diff --git a/_freeze/index/execute-results/html.json b/_freeze/index/execute-results/html.json index 84f2dff..5fb3bf9 100644 --- a/_freeze/index/execute-results/html.json +++ b/_freeze/index/execute-results/html.json @@ -1,11 +1,9 @@ { - "hash": "05073b6be830a860edae5533f98c6bfa", + "hash": "bd5e899c4855a84d6ccaf8793ad30381", "result": { "engine": "knitr", - "markdown": "---\ntitle: Reproducibility and Data Science in R\nsubtitle: \"Fall 2024\"\nformat: html\ncitation:\n title: Syllabus\n---\n\n\n\n\nWelcome to the syllabus for the CCT Data Science fall workshop series: **Reproducibility and Data Science in R.** If you didn't register for the course this year, sign up for our [mailing list](https://datascience.cct.arizona.edu/contact) to be notified when enrollment opens for next year's iteration and to be notified of our other monthly workshops.\n\n## Schedule\n\nWe'll meet on Tuesdays and Thursdays from 11am to 1pm via Zoom (link pinned in Slack channel)\n\n\n\n\n\n\n\n::: {.cell}\n::: {.cell-output-display}\n\n```{=html}\n
\n\n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n \n \n
LessonDateThemeTopicLinks
1Tue, 9/3Manage & OrganizeProject managment and documentation
\n
2Thu, 9/5Document & PublishLiterate programming with Quarto
\n
3Tue, 9/10Share & CollaborateFile systems and command line
\n
4Thu, 9/12Share & CollaborateVersion control with git
\n
5Tue, 9/17Share & CollaborateDeveloping code on GitHub
\n
6Thu, 9/19Share & CollaborateCollaborating with GitHub
\n
7Tue, 9/24Tidy & WrangleData manipulation & coding best practices
\n
8Thu, 9/26Repeat & ReproduceIntermediate R programming I
\n
9Tue, 10/1Repeat & ReproduceIntermediate R programming II—
10Thu, 10/3Document & PublishGetting credit for your hard work—
11Tue, 10/8ReviewDrop-in co-working—
12Thu, 10/10Reproducibility ColloquiumAn opportunity for you to show off what you've learned—
\n
\n```\n\n:::\n:::\n\n\n\n\n## Code of Conduct\n\n> Our group's mission is to enable scientists.\n> This means treating people with respect and responding in a polite and helpful way.\n>\n> Our group is committed to ensuring a harassment-free experience for everyone, regardless of level of experience, gender, gender identity and expression, sexual orientation, disability, personal appearance, body size, race, ethnicity, age, or religion.\n>\n> Examples of unacceptable behavior by members, collaborators, and contributors include: the use of sexual language or imagery, derogatory comments or personal attacks, trolling, public or private harassment, insults, or other unprofessional conduct.\n\nRead our full [code of conduct](https://cct-datascience.github.io/group-procedures/code-of-conduct.html) and please report any violations or concerns to the course instructors or to Kristina Riemer ([kristinariemer\\@arizona.edu](mailto:kristinariemer@arizona.edu)).\n\n## Helpful Reads\n\nThis workshop series doesn't have anything like \"required reading\", but we think these books and websites are good companions.