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This repository includes code to conduct a clone-censor-weighted study of "initiate treatment within X days" using a modified cohort created from the Synthetic Medicare Public Use Files (SynPUF), as well as the base cohort itself. It includes code to study four different regimens: start treatment within 30 days of MI, start treatment within 90 days of MI, start treatment between 30 and 90 days of MI, and never start treatment. The first three regimens are the focus of the associated manuscript.

In addition to the base cohort file built from a modified version of the SynPUF data (baseccwcohort.sas7bdat) and included in the Data folder, this repository includes commented SAS (in the SAS_code folder) and R (in the R_code folder) code walking through a key aspects of a CCW study step-by-step including:

-Cloning and censoring the cohort (01_cloning_and_censoring_FINAL)

-Weighting each set of clones to account for selection bias (02a_weighting_0_30_FINAL, 02b_weighting_0_90_FINAL, 02c_weighting_30_90_FINAL, 02d_weighting_no_trt_FINAL)

-Estimating contrasts between each set of clones (03_estimating_effects_FINAL)

-Visualizing the difference in initiation timings across the different regimens (04_visualizing_exposure_FINAL)

-Calculating standardized mean differences to evaluate how well the IPCW balanced covariates at 30 or 90 days, depending on regimen (05a_SMD_assessment_0_30_FINAL, 05b_SMD_assessment_0_90_FINAL, and 05c_SMD_assessment_30_90_FINAL).

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, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
 blocks\n(function() {\n function addCopyButtons() {\n document.querySelectorAll('pre code').forEach(function(codeBlock) {\n if (codeBlock.parentElement.hasAttribute('data-copy-added')) return;\n codeBlock.parentElement.setAttribute('data-copy-added', 'true');\n \n var btn = document.createElement('button');\n btn.textContent = 'Copy';\n btn.style.cssText = 'position:absolute;top:4px;right:4px;padding:2px 8px;font-size:11px;background:#4ecdc4;border:none;border-radius:4px;color:#1a1a2e;cursor:pointer;opacity:0.7;transition:opacity 0.2s;';\n btn.onmouseover = function() { this.style.opacity = '1'; };\n btn.onmouseout = function() { this.style.opacity = '0.7'; };\n btn.onclick = function() {\n navigator.clipboard.writeText(codeBlock.textContent).then(function() {\n btn.textContent = 'Copied!';\n setTimeout(function() { btn.textContent = 'Copy'; }, 1500);\n });\n };\n codeBlock.parentElement.style.position = 'relative';\n codeBlock.parentElement.appendChild(btn);\n });\n }\n \n addCopyButtons();\n \n // Re-run on dynamic content\n var observer = new MutationObserver(addCopyButtons);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Add Copy Buttons to Code Blocks");
}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

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CCW_tutorial
This repository includes code to conduct a clone-censor-weighted study of "initiate treatment within X days" using a modified cohort created from the Synthetic Medicare Public Use Files (SynPUF), as well as the base cohort itself. It includes code to study four different regimens: start treatment within 30 days of MI, start treatment within 90 days of MI, start treatment between 30 and 90 days of MI, and never start treatment. The first three regimens are the focus of the associated manuscript.
In addition to the base cohort file built from a modified version of the SynPUF data (baseccwcohort.sas7bdat) and included in the Data folder, this repository includes commented SAS (in the SAS_code folder) and R (in the R_code folder) code walking through a key aspects of a CCW study step-by-step including:
-Cloning and censoring the cohort (01_cloning_and_censoring_FINAL)
-Weighting each set of clones to account for selection bias (02a_weighting_0_30_FINAL, 02b_weighting_0_90_FINAL, 02c_weighting_30_90_FINAL, 02d_weighting_no_trt_FINAL)
-Estimating contrasts between each set of clones (03_estimating_effects_FINAL)
-Visualizing the difference in initiation timings across the different regimens (04_visualizing_exposure_FINAL)
-Calculating standardized mean differences to evaluate how well the IPCW balanced covariates at 30 or 90 days, depending on regimen (05a_SMD_assessment_0_30_FINAL, 05b_SMD_assessment_0_90_FINAL, and 05c_SMD_assessment_30_90_FINAL).
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Force GitHub README to respect dark mode\n(function() {\n var style = document.createElement('style');\n style.textContent = '\n .markdown-body {\n color-scheme: dark light;\n }\n .markdown-body pre { background: #161b22 !important; }\n .markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }\n .markdown-body table th, .markdown-body table td { border-color: #30363d !important; }\n .markdown-body img { background: #0d1117; }\n .markdown-body blockquote { border-left-color: #8b949e; }\n .markdown-body hr { border-color: #30363d; }\n ';\n document.head.appendChild(style);\n})();", "GitHub Dark Mode README Fix");
}
} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
})();
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var __m = "*";
var __re = new RegExp('^' + ".*" + '

