diff --git a/README.md b/README.md index 5349f23..ea05a92 100644 --- a/README.md +++ b/README.md @@ -27,7 +27,7 @@ them. | 11/19 and 11/21 | R packages II | | | | 11/26 and 11/28 (off) | Automatic Reports with GitHub Actions | [slides](https://UofUEpiBio.github.io/PHS7045-advanced-programming/15-autoreport/slides.html) ([source](https://github.com/UofUEpiBio/PHS7045-advanced-programming//tree/main/15-autoreport/slides.qmd)) | | | 12/03 and 12/05 (hybrid) | Final Prep (Hackathon) | | | -| 12/12 | Final | | | +| 12/10 (pkg) and 12/12 (talk) | Final ([Requirements](https://UofUEpiBio.github.io/PHS7045-advanced-programming/exams/final.html)) | | | ## Assignment workflow diff --git a/exams/02-final.html b/exams/02-final.html index dea0e6b..47908d3 100644 --- a/exams/02-final.html +++ b/exams/02-final.html @@ -2,7 +2,7 @@ - + @@ -19,6 +19,40 @@ width: 0.8em; margin: 0 0.8em 0.2em -1em; vertical-align: middle; } + +pre > code.sourceCode { white-space: pre; position: relative; } +pre > code.sourceCode > span { line-height: 1.25; } +pre > code.sourceCode > span:empty { height: 1.2em; } +.sourceCode { overflow: visible; } +code.sourceCode > span { color: inherit; text-decoration: inherit; } +div.sourceCode { margin: 1em 0; } +pre.sourceCode { margin: 0; } +@media screen { +div.sourceCode { overflow: auto; } +} +@media print { +pre > code.sourceCode { white-space: pre-wrap; } +pre > code.sourceCode > span { display: inline-block; text-indent: -5em; padding-left: 5em; } +} +pre.numberSource code +{ counter-reset: source-line 0; } +pre.numberSource code > span +{ position: relative; left: -4em; counter-increment: source-line; } +pre.numberSource code > span > a:first-child::before +{ content: counter(source-line); +position: relative; left: -1em; text-align: right; vertical-align: baseline; +border: none; display: inline-block; +-webkit-touch-callout: none; -webkit-user-select: none; +-khtml-user-select: none; -moz-user-select: none; +-ms-user-select: none; user-select: none; +padding: 0 4px; width: 4em; +} +pre.numberSource { margin-left: 3em; padding-left: 4px; } +div.sourceCode +{ } +@media screen { +pre > code.sourceCode > span > a:first-child::before { text-decoration: underline; } +} @@ -36,7 +70,49 @@ composed: false, }); +const layoutMarginEls = () => { + // Find any conflicting margin elements and add margins to the + // top to prevent overlap + const marginChildren = window.document.querySelectorAll( + ".column-margin.column-container > *, .margin-caption, .aside" + ); + + let lastBottom = 0; + for (const marginChild of marginChildren) { + if (marginChild.offsetParent !== null) { + // clear the top margin so we recompute it + marginChild.style.marginTop = null; + const top = marginChild.getBoundingClientRect().top + window.scrollY; + if (top < lastBottom) { + const marginChildStyle = window.getComputedStyle(marginChild); + const marginBottom = parseFloat(marginChildStyle["marginBottom"]); + const margin = lastBottom - top + marginBottom; + marginChild.style.marginTop = `${margin}px`; + } + const styles = window.getComputedStyle(marginChild); + const marginTop = parseFloat(styles["marginTop"]); + lastBottom = top + marginChild.getBoundingClientRect().height + marginTop; + } + } +}; + window.document.addEventListener("DOMContentLoaded", function (_event) { + // Recompute the position of margin elements anytime the body size changes + if (window.ResizeObserver) { + const resizeObserver = new window.ResizeObserver( + throttle(() => { + layoutMarginEls(); + if ( + window.document.body.getBoundingClientRect().width < 990 && + isReaderMode() + ) { + quartoToggleReader(); + } + }, 50) + ); + resizeObserver.observe(window.document.body); + } + const tocEl = window.document.querySelector('nav.toc-active[role="doc-toc"]'); const sidebarEl = window.document.getElementById("quarto-sidebar"); const leftTocEl = window.document.getElementById("quarto-sidebar-toc-left"); @@ -83,7 +159,7 @@ if (link.href.indexOf("#") !