\n\nData analysis in R:\n\n- [R for Data Science (2e)](https://r4ds.hadley.nz/)\n- [Building reproducible analytical pipelines with R](https://raps-with-r.dev/) \n\nBest practices for reproducibility:\n\n- [Good enough practices in scientific computing](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005510)\n- [Data organization in spreadsheets](https://doi.org/10.1080/00031305.2017.1375989)\n- [A beginner's guide to conducting reproducible research](https://doi.org/10.1002/bes2.1801)\n- [The Turing Way: Guide for Reproducible Research](https://the-turing-way.netlify.app/reproducible-research/reproducible-research)\n- [6 Steps Toward Reproducible Research](https://zenodo.org/records/12744715)\n\nVersion control:\n\n- [Excuse me, do you have a moment to talk about version control?](https://doi.org/10.7287/peerj.preprints.3159v2)\n- [Happy Git and GitHub for the useR](https://happygitwithr.com/)\n", - "supporting": [ - "index_files" - ], + "markdown": "---\ntitle: Reproducibility and Data Science in R\nsubtitle: \"Fall 2024\"\nformat: html\ncitation:\n title: Syllabus\n---\n\n\n\n\nWelcome to the syllabus for the CCT Data Science fall workshop series: **Reproducibility and Data Science in R.** If you didn't register for the course this year, sign up for our [mailing list](https://datascience.cct.arizona.edu/contact) to be notified when enrollment opens for next year's iteration and to be notified of our other monthly workshops.\n\n## Schedule\n\nWe'll meet on Tuesdays and Thursdays from 11am to 1pm via Zoom (link pinned in Slack channel)\n\n\n\n\n\n\n::: {.cell}\n::: {.cell-output-display}\n\n```{=html}\n
\n\n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n \n \n
LessonDateThemeTopicLinks
1Tue, 9/3Manage & OrganizeProject managment and documentation
\n
2Thu, 9/5Document & PublishLiterate programming with Quarto
\n
3Tue, 9/10Share & CollaborateFile systems and command line
\n
4Thu, 9/12Share & CollaborateVersion control with git
\n
5Tue, 9/17Share & CollaborateDeveloping code on GitHub
\n
6Thu, 9/19Share & CollaborateCollaborating with GitHub
\n
7Tue, 9/24Tidy & WrangleData manipulation & coding best practices
\n
8Thu, 9/26Repeat & ReproduceIntermediate R programming I
\n
9Tue, 10/1Repeat & ReproduceIntermediate R programming II—
10Thu, 10/3Document & PublishGetting credit for your hard work—
11Tue, 10/8ReviewDrop-in co-working—
12Thu, 10/10Reproducibility ColloquiumAn opportunity for you to show off what you've learned
\n
\n```\n\n:::\n:::\n\n\n\n\n## Code of Conduct\n\n> Our group's mission is to enable scientists.\n> This means treating people with respect and responding in a polite and helpful way.\n>\n> Our group is committed to ensuring a harassment-free experience for everyone, regardless of level of experience, gender, gender identity and expression, sexual orientation, disability, personal appearance, body size, race, ethnicity, age, or religion.\n>\n> Examples of unacceptable behavior by members, collaborators, and contributors include: the use of sexual language or imagery, derogatory comments or personal attacks, trolling, public or private harassment, insults, or other unprofessional conduct.\n\nRead our full [code of conduct](https://cct-datascience.github.io/group-procedures/code-of-conduct.html) and please report any violations or concerns to the course instructors or to Kristina Riemer ([kristinariemer\\@arizona.edu](mailto:kristinariemer@arizona.edu)).\n\n## Helpful Reads\n\nThis workshop series doesn't have anything like \"required reading\", but we think these books and websites are good companions.