databases). // // For this example, these parameters are ignored as standard age adjusted rates are used // "vm_parameters" : { // "VM_D76.M6_D76.V10": "", // Location // "VM_D76.M6_D76.V17": "*All*", // Hispanic-Origin // "VM_D76.M6_D76.V1_S": "*All*", // Year // "VM_D76.M6_D76.V7": "*All*", // Gender // "VM_D76.M6_D76.V8": "*All*" // Race // }, // // Miscellaneous hidden inputs/parameters usually passed by web form. These do not change. // "misc_parameters" : { // "action-Send": "Send", // "finder-stage-D76.V1": "codeset", // "finder-stage-D76.V1": "codeset", // "finder-stage-D76.V2": "codeset", // "finder-stage-D76.V27": "codeset", // "finder-stage-D76.V9": "codeset", // "stage": "request" // } //} // return data 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2f:{"title":"drugUtilization","cells":[{"id":3,"value":"# drugUtilization","pinned":false,"hidden":false,"mode":"md"},{"id":6,"value":"$31","pinned":false,"hidden":false,"mode":"md"},{"id":175,"value":"## CDC Detailed Mortality 1999-2013","pinned":false,"hidden":false,"mode":"md"},{"id":241,"value":"Parameters: https://github.com/alipphardt/cdc-wonder-api","pinned":false,"hidden":false,"mode":"md"},{"id":177,"value":"D76 is the online database for Detailed Mortality 1999-2013, at https://wonder.cdc.gov/ucd-icd10.html.","pinned":false,"hidden":false,"mode":"md"},{"id":362,"value":"cdcData2 = await fetchp(\"https://wonder.cdc.gov/controller/datarequest/D76\")","pinned":true,"hidden":false,"mode":"ojs"},{"id":33,"value":"$32","pinned":true,"hidden":false,"mode":"ojs"},{"id":187,"value":"## _ Parse XML_","pinned":false,"hidden":false,"mode":"md"},{"id":165,"value":"xml = (new DOMParser).parseFromString(cdcData,\"application/xml\")","pinned":true,"hidden":false,"mode":"ojs"},{"id":167,"value":"xmlTitle = xml.querySelector('html').textContent","pinned":true,"hidden":false,"mode":"ojs"},{"id":179,"value":"_Can't get the data into the notebook, just on the console here:_","pinned":false,"hidden":false,"mode":"md"},{"id":83,"value":"dt = {\nlet parseXml;\nif (typeof window.DOMParser != \"undefined\") {\n parseXml = function(xmlStr) {\n console.log('xmlDoc',new window.DOMParser().parseFromString(xmlStr, \"text/xml\"))\n \n return new window.DOMParser().parseFromString(xmlStr, \"text/xml\");\n };\n} else if (typeof window.ActiveXObject != \"undefined\" &&\n new window.ActiveXObject(\"Microsoft.XMLDOM\")) {\n parseXml = function(xmlStr) {\n var xmlDoc = new window.ActiveXObject(\"Microsoft.XMLDOM\");\n xmlDoc.async = \"false\";\n xmlDoc.loadXML(xmlStr);\n console.log('xmlDoc',xmlDoc)\n return xmlDoc;\n };\n} else {\n throw new Error(\"No XML parser found\");\n}\nreturn parseXml(cdcData);\n}","pinned":true,"hidden":true,"mode":"ojs"},{"id":118,"value":"---","pinned":false,"hidden":false,"mode":"md"},{"id":113,"value":"# Appendix","pinned":false,"hidden":false,"mode":"md"},{"id":258,"value":"xml2js = require(await FileAttachment(\"xml2js.js\").url())","pinned":true,"hidden":false,"mode":"ojs"},{"id":270,"value":"parser = new xml2js.Parser();","pinned":true,"hidden":false,"mode":"ojs"},{"id":246,"value":"function xmlToObject(xml) {\n\n return new Promise( function (resolve, reject) {\n\n // transform xml string to an object using xml2js for example\n parser.parseString(xml, function(error, obj) {\n\n if (error) reject(error)\n console.log(\"error----------------\",error)\n resolve(obj)\n })\n })\n}","pinned":true,"hidden":false,"mode":"ojs"},{"id":155,"value":"import {scrape,requireFromGithub,requireScript,load } from \"@bumbeishvili/fetcher\"","pinned":true,"hidden":false,"mode":"ojs"},{"id":126,"value":"d3 = require('d3')","pinned":true,"hidden":false,"mode":"ojs"},{"id":209,"value":"import {fetchp} from \"@tomlarkworthy/fetchp\"","pinned":true,"hidden":false,"mode":"ojs"},{"id":195,"value":"$33","pinned":true,"hidden":false,"mode":"ojs"},{"id":223,"value":"cdcData.split(\"\\n\").slice(150,170)","pinned":true,"hidden":false,"mode":"ojs"},{"id":321,"value":"// {\n// var jdata = new Object();\n// var params = xmlParameters;\n// var url = \"https://corsproxy.io/?https://wonder.cdc.gov/controller/datarequest/D76\"\n// var xhttp = new XMLHttpRequest();\n// xhttp.open(\"POST\", url, true);\n// xhttp.setRequestHeader('Content-Type', 'application/xml');\n\n// console.log(\"xhttp\",xhttp);\n\n// xhttp.onreadystatechange = function() {\n// console.log(\"this.status,this.readyState\",this.status,this.readyState);\n// console.log(\"this.readyState == 4 && this.status == 200\",this.readyState == 4 && this.status == 200);\n// if (this.readyState == 4 && this.status == 200) {\n// console.log(\"this.responseText:\",this);\n// }\n// console.log(\"this.responseText:\",this);\n\n// //console.log(\"this.status,this.readyState\",this.status,this.readyState);\n// }\n// xhttp.send(params);\n// }","pinned":true,"hidden":false,"mode":"ojs"},{"id":58,"value":"$34","pinned":true,"hidden":false,"mode":"ojs"}],"files":"$W35","stdlib":"1","titling":"auto"}