== -1) { const anchor = link.href.split("#")[1]; const heading = window.document.querySelector( - `[data-anchor-id=${anchor}]` + `[data-anchor-id="${anchor}"]` ); if (heading) { // Add the class @@ -123,8 +199,10 @@ window.innerHeight + window.pageYOffset >= window.document.body.offsetHeight ) { + // This is the no-scroll case where last section should be the active one sectionIndex = 0; } else { + // This finds the last section visible on screen that should be made active sectionIndex = [...sections].reverse().findIndex((section) => { if (section) { return window.pageYOffset >= section.offsetTop - sectionMargin; @@ -306,6 +384,7 @@ for (const child of el.children) { child.style.opacity = 0; child.style.overflow = "hidden"; + child.style.pointerEvents = "none"; } nexttick(() => { @@ -347,6 +426,7 @@ const clone = child.cloneNode(true); clone.style.opacity = 1; + clone.style.pointerEvents = null; clone.style.display = null; toggleContents.append(clone); } @@ -421,6 +501,7 @@ for (const child of el.children) { child.style.opacity = 1; child.style.overflow = null; + child.style.pointerEvents = null; } const placeholderEl = window.document.getElementById( @@ -462,32 +543,6 @@ }; }; - // Find any conflicting margin elements and add margins to the - // top to prevent overlap - const marginChildren = window.document.querySelectorAll( - ".column-margin.column-container > * " - ); - - const layoutMarginEls = () => { - let lastBottom = 0; - for (const marginChild of marginChildren) { - if (marginChild.offsetParent !== null) { - // clear the top margin so we recompute it - marginChild.style.marginTop = null; - const top = marginChild.getBoundingClientRect().top + window.scrollY; - if (top < lastBottom) { - const margin = lastBottom - top; - marginChild.style.marginTop = `${margin}px`; - } - const styles = window.getComputedStyle(marginChild); - const marginTop = parseFloat(styles["marginTop"]); - lastBottom = - top + marginChild.getBoundingClientRect().height + marginTop; - } - } - }; - nexttick(layoutMarginEls); - const tabEls = document.querySelectorAll('a[data-bs-toggle="tab"]'); for (const tabEl of tabEls) { const id = tabEl.getAttribute("data-bs-target"); @@ -497,7 +552,6 @@ ); if (columnEl) tabEl.addEventListener("shown.bs.tab", function (event) { - const el = event.srcElement; if (el) { const visibleCls = `${el.id}-margin-content`; @@ -755,6 +809,7 @@ // Process the collapse state if this is an UL if (el.tagName === "UL") { if (tocOpenDepth === -1 && depth > 1) { + // toc-expand: false el.classList.add("collapse"); } else if ( depth <= tocOpenDepth || @@ -773,10 +828,9 @@ }; // walk the TOC and expand / collapse any items that should be shown - if (tocEl) { - walk(tocEl, 0); updateActiveLink(); + walk(tocEl, 0); } // Throttle the scroll event and walk peridiocally @@ -795,6 +849,10 @@ window.addEventListener( "resize", throttle(() => { + if (tocEl) { + updateActiveLink(); + walk(tocEl, 0); + } if (!isReaderMode()) { hideOverlappedSidebars(); } @@ -915,10 +973,10 @@ } - + - - + @@ -2984,38 +3097,38 @@