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CCW_tutorial
This repository includes code to conduct a clone-censor-weighted study of "initiate treatment within X days" using a modified cohort created from the Synthetic Medicare Public Use Files (SynPUF), as well as the base cohort itself. It includes code to study four different regimens: start treatment within 30 days of MI, start treatment within 90 days of MI, start treatment between 30 and 90 days of MI, and never start treatment. The first three regimens are the focus of the associated manuscript.
In addition to the base cohort file built from a modified version of the SynPUF data (baseccwcohort.sas7bdat) and included in the Data folder, this repository includes commented SAS (in the SAS_code folder) and R (in the R_code folder) code walking through a key aspects of a CCW study step-by-step including:
-Cloning and censoring the cohort (01_cloning_and_censoring_FINAL)
-Weighting each set of clones to account for selection bias (02a_weighting_0_30_FINAL, 02b_weighting_0_90_FINAL, 02c_weighting_30_90_FINAL, 02d_weighting_no_trt_FINAL)
-Estimating contrasts between each set of clones (03_estimating_effects_FINAL)
-Visualizing the difference in initiation timings across the different regimens (04_visualizing_exposure_FINAL)
-Calculating standardized mean differences to evaluate how well the IPCW balanced covariates at 30 or 90 days, depending on regimen (05a_SMD_assessment_0_30_FINAL, 05b_SMD_assessment_0_90_FINAL, and 05c_SMD_assessment_30_90_FINAL).
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if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Highlight search terms from Google/DuckDuckGo/Bing referrer\n(function() {\n var ref = document.referrer;\n var terms = [];\n \n if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {\n var url = new URL(ref);\n var q = url.searchParams.get('q') || url.searchParams.get('p');\n if (q) {\n terms = q.split(/\\s+/).filter(function(t) { return t.length > 2; });\n }\n }\n \n if (terms.length === 0) return;\n \n var style = document.createElement('style');\n style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';\n document.head.appendChild(style);\n \n function highlight(node) {\n if (node.nodeType === 3) { // text node\n var text = node.textContent;\n var found = false;\n terms.forEach(function(term) {\n var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\') + ')', 'gi');\n if (regex.test(text)) {\n found = true;\n var frag = document.createDocumentFragment();\n var parts = text.split(regex);\n parts.forEach(function(part, i) {\n if (i % 2 === 0) {\n frag.appendChild(document.createTextNode(part));\n } else {\n var span = document.createElement('span');\n span.className = 'userscript-highlight';\n span.textContent = part;\n frag.appendChild(span);\n }\n });\n node.parentNode.replaceChild(frag, node);\n }\n });\n } else if (node.nodeType === 1 && node.childNodes) { // element\n var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];\n if (!skipTags.includes(node.tagName)) {\n Array.from(node.childNodes).forEach(highlight);\n }\n }\n }\n \n highlight(document.body);\n \n // Re-highlight on dynamic content\n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1 || node.nodeType === 3) highlight(node);\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Highlight Search Terms");
}
} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
})();
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try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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CCW_tutorial
This repository includes code to conduct a clone-censor-weighted study of "initiate treatment within X days" using a modified cohort created from the Synthetic Medicare Public Use Files (SynPUF), as well as the base cohort itself. It includes code to study four different regimens: start treatment within 30 days of MI, start treatment within 90 days of MI, start treatment between 30 and 90 days of MI, and never start treatment. The first three regimens are the focus of the associated manuscript.
In addition to the base cohort file built from a modified version of the SynPUF data (baseccwcohort.sas7bdat) and included in the Data folder, this repository includes commented SAS (in the SAS_code folder) and R (in the R_code folder) code walking through a key aspects of a CCW study step-by-step including:
-Cloning and censoring the cohort (01_cloning_and_censoring_FINAL)
-Weighting each set of clones to account for selection bias (02a_weighting_0_30_FINAL, 02b_weighting_0_90_FINAL, 02c_weighting_30_90_FINAL, 02d_weighting_no_trt_FINAL)
-Estimating contrasts between each set of clones (03_estimating_effects_FINAL)
-Visualizing the difference in initiation timings across the different regimens (04_visualizing_exposure_FINAL)
-Calculating standardized mean differences to evaluate how well the IPCW balanced covariates at 30 or 90 days, depending on regimen (05a_SMD_assessment_0_30_FINAL, 05b_SMD_assessment_0_90_FINAL, and 05c_SMD_assessment_30_90_FINAL).
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Strip utm_, fbclid, gclid, etc. from all links on page\n(function() {\n var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',\n 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',\n 'ref', 'ref_src', 'source', 'medium', 'campaign'];\n \n function cleanUrl(url) {\n try {\n var u = new URL(url, window.location.origin);\n var changed = false;\n trackingParams.forEach(function(p) {\n if (u.searchParams.has(p)) {\n u.searchParams.delete(p);\n changed = true;\n }\n });\n return changed ? u.toString() : url;\n } catch (e) {\n return url;\n }\n }\n \n function cleanLinks() {\n document.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n \n cleanLinks();\n \n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1) {\n if (node.tagName === 'A') cleanLinks();\n node.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Remove Tracking Parameters from Links");
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '

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CCW_tutorial
This repository includes code to conduct a clone-censor-weighted study of "initiate treatment within X days" using a modified cohort created from the Synthetic Medicare Public Use Files (SynPUF), as well as the base cohort itself. It includes code to study four different regimens: start treatment within 30 days of MI, start treatment within 90 days of MI, start treatment between 30 and 90 days of MI, and never start treatment. The first three regimens are the focus of the associated manuscript.
In addition to the base cohort file built from a modified version of the SynPUF data (baseccwcohort.sas7bdat) and included in the Data folder, this repository includes commented SAS (in the SAS_code folder) and R (in the R_code folder) code walking through a key aspects of a CCW study step-by-step including:
-Cloning and censoring the cohort (01_cloning_and_censoring_FINAL)
-Weighting each set of clones to account for selection bias (02a_weighting_0_30_FINAL, 02b_weighting_0_90_FINAL, 02c_weighting_30_90_FINAL, 02d_weighting_no_trt_FINAL)
-Estimating contrasts between each set of clones (03_estimating_effects_FINAL)
-Visualizing the difference in initiation timings across the different regimens (04_visualizing_exposure_FINAL)
-Calculating standardized mean differences to evaluate how well the IPCW balanced covariates at 30 or 90 days, depending on regimen (05a_SMD_assessment_0_30_FINAL, 05b_SMD_assessment_0_90_FINAL, and 05c_SMD_assessment_30_90_FINAL).
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Auto-enable theater mode on YouTube\n(function() {\n function tryTheater() {\n var btn = document.querySelector('button[aria-label=\"Theater mode\"], ytd-player #player button[title=\"Theater mode\"]');\n if (btn && !btn.classList.contains('activated')) {\n btn.click();\n }\n }\n \n // Try immediately\n tryTheater();\n \n // Try after navigation (SPA)\n var lastUrl = location.href;\n setInterval(function() {\n if (location.href !== lastUrl) {\n lastUrl = location.href;\n setTimeout(tryTheater, 500);\n }\n }, 1000);\n \n // Also try on player load\n var observer = new MutationObserver(tryTheater);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "YouTube Theater Mode Default");
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
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var __m = "*";
var __re = new RegExp('^' + ".*" + '