\n\nData analysis in R:\n\n- [R for Data Science (2e)](https://r4ds.hadley.nz/)\n- [Building reproducible analytical pipelines with R](https://raps-with-r.dev/) \n\nBest practices for reproducibility:\n\n- [Good enough practices in scientific computing](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005510)\n- [Data organization in spreadsheets](https://doi.org/10.1080/00031305.2017.1375989)\n- [A beginner's guide to conducting reproducible research](https://doi.org/10.1002/bes2.1801)\n- [The Turing Way: Guide for Reproducible Research](https://the-turing-way.netlify.app/reproducible-research/reproducible-research)\n- [6 Steps Toward Reproducible Research](https://zenodo.org/records/12744715)\n\nVersion control:\n\n- [Excuse me, do you have a moment to talk about version control?](https://doi.org/10.7287/peerj.preprints.3159v2)\n- [Happy Git and GitHub for the useR](https://happygitwithr.com/)\n", + "supporting": [], "filters": [ "rmarkdown/pagebreak.lua" ], diff --git a/_freeze/site_libs/revealjs/dist/theme/quarto.css b/_freeze/site_libs/revealjs/dist/theme/quarto.css index c35eaa0..e96ab76 100644 --- a/_freeze/site_libs/revealjs/dist/theme/quarto.css +++ b/_freeze/site_libs/revealjs/dist/theme/quarto.css @@ -5,4 +5,4 @@ * we also add `bright-[color]-` synonyms for the `-[color]-intense` classes since * that seems to be what ansi_up emits * -*/.ansi-black-fg{color:#3e424d}.ansi-black-bg{background-color:#3e424d}.ansi-black-intense-black,.ansi-bright-black-fg{color:#282c36}.ansi-black-intense-black,.ansi-bright-black-bg{background-color:#282c36}.ansi-red-fg{color:#e75c58}.ansi-red-bg{background-color:#e75c58}.ansi-red-intense-red,.ansi-bright-red-fg{color:#b22b31}.ansi-red-intense-red,.ansi-bright-red-bg{background-color:#b22b31}.ansi-green-fg{color:#00a250}.ansi-green-bg{background-color:#00a250}.ansi-green-intense-green,.ansi-bright-green-fg{color:#007427}.ansi-green-intense-green,.ansi-bright-green-bg{background-color:#007427}.ansi-yellow-fg{color:#ddb62b}.ansi-yellow-bg{background-color:#ddb62b}.ansi-yellow-intense-yellow,.ansi-bright-yellow-fg{color:#b27d12}.ansi-yellow-intense-yellow,.ansi-bright-yellow-bg{background-color:#b27d12}.ansi-blue-fg{color:#208ffb}.ansi-blue-bg{background-color:#208ffb}.ansi-blue-intense-blue,.ansi-bright-blue-fg{color:#0065ca}.ansi-blue-intense-blue,.ansi-bright-blue-bg{background-color:#0065ca}.ansi-magenta-fg{color:#d160c4}.ansi-magenta-bg{background-color:#d160c4}.ansi-magenta-intense-magenta,.ansi-bright-magenta-fg{color:#a03196}.ansi-magenta-intense-magenta,.ansi-bright-magenta-bg{background-color:#a03196}.ansi-cyan-fg{color:#60c6c8}.ansi-cyan-bg{background-color:#60c6c8}.ansi-cyan-intense-cyan,.ansi-bright-cyan-fg{color:#258f8f}.ansi-cyan-intense-cyan,.ansi-bright-cyan-bg{background-color:#258f8f}.ansi-white-fg{color:#c5c1b4}.ansi-white-bg{background-color:#c5c1b4}.ansi-white-intense-white,.ansi-bright-white-fg{color:#a1a6b2}.ansi-white-intense-white,.ansi-bright-white-bg{background-color:#a1a6b2}.ansi-default-inverse-fg{color:#fff}.ansi-default-inverse-bg{background-color:#000}.ansi-bold{font-weight:bold}.ansi-underline{text-decoration:underline}:root{--quarto-body-bg: #1E5288;--quarto-body-color: #E2E9EB;--quarto-text-muted: white;--quarto-border-color: white;--quarto-border-width: 1px;--quarto-border-radius: 4px}table.gt_table{color:var(--quarto-body-color);font-size:1em;width:100%;background-color:rgba(0,0,0,0);border-top-width:inherit;border-bottom-width:inherit;border-color:var(--quarto-border-color)}table.gt_table th.gt_column_spanner_outer{color:var(--quarto-body-color);background-color:rgba(0,0,0,0);border-top-width:inherit;border-bottom-width:inherit;border-color:var(--quarto-border-color)}table.gt_table th.gt_col_heading{color:var(--quarto-body-color);font-weight:bold;background-color:rgba(0,0,0,0)}table.gt_table thead.gt_col_headings{border-bottom:1px solid