Advanced Programming with R: Final

+ +

Due date

-

There are two due dates: Thursday, May 2nd (presentation) and May 4th (R package), 2023.

+

The R package is due by the end of Tuesday December 10th.

+

The in-class presentation will be Thursday, December 12th.

Task

-

This will be an extension of the package submitted for the midterm. The new component will be agreed upon on the week of April 17th.

+

Expand upon midterm project with a new component and create an R package. The new component will be agreed upon on by Thursday November 21.

Deliverables

Requirements

-

The presentation (May 2nd):

-
-
-

Grading

-

The grade will be based on clear communication and coding.

+
+

Misc

+
+

Installing the package with the vignettes

+

You can install this package from the source using the following commands from the command line:

+
R CMD build .
+R CMD INSTALL egpkg2024_1.0.tar.gz
+

The first command builds a tar.gz file that can be shared. This is what you share when you submit to CRAN. The second command installs the package in your computer. Notice that this approach builds the vignettes, making them available to your R session. Recall you can access vignettes using the vignette command like this:

+
vignette(package="dplyr")
+

Which will list the vignettes available to the dplyr R package (learn more typing ?vignette in your R console).

+
@@ -3085,18 +3207,7 @@

Grading

} return false; } - const clipboard = new window.ClipboardJS('.code-copy-button', { - text: function(trigger) { - const codeEl = trigger.previousElementSibling.cloneNode(true); - for (const childEl of codeEl.children) { - if (isCodeAnnotation(childEl)) { - childEl.remove(); - } - } - return codeEl.innerText; - } - }); - clipboard.on('success', function(e) { + const onCopySuccess = function(e) { // button target const button = e.trigger; // don't keep focus @@ -3128,11 +3239,50 @@

Grading

}, 1000); // clear code selection e.clearSelection(); + } + const getTextToCopy = function(trigger) { + const codeEl = trigger.previousElementSibling.cloneNode(true); + for (const childEl of codeEl.children) { + if (isCodeAnnotation(childEl)) { + childEl.remove(); + } + } + return codeEl.innerText; + } + const clipboard = new window.ClipboardJS('.code-copy-button:not([data-in-quarto-modal])', { + text: getTextToCopy }); - function tippyHover(el, contentFn) { + clipboard.on('success', onCopySuccess); + if (window.document.getElementById('quarto-embedded-source-code-modal')) { + // For code content inside modals, clipBoardJS needs to be initialized with a container option + // TODO: Check when it could be a function (https://github.com/zenorocha/clipboard.js/issues/860) + const clipboardModal = new window.ClipboardJS('.code-copy-button[data-in-quarto-modal]', { + text: getTextToCopy, + container: window.document.getElementById('quarto-embedded-source-code-modal') + }); + clipboardModal.on('success', onCopySuccess); + } + var localhostRegex = new RegExp(/^(?:http|https):\/\/localhost\:?[0-9]*\//); + var mailtoRegex = new RegExp(/^mailto:/); + var filterRegex = new RegExp('/' + window.location.host + '/'); + var isInternal = (href) => { + return filterRegex.test(href) || localhostRegex.test(href) || mailtoRegex.test(href); + } + // Inspect non-navigation links and adorn them if external + var links = window.document.querySelectorAll('a[href]:not(.nav-link):not(.navbar-brand):not(.toc-action):not(.sidebar-link):not(.sidebar-item-toggle):not(.pagination-link):not(.no-external):not([aria-hidden]):not(.dropdown-item):not(.quarto-navigation-tool):not(.about-link)'); + for (var i=0; iGrading interactive: true, interactiveBorder: 10, theme: 'quarto', - placement: 'bottom-start' + placement: 'bottom-start', }; + if (contentFn) { + config.content = contentFn; + } + if (onTriggerFn) { + config.onTrigger = onTriggerFn; + } + if (onUntriggerFn) { + config.onUntrigger = onUntriggerFn; + } window.tippy(el, config); } const noterefs = window.document.querySelectorAll('a[role="doc-noteref"]'); @@ -3155,7 +3314,130 @@

