1 + 1
[1] 2
+diff --git a/Open-Source-Technology-in-Clinical-Data-Analysis.docx b/Open-Source-Technology-in-Clinical-Data-Analysis.docx new file mode 100644 index 0000000..e34b317 Binary files /dev/null and b/Open-Source-Technology-in-Clinical-Data-Analysis.docx differ diff --git a/Open-Source-Technology-in-Clinical-Data-Analysis.pdf b/Open-Source-Technology-in-Clinical-Data-Analysis.pdf new file mode 100644 index 0000000..540c269 Binary files /dev/null and b/Open-Source-Technology-in-Clinical-Data-Analysis.pdf differ diff --git a/assets/phuse.png b/assets/phuse.png new file mode 100644 index 0000000..82fee71 Binary files /dev/null and b/assets/phuse.png differ diff --git a/index.html b/index.html new file mode 100644 index 0000000..74f6bf5 --- /dev/null +++ b/index.html @@ -0,0 +1,506 @@ + +
+ + + + + + + + +This is a Quarto book.
+To learn more about Quarto books visit https://quarto.org/docs/books.
+1 + 1
[1] 2
+Open Source Technology in Clinical Data Analysis
+A significant amount of time and energy has been invested in recent years exploring the desirability (do we want it?), feasibility (can we do it?), and viability (is it worth it?) of integrating open source solutions into our clinical data pipelines which transform source data into clinical study reports and submission data packages.
+This repository will serve to collect and synthesize expert opinions and resources for a (hopefully) comprehensive set of questions which arise as organizations travel this journey.
+The discussions will provide citable (and sometimes quotable) input from industry experts, resulting in a “state of the union”-style manuscript that will help us move past questions that have already been sufficiently addressed and focus on those that remain.
+We invite you to navigate to the Discussions section section to provide your thoughts, resources, or perspectives that help address any or all of the questions. If we’ve overlooked a key question - start up a new discussion thread!
+There are many questions around understanding and using open source for clinical data analysis. We want to create a comprehesive knowledge base about the “state of the union” and provide an overview and ideally also answers for core questions. We need and collect input from our community to compile the knowledge base, so please join the discussions to allow a broad and complete picutre.
+If you like to know more, please join the R/Pharma talk “The State of Open Source Technology in Clinical Data Analysis, Reporting, and Submissions”. The recording will be made available after the conference.
+ + +${missingFields[0]}
field.`,
+ message: `The items being returned for this search do not include all the required fields. Please ensure that your index items include the ${missingFields[0]}
field or use index-fields
in your _quarto.yml
file to specify the field names.`,
+ };
+ } else if (missingFields.length > 1) {
+ const missingFieldList = missingFields
+ .map((field) => {
+ return `${field}
`;
+ })
+ .join(", ");
+
+ throw {
+ name: `Error: Search index is missing the following fields: ${missingFieldList}.`,
+ message: `The items being returned for this search do not include all the required fields. Please ensure that your index items includes the following fields: ${missingFieldList}, or use index-fields
in your _quarto.yml
file to specify the field names.`,
+ };
+ }
+ }
+}
+
+let lastQuery = null;
+function showCopyLink(query, options) {
+ const language = options.language;