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CCW_tutorial
This repository includes code to conduct a clone-censor-weighted study of "initiate treatment within X days" using a modified cohort created from the Synthetic Medicare Public Use Files (SynPUF), as well as the base cohort itself. It includes code to study four different regimens: start treatment within 30 days of MI, start treatment within 90 days of MI, start treatment between 30 and 90 days of MI, and never start treatment. The first three regimens are the focus of the associated manuscript.
In addition to the base cohort file built from a modified version of the SynPUF data (baseccwcohort.sas7bdat) and included in the Data folder, this repository includes commented SAS (in the SAS_code folder) and R (in the R_code folder) code walking through a key aspects of a CCW study step-by-step including:
-Cloning and censoring the cohort (01_cloning_and_censoring_FINAL)
-Weighting each set of clones to account for selection bias (02a_weighting_0_30_FINAL, 02b_weighting_0_90_FINAL, 02c_weighting_30_90_FINAL, 02d_weighting_no_trt_FINAL)
-Estimating contrasts between each set of clones (03_estimating_effects_FINAL)
-Visualizing the difference in initiation timings across the different regimens (04_visualizing_exposure_FINAL)
-Calculating standardized mean differences to evaluate how well the IPCW balanced covariates at 30 or 90 days, depending on regimen (05a_SMD_assessment_0_30_FINAL, 05b_SMD_assessment_0_90_FINAL, and 05c_SMD_assessment_30_90_FINAL).
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Remove or un-stick sticky/fixed headers that block content\n(function() {\n function unstick() {\n document.querySelectorAll('header, nav, [role=\"banner\"], .header, .navbar, .sticky, .fixed-top, [style*=\"position: fixed\"], [style*=\"position:sticky\"]').forEach(function(el) {\n if (el.style.position === 'fixed' || el.style.position === 'sticky' || \n getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {\n el.style.position = 'static';\n el.style.top = 'auto';\n el.style.zIndex = 'auto';\n }\n });\n }\n \n unstick();\n \n var observer = new MutationObserver(unstick);\n observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });\n})();", "Kill Sticky Headers");
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
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var __m = "*";
var __re = new RegExp('^' + ".*" + '