Grading

try { href = new URL(href).hash; } catch {} const id = href.replace(/^#\/?/, ""); const note = window.document.getElementById(id); - return note.innerHTML; + if (note) { + return note.innerHTML; + } else { + return ""; + } + }); + } + const xrefs = window.document.querySelectorAll('a.quarto-xref'); + const processXRef = (id, note) => { + // Strip column container classes + const stripColumnClz = (el) => { + el.classList.remove("page-full", "page-columns"); + if (el.children) { + for (const child of el.children) { + stripColumnClz(child); + } + } + } + stripColumnClz(note) + if (id === null || id.startsWith('sec-')) { + // Special case sections, only their first couple elements + const container = document.createElement("div"); + if (note.children && note.children.length > 2) { + container.appendChild(note.children[0].cloneNode(true)); + for (let i = 1; i < note.children.length; i++) { + const child = note.children[i]; + if (child.tagName === "P" && child.innerText === "") { + continue; + } else { + container.appendChild(child.cloneNode(true)); + break; + } + } + if (window.Quarto?.typesetMath) { + window.Quarto.typesetMath(container); + } + return container.innerHTML + } else { + if (window.Quarto?.typesetMath) { + window.Quarto.typesetMath(note); + } + return note.innerHTML; + } + } else { + // Remove any anchor links if they are present + const anchorLink = note.querySelector('a.anchorjs-link'); + if (anchorLink) { + anchorLink.remove(); + } + if (window.Quarto?.typesetMath) { + window.Quarto.typesetMath(note); + } + // TODO in 1.5, we should make sure this works without a callout special case + if (note.classList.contains("callout")) { + return note.outerHTML; + } else { + return note.innerHTML; + } + } + } + for (var i=0; i res.text()) + .then(html => { + const parser = new DOMParser(); + const htmlDoc = parser.parseFromString(html, "text/html"); + const note = htmlDoc.getElementById(id); + if (note !== null) { + const html = processXRef(id, note); + instance.setContent(html); + } + }).finally(() => { + instance.enable(); + instance.show(); + }); + } + } else { + // See if we can fetch a full url (with no hash to target) + // This is a special case and we should probably do some content thinning / targeting + fetch(url) + .then(res => res.text()) + .then(html => { + const parser = new DOMParser(); + const htmlDoc = parser.parseFromString(html, "text/html"); + const note = htmlDoc.querySelector('main.content'); + if (note !== null) { + // This should only happen for chapter cross references + // (since there is no id in the URL) + // remove the first header + if (note.children.length > 0 && note.children[0].tagName === "HEADER") { + note.children[0].remove(); + } + const html = processXRef(null, note); + instance.setContent(html); + } + }).finally(() => { + instance.enable(); + instance.show(); + }); + } + }, function(instance) { }); } let selectedAnnoteEl; @@ -3199,6 +3481,7 @@

Grading

} div.style.top = top - 2 + "px"; div.style.height = height + 4 + "px"; + div.style.left = 0; let gutterDiv = window.document.getElementById("code-annotation-line-highlight-gutter"); if (gutterDiv === null) { gutterDiv = window.document.createElement("div"); @@ -3224,6 +3507,32 @@

Grading

}); selectedAnnoteEl = undefined; }; + // Handle positioning of the toggle + window.addEventListener( + "resize", + throttle(() => { + elRect = undefined; + if (selectedAnnoteEl) { + selectCodeLines(selectedAnnoteEl); + } + }, 10) + ); + function throttle(fn, ms) { + let throttle = false; + let timer; + return (...args) => { + if(!throttle) { // first call gets through + fn.apply(this, args); + throttle = true; + } else { // all the others get throttled + if(timer) clearTimeout(timer); // cancel #2 + timer = setTimeout(() => { + fn.apply(this, args); + timer = throttle = false; + }, ms); + } + }; + } // Attach click handler to the DT const annoteDls = window.document.querySelectorAll('dt[data-target-cell]'); for (const annoteDlNode of annoteDls) { @@ -3287,4 +3596,5 @@