+ lastQuery = query;
+ // Insert share icon
+ const inputSuffixEl = window.document.body.querySelector(
+ ".aa-Form .aa-InputWrapperSuffix"
+ );
+
+ if (inputSuffixEl) {
+ let copyButtonEl = window.document.body.querySelector(
+ ".aa-Form .aa-InputWrapperSuffix .aa-CopyButton"
+ );
+
+ if (copyButtonEl === null) {
+ copyButtonEl = window.document.createElement("button");
+ copyButtonEl.setAttribute("class", "aa-CopyButton");
+ copyButtonEl.setAttribute("type", "button");
+ copyButtonEl.setAttribute("title", language["search-copy-link-title"]);
+ copyButtonEl.onmousedown = (e) => {
+ e.preventDefault();
+ e.stopPropagation();
+ };
+
+ const linkIcon = "bi-clipboard";
+ const checkIcon = "bi-check2";
+
+ const shareIconEl = window.document.createElement("i");
+ shareIconEl.setAttribute("class", `bi ${linkIcon}`);
+ copyButtonEl.appendChild(shareIconEl);
+ inputSuffixEl.prepend(copyButtonEl);
+
+ const clipboard = new window.ClipboardJS(".aa-CopyButton", {
+ text: function (_trigger) {
+ const copyUrl = new URL(window.location);
+ copyUrl.searchParams.set(kQueryArg, lastQuery);
+ copyUrl.searchParams.set(kResultsArg, "1");
+ return copyUrl.toString();
+ },
+ });
+ clipboard.on("success", function (e) {
+ // Focus the input
+
+ // button target
+ const button = e.trigger;
+ const icon = button.querySelector("i.bi");
+
+ // flash "checked"
+ icon.classList.add(checkIcon);
+ icon.classList.remove(linkIcon);
+ setTimeout(function () {
+ icon.classList.remove(checkIcon);
+ icon.classList.add(linkIcon);
+ }, 1000);
+ });
+ }
+
+ // If there is a query, show the link icon
+ if (copyButtonEl) {
+ if (lastQuery && options["copy-button"]) {
+ copyButtonEl.style.display = "flex";
+ } else {
+ copyButtonEl.style.display = "none";
+ }
+ }
+ }
+}
+
+/* Search Index Handling */
+// create the index
+var fuseIndex = undefined;
+async function readSearchData() {
+ // Initialize the search index on demand
+ if (fuseIndex === undefined) {
+ // create fuse index
+ const options = {
+ keys: [
+ { name: "title", weight: 20 },
+ { name: "section", weight: 20 },
+ { name: "text", weight: 10 },
+ ],
+ ignoreLocation: true,
+ threshold: 0.1,
+ };
+ const fuse = new window.Fuse([], options);
+
+ // fetch the main search.json
+ const response = await fetch(offsetURL("search.json"));
+ if (response.status == 200) {
+ return response.json().then(function (searchDocs) {
+ searchDocs.forEach(function (searchDoc) {
+ fuse.add(searchDoc);
+ });
+ fuseIndex = fuse;
+ return fuseIndex;
+ });
+ } else {
+ return Promise.reject(
+ new Error(
+ "Unexpected status from search index request: " + response.status
+ )
+ );
+ }
+ }
+ return fuseIndex;
+}
+
+function inputElement() {
+ return window.document.body.querySelector(".aa-Form .aa-Input");
+}
+
+function focusSearchInput() {
+ setTimeout(() => {
+ const inputEl = inputElement();
+ if (inputEl) {
+ inputEl.focus();
+ }
+ }, 50);
+}
+
+/* Panels */
+const kItemTypeDoc = "document";
+const kItemTypeMore = "document-more";
+const kItemTypeItem = "document-item";
+const kItemTypeError = "error";
+
+function renderItem(
+ item,
+ createElement,
+ state,
+ setActiveItemId,
+ setContext,
+ refresh
+) {
+ switch (item.type) {
+ case kItemTypeDoc:
+ return createDocumentCard(
+ createElement,
+ "file-richtext",
+ item.title,
+ item.section,
+ item.text,
+ item.href
+ );
+ case kItemTypeMore:
+ return createMoreCard(
+ createElement,
+ item,
+ state,
+ setActiveItemId,
+ setContext,
+ refresh
+ );
+ case kItemTypeItem:
+ return createSectionCard(
+ createElement,
+ item.section,
+ item.text,
+ item.href
+ );
+ case kItemTypeError:
+ return createErrorCard(createElement, item.title, item.text);
+ default:
+ return undefined;
+ }
+}
+
+function createDocumentCard(createElement, icon, title, section, text, href) {
+ const iconEl = createElement("i", {
+ class: `bi bi-${icon} search-result-icon`,
+ });
+ const titleEl = createElement("p", { class: "search-result-title" }, title);
+ const titleContainerEl = createElement(
+ "div",
+ { class: "search-result-title-container" },
+ [iconEl, titleEl]
+ );
+
+ const textEls = [];
+ if (section) {
+ const sectionEl = createElement(
+ "p",
+ { class: "search-result-section" },
+ section
+ );
+ textEls.push(sectionEl);
+ }
+ const descEl = createElement("p", {
+ class: "search-result-text",
+ dangerouslySetInnerHTML: {
+ __html: text,
+ },
+ });
+ textEls.push(descEl);
+
+ const textContainerEl = createElement(
+ "div",
+ { class: "search-result-text-container" },
+ textEls
+ );
+
+ const containerEl = createElement(
+ "div",
+ {
+ class: "search-result-container",
+ },
+ [titleContainerEl, textContainerEl]
+ );
+
+ const linkEl = createElement(
+ "a",
+ {
+ href: offsetURL(href),
+ class: "search-result-link",
+ },
+ containerEl
+ );
+
+ const classes = ["search-result-doc", "search-item"];
+ if (!section) {
+ classes.push("document-selectable");
+ }
+
+ return createElement(
+ "div",
+ {
+ class: classes.join(" "),
+ },
+ linkEl
+ );
+}
+
+function createMoreCard(
+ createElement,
+ item,
+ state,
+ setActiveItemId,
+ setContext,
+ refresh
+) {
+ const moreCardEl = createElement(
+ "div",
+ {
+ class: "search-result-more search-item",
+ onClick: (e) => {
+ // Handle expanding the sections by adding the expanded
+ // section to the list of expanded sections
+ toggleExpanded(item, state, setContext, setActiveItemId, refresh);
+ e.stopPropagation();
+ },
+ },
+ item.title
+ );
+
+ return moreCardEl;
+}
+
+function toggleExpanded(item, state, setContext, setActiveItemId, refresh) {
+ const expanded = state.context.expanded || [];
+ if (expanded.includes(item.target)) {
+ setContext({
+ expanded: expanded.filter((target) => target !== item.target),
+ });
+ } else {
+ setContext({ expanded: [...expanded, item.target] });
+ }
+
+ refresh();
+ setActiveItemId(item.__autocomplete_id);
+}
+
+function createSectionCard(createElement, section, text, href) {
+ const sectionEl = createSection(createElement, section, text, href);
+ return createElement(
+ "div",
+ {
+ class: "search-result-doc-section search-item",
+ },
+ sectionEl
+ );
+}
+
+function createSection(createElement, title, text, href) {
+ const descEl = createElement("p", {
+ class: "search-result-text",
+ dangerouslySetInnerHTML: {
+ __html: text,
+ },
+ });
+
+ const titleEl = createElement("p", { class: "search-result-section" }, title);
+ const linkEl = createElement(
+ "a",
+ {
+ href: offsetURL(href),
+ class: "search-result-link",
+ },
+ [titleEl, descEl]
+ );
+ return linkEl;
+}
+
+function createErrorCard(createElement, title, text) {
+ const descEl = createElement("p", {
+ class: "search-error-text",
+ dangerouslySetInnerHTML: {
+ __html: text,
+ },
+ });
+
+ const titleEl = createElement("p", {
+ class: "search-error-title",
+ dangerouslySetInnerHTML: {
+ __html: ` ${title}`,
+ },
+ });
+ const errorEl = createElement("div", { class: "search-error" }, [
+ titleEl,
+ descEl,
+ ]);
+ return errorEl;
+}
+
+function positionPanel(pos) {