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CCW_tutorial
This repository includes code to conduct a clone-censor-weighted study of "initiate treatment within X days" using a modified cohort created from the Synthetic Medicare Public Use Files (SynPUF), as well as the base cohort itself. It includes code to study four different regimens: start treatment within 30 days of MI, start treatment within 90 days of MI, start treatment between 30 and 90 days of MI, and never start treatment. The first three regimens are the focus of the associated manuscript.
In addition to the base cohort file built from a modified version of the SynPUF data (baseccwcohort.sas7bdat) and included in the Data folder, this repository includes commented SAS (in the SAS_code folder) and R (in the R_code folder) code walking through a key aspects of a CCW study step-by-step including:
-Cloning and censoring the cohort (01_cloning_and_censoring_FINAL)
-Weighting each set of clones to account for selection bias (02a_weighting_0_30_FINAL, 02b_weighting_0_90_FINAL, 02c_weighting_30_90_FINAL, 02d_weighting_no_trt_FINAL)
-Estimating contrasts between each set of clones (03_estimating_effects_FINAL)
-Visualizing the difference in initiation timings across the different regimens (04_visualizing_exposure_FINAL)
-Calculating standardized mean differences to evaluate how well the IPCW balanced covariates at 30 or 90 days, depending on regimen (05a_SMD_assessment_0_30_FINAL, 05b_SMD_assessment_0_90_FINAL, and 05c_SMD_assessment_30_90_FINAL).
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Universal Dark Mode - works on any site\n(function() {\n var enabled = true;\n \n function applyDarkMode() {\n if (!enabled) return;\n \n // Create style element if it doesn't exist\n var style = document.getElementById('universal-dark-mode-style');\n if (!style) {\n style = document.createElement('style');\n style.id = 'universal-dark-mode-style';\n document.head.appendChild(style);\n }\n \n // Dark mode CSS - inverts colors but preserves images/video\n style.textContent = '\n /* Invert everything except media */\n html {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #1a1a2e !important;\n }\n \n /* Restore images, videos, iframes, canvas */\n img, video, iframe, canvas, svg, picture, [style*=\"background-image\"] {\n filter: invert(1) hue-rotate(180deg) !important;\n }\n \n /* Preserve specific elements that should not be inverted */\n .no-dark-mode, .no-dark-mode *,\n [data-theme=\"light\"], [data-theme=\"light\"],\n .ace_editor, .ace_editor *,\n .CodeMirror, .CodeMirror *,\n .monaco-editor, .monaco-editor *,\n .markdown-body pre, .markdown-body pre *,\n .highlight, .highlight *,\n pre code, pre code * {\n filter: none !important;\n }\n \n /* Fix common UI elements */\n .modal, .popup, .dropdown-menu, .tooltip, .popover {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #2d2d44 !important;\n border-color: #444 !important;\n }\n \n /* Scrollbars */\n ::-webkit-scrollbar { background: #1a1a2e !important; }\n ::-webkit-scrollbar-thumb { background: #444 !important; }\n ::-webkit-scrollbar-thumb:hover { background: #555 !important; }\n \n /* Selection */\n ::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ';\n }\n \n function removeDarkMode() {\n var style = document.getElementById('universal-dark-mode-style');\n if (style) style.remove();\n }\n \n // Toggle with Alt+Shift+D\n document.addEventListener('keydown', function(e) {\n if (e.altKey && e.shiftKey && e.key === 'D') {\n e.preventDefault();\n enabled = !enabled;\n if (enabled) {\n applyDarkMode();\n console.log('[Universal Dark Mode] Enabled');\n } else {\n removeDarkMode();\n console.log('[Universal Dark Mode] Disabled');\n }\n }\n });\n \n // Apply on load\n applyDarkMode();\n \n // Re-apply on dynamic content\n var observer = new MutationObserver(function(mutations) {\n if (enabled && !document.getElementById('universal-dark-mode-style')) {\n applyDarkMode();\n }\n });\n observer.observe(document.head, { childList: true });\n \n console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');\n})();", "Universal Dark Mode");
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
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This repository includes code to conduct a clone-censor-weighted study of "initiate treatment within X days" using a modified cohort created from the Synthetic Medicare Public Use Files (SynPUF), as well as the base cohort itself. It includes code to study four different regimens: start treatment within 30 days of MI, start treatment within 90 days of MI, start treatment between 30 and 90 days of MI, and never start treatment. The first three regimens are the focus of the associated manuscript.
In addition to the base cohort file built from a modified version of the SynPUF data (baseccwcohort.sas7bdat) and included in the Data folder, this repository includes commented SAS (in the SAS_code folder) and R (in the R_code folder) code walking through a key aspects of a CCW study step-by-step including:
-Cloning and censoring the cohort (01_cloning_and_censoring_FINAL)
-Weighting each set of clones to account for selection bias (02a_weighting_0_30_FINAL, 02b_weighting_0_90_FINAL, 02c_weighting_30_90_FINAL, 02d_weighting_no_trt_FINAL)
-Estimating contrasts between each set of clones (03_estimating_effects_FINAL)
-Visualizing the difference in initiation timings across the different regimens (04_visualizing_exposure_FINAL)
-Calculating standardized mean differences to evaluate how well the IPCW balanced covariates at 30 or 90 days, depending on regimen (05a_SMD_assessment_0_30_FINAL, 05b_SMD_assessment_0_90_FINAL, and 05c_SMD_assessment_30_90_FINAL).
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Code to conduct a clone-censor-weighted study of "initiate treatment within X days" in synthetic Medicare data
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