Grading

+ \ No newline at end of file diff --git a/exams/02-final.qmd b/exams/02-final.qmd index bab149d..2477ab4 100644 --- a/exams/02-final.qmd +++ b/exams/02-final.qmd @@ -7,38 +7,38 @@ format: ## Due date -There are two due dates: Thursday, May 2nd (presentation) and May 4th (R package), 2023. +The R package is due by the end of Tuesday December 10th. + +The in-class presentation will be Thursday, December 12th. ## Task -This will be an extension of the package submitted for the midterm. The new component will be agreed upon on the week of April 17th. +Expand upon midterm project with a new component and create an R package. The new component will be agreed upon on by Thursday November 21. ## Deliverables -* An extension of the package developed for the midterm (70% of grade). +* An extension of the midterm project and package creation (70% of grade). * An oral presentation of no more than seven minutes (30% of grade). ## Requirements -The presentation (May 2nd): - - - The time allocation will be the same as the midterm (7 minutes). +Grading will be based on the following: - - It Should be presented with slides (PowerPoint/quarto::revealjs/google slides/etc.) +The presentation: - - It should have the following structure (roughly): +- [ ] The time allocation will be 7 minutes (5/100 points of penalty per extra minute). - a. Review of the problem which highlights the issue or “why” the problem needs solving (may consider including visuals to highlight the issue; ~2 slides) +- [ ] Presentation should be clear. - b. Overview of the package until the midterm (~1 slide) +- [ ] It Should be presented with slides using quarto. - c. The new feature of the package (~ 1 slide each) +- [ ] Review of the problem which highlights the issue or “why” the problem needs solving (may consider including visuals to highlight the issue; ~2 slides) - d. Problem/motive +- [ ] Overview of the package until the midterm (~1 slide) - e. Solution +- [ ] The new feature of the coding solution (other than the R package itself; ~ 1 slide each) - f. Example +- [ ] Provide a single example highlighting the package (~1-3 slides). ::: {.callout-tip} @@ -46,7 +46,6 @@ The presentation (May 2nd): (ii) More figures and less text, *i.e.*, avoid paragraphs. (iii) Avoid diving into the details (or at least, most of your talk should be to the general audience). (iv) Focus on what your audience would value the most. -(v) Cluttered slides are never good: It probably needs to be split if they are too long. ::: ```{r} @@ -54,17 +53,40 @@ The presentation (May 2nd): fa <- fontawesome::fa("jedi-order") ``` -The R package (May 4th `r fa`): +The R package: + +- [ ] Add a new function/feature to the R package using parallel computing or `Rcpp` (a must.) + +- [ ] The package should have a `README.md` file with a brief description of the package. + +- [ ] The package should pass `R CMD check`s using macOS, Ubuntu, and Windows for the R release and development versions (x6 `R CMD check`s). Notes are OK, but warnings are not (recall the `usethis::use_github_action...` function). -- Add a new function/feature to the R package using parallel computing or `Rcpp` (a must.) +- [ ] The package should pass the `R CMD check` on Ubuntu using the R release version with the option [`--as-cran`](https://cran.r-project.org/web/packages/submission_checklist.html) (more strict `R CMD check`.) -- The package should pass `R CMD check`s using macOS, Ubuntu, and Windows for the R release and development versions (x6 `R CMD check`s). Notes are OK, but warnings are not. +- [ ] The package should have a vignette that illustrates the use of the functions in the package. -- The package should pass the `R CMD check` on Ubuntu using the R release version with the option [`--as-cran`](https://cran.r-project.org/web/packages/submission_checklist.html) (more strict `R CMD check`.) +# Misc +## Installing the package with the vignettes +You can install this package from the source using the following +commands from the command line: -## Grading +``` bash +R CMD build . +R CMD INSTALL egpkg2024_1.0.tar.gz +``` + +The first command builds a tar.gz file that can be shared. This is what +you share when you submit to CRAN. The second command installs the +package in your computer. Notice that this approach builds the +vignettes, making them available to your R session. Recall you can +access vignettes using the `vignette` command like this: + +``` r +vignette(package="dplyr") +``` -The grade will be based on clear communication and coding. \ No newline at end of file +Which will list the vignettes available to the dplyr R package (learn +more typing `?vignette` in your R console). diff --git a/pages.csv b/pages.csv index aaad61c..ff9f056 100644 --- a/pages.csv +++ b/pages.csv @@ -15,4 +15,4 @@ date,week,name,id,issue,extra 11/19 and 11/21,14,R packages II,,, 11/26 and 11/28 (off),15,Automatic Reports with GitHub Actions,15-autoreport,, 12/03 and 12/05 (hybrid),16,Final Prep (Hackathon),,, -12/12,17,Final,,, +12/10 (pkg) and 12/12 (talk),17,Final,,,([Requirements](https://UofUEpiBio.github.io/PHS7045-advanced-programming/exams/final.html))