+ const panelEl = window.document.querySelector(
+ "#quarto-search-results .aa-Panel"
+ );
+ const inputEl = window.document.querySelector(
+ "#quarto-search .aa-Autocomplete"
+ );
+
+ if (panelEl && inputEl) {
+ panelEl.style.top = `${Math.round(panelEl.offsetTop)}px`;
+ if (pos === "start") {
+ panelEl.style.left = `${Math.round(inputEl.left)}px`;
+ } else {
+ panelEl.style.right = `${Math.round(inputEl.offsetRight)}px`;
+ }
+ }
+}
+
+/* Highlighting */
+// highlighting functions
+function highlightMatch(query, text) {
+ if (text) {
+ const start = text.toLowerCase().indexOf(query.toLowerCase());
+ if (start !== -1) {
+ const startMark = "";
+ const endMark = "";
+
+ const end = start + query.length;
+ text =
+ text.slice(0, start) +
+ startMark +
+ text.slice(start, end) +
+ endMark +
+ text.slice(end);
+ const startInfo = clipStart(text, start);
+ const endInfo = clipEnd(
+ text,
+ startInfo.position + startMark.length + endMark.length
+ );
+ text =
+ startInfo.prefix +
+ text.slice(startInfo.position, endInfo.position) +
+ endInfo.suffix;
+
+ return text;
+ } else {
+ return text;
+ }
+ } else {
+ return text;
+ }
+}
+
+function clipStart(text, pos) {
+ const clipStart = pos - 50;
+ if (clipStart < 0) {
+ // This will just return the start of the string
+ return {
+ position: 0,
+ prefix: "",
+ };
+ } else {
+ // We're clipping before the start of the string, walk backwards to the first space.
+ const spacePos = findSpace(text, pos, -1);
+ return {
+ position: spacePos.position,
+ prefix: "",
+ };
+ }
+}
+
+function clipEnd(text, pos) {
+ const clipEnd = pos + 200;
+ if (clipEnd > text.length) {
+ return {
+ position: text.length,
+ suffix: "",
+ };
+ } else {
+ const spacePos = findSpace(text, clipEnd, 1);
+ return {
+ position: spacePos.position,
+ suffix: spacePos.clipped ? "…" : "",
+ };
+ }
+}
+
+function findSpace(text, start, step) {
+ let stepPos = start;
+ while (stepPos > -1 && stepPos < text.length) {
+ const char = text[stepPos];
+ if (char === " " || char === "," || char === ":") {
+ return {
+ position: step === 1 ? stepPos : stepPos - step,
+ clipped: stepPos > 1 && stepPos < text.length,
+ };
+ }
+ stepPos = stepPos + step;
+ }
+
+ return {
+ position: stepPos - step,
+ clipped: false,
+ };
+}
+
+// removes highlighting as implemented by the mark tag
+function clearHighlight(searchterm, el) {
+ const childNodes = el.childNodes;
+ for (let i = childNodes.length - 1; i >= 0; i--) {
+ const node = childNodes[i];
+ if (node.nodeType === Node.ELEMENT_NODE) {
+ if (
+ node.tagName === "MARK" &&
+ node.innerText.toLowerCase() === searchterm.toLowerCase()
+ ) {
+ el.replaceChild(document.createTextNode(node.innerText), node);
+ } else {
+ clearHighlight(searchterm, node);
+ }
+ }
+ }
+}
+
+function escapeRegExp(string) {
+ return string.replace(/[.*+?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string
+}
+
+// highlight matches
+function highlight(term, el) {
+ const termRegex = new RegExp(term, "ig");
+ const childNodes = el.childNodes;
+
+ // walk back to front avoid mutating elements in front of us
+ for (let i = childNodes.length - 1; i >= 0; i--) {
+ const node = childNodes[i];
+
+ if (node.nodeType === Node.TEXT_NODE) {
+ // Search text nodes for text to highlight
+ const text = node.nodeValue;
+
+ let startIndex = 0;
+ let matchIndex = text.search(termRegex);
+ if (matchIndex > -1) {
+ const markFragment = document.createDocumentFragment();
+ while (matchIndex > -1) {
+ const prefix = text.slice(startIndex, matchIndex);
+ markFragment.appendChild(document.createTextNode(prefix));
+
+ const mark = document.createElement("mark");
+ mark.appendChild(
+ document.createTextNode(
+ text.slice(matchIndex, matchIndex + term.length)
+ )
+ );
+ markFragment.appendChild(mark);
+
+ startIndex = matchIndex + term.length;
+ matchIndex = text.slice(startIndex).search(new RegExp(term, "ig"));
+ if (matchIndex > -1) {
+ matchIndex = startIndex + matchIndex;
+ }
+ }
+ if (startIndex < text.length) {
+ markFragment.appendChild(
+ document.createTextNode(text.slice(startIndex, text.length))
+ );
+ }
+
+ el.replaceChild(markFragment, node);
+ }
+ } else if (node.nodeType === Node.ELEMENT_NODE) {
+ // recurse through elements
+ highlight(term, node);
+ }
+ }
+}
+
+/* Link Handling */
+// get the offset from this page for a given site root relative url
+function offsetURL(url) {
+ var offset = getMeta("quarto:offset");
+ return offset ? offset + url : url;
+}
+
+// read a meta tag value
+function getMeta(metaName) {
+ var metas = window.document.getElementsByTagName("meta");
+ for (let i = 0; i < metas.length; i++) {
+ if (metas[i].getAttribute("name") === metaName) {
+ return metas[i].getAttribute("content");
+ }
+ }
+ return "";
+}
+
+function algoliaSearch(query, limit, algoliaOptions) {
+ const { getAlgoliaResults } = window["@algolia/autocomplete-preset-algolia"];
+
+ const applicationId = algoliaOptions["application-id"];
+ const searchOnlyApiKey = algoliaOptions["search-only-api-key"];
+ const indexName = algoliaOptions["index-name"];
+ const indexFields = algoliaOptions["index-fields"];
+ const searchClient = window.algoliasearch(applicationId, searchOnlyApiKey);
+ const searchParams = algoliaOptions["params"];
+ const searchAnalytics = !!algoliaOptions["analytics-events"];
+
+ return getAlgoliaResults({
+ searchClient,
+ queries: [
+ {
+ indexName: indexName,
+ query,
+ params: {
+ hitsPerPage: limit,
+ clickAnalytics: searchAnalytics,
+ ...searchParams,
+ },
+ },
+ ],
+ transformResponse: (response) => {
+ if (!indexFields) {
+ return response.hits.map((hit) => {
+ return hit.map((item) => {
+ return {
+ ...item,
+ text: highlightMatch(query, item.text),
+ };
+ });
+ });
+ } else {
+ const remappedHits = response.hits.map((hit) => {
+ return hit.map((item) => {
+ const newItem = { ...item };
+ ["href", "section", "title", "text"].forEach((keyName) => {
+ const mappedName = indexFields[keyName];
+ if (
+ mappedName &&
+ item[mappedName] !== undefined &&
+ mappedName !== keyName
+ ) {
+ newItem[keyName] = item[mappedName];
+ delete newItem[mappedName];
+ }
+ });
+ newItem.text = highlightMatch(query, newItem.text);
+ return newItem;
+ });
+ });
+ return remappedHits;
+ }
+ },
+ });
+}
+
+function fuseSearch(query, fuse, fuseOptions) {
+ return fuse.search(query, fuseOptions).map((result) => {
+ const addParam = (url, name, value) => {
+ const anchorParts = url.split("#");
+ const baseUrl = anchorParts[0];
+ const sep = baseUrl.search("\\?") > 0 ? "&" : "?";
+ anchorParts[0] = baseUrl + sep + name + "=" + value;
+ return anchorParts.join("#");
+ };
+
+ return {
+ title: result.item.title,
+ section: result.item.section,
+ href: addParam(result.item.href, kQueryArg, query),
+ text: highlightMatch(query, result.item.text),
+ };
+ });
+}
diff --git a/summary.html b/summary.html
new file mode 100644
index 0000000..d4d8676
--- /dev/null
+++ b/summary.html
@@ -0,0 +1,487 @@
+
+
+
+
+
+
+
+
+
+In summary, this book has no content whatsoever.
+1 + 1
[1] 2
+