currentColor;border-top-width:inherit;border-top-color:var(--quarto-border-color)}table.gt_table thead.gt_col_headings:not(:first-child){border-top-width:1px;border-top-color:var(--quarto-border-color)}table.gt_table td.gt_row{border-bottom-width:1px;border-bottom-color:var(--quarto-border-color);border-top-width:0px}table.gt_table tbody.gt_table_body{border-top-width:1px;border-bottom-width:1px;border-bottom-color:var(--quarto-border-color);border-top-color:currentColor}div.columns{display:initial;gap:initial}div.column{display:inline-block;overflow-x:initial;vertical-align:top;width:50%}.code-annotation-tip-content{word-wrap:break-word}.code-annotation-container-hidden{display:none !important}dl.code-annotation-container-grid{display:grid;grid-template-columns:min-content auto}dl.code-annotation-container-grid dt{grid-column:1}dl.code-annotation-container-grid dd{grid-column:2}pre.sourceCode.code-annotation-code{padding-right:0}code.sourceCode .code-annotation-anchor{z-index:100;position:relative;float:right;background-color:rgba(0,0,0,0)}input[type=checkbox]{margin-right:.5ch}:root{--mermaid-bg-color: #1E5288;--mermaid-edge-color: #999;--mermaid-node-fg-color: #E2E9EB;--mermaid-fg-color: #E2E9EB;--mermaid-fg-color--lighter: white;--mermaid-fg-color--lightest: white;--mermaid-font-family: Proxima Nova, Calibri, sans-serif;--mermaid-label-bg-color: #1E5288;--mermaid-label-fg-color: #468;--mermaid-node-bg-color: rgba(68, 102, 136, 0.1);--mermaid-node-fg-color: #E2E9EB}@media print{:root{font-size:11pt}#quarto-sidebar,#TOC,.nav-page{display:none}.page-columns .content{grid-column-start:page-start}.fixed-top{position:relative}.panel-caption,.figure-caption,figcaption{color:#666}}.code-copy-button{position:absolute;top:0;right:0;border:0;margin-top:5px;margin-right:5px;background-color:rgba(0,0,0,0);z-index:3}.code-copy-button:focus{outline:none}.code-copy-button-tooltip{font-size:.75em}pre.sourceCode:hover>.code-copy-button>.bi::before{display:inline-block;height:1rem;width:1rem;content:"";vertical-align:-0.125em;background-image:url('data:image/svg+xml,');background-repeat:no-repeat;background-size:1rem 1rem}pre.sourceCode:hover>.code-copy-button-checked>.bi::before{background-image:url('data:image/svg+xml,')}pre.sourceCode:hover>.code-copy-button:hover>.bi::before{background-image:url('data:image/svg+xml,')}pre.sourceCode:hover>.code-copy-button-checked:hover>.bi::before{background-image:url('data:image/svg+xml,')}.panel-tabset [role=tablist]{border-bottom:1px solid #e2e9eb;list-style:none;margin:0;padding:0;width:100%}.panel-tabset [role=tablist] *{-webkit-box-sizing:border-box;box-sizing:border-box}@media(min-width: 30em){.panel-tabset [role=tablist] li{display:inline-block}}.panel-tabset [role=tab]{border:1px solid rgba(0,0,0,0);border-top-color:#e2e9eb;display:block;padding:.5em 1em;text-decoration:none}@media(min-width: 30em){.panel-tabset [role=tab]{border-top-color:rgba(0,0,0,0);display:inline-block;margin-bottom:-1px}}.panel-tabset [role=tab][aria-selected=true]{background-color:#e2e9eb}@media(min-width: 30em){.panel-tabset [role=tab][aria-selected=true]{background-color:rgba(0,0,0,0);border:1px solid #e2e9eb;border-bottom-color:#1e5288}}@media(min-width: 30em){.panel-tabset [role=tab]:hover:not([aria-selected=true]){border:1px solid #e2e9eb}}.code-with-filename .code-with-filename-file{margin-bottom:0;padding-bottom:2px;padding-top:2px;padding-left:.7em;border:var(--quarto-border-width) solid var(--quarto-border-color);border-radius:var(--quarto-border-radius);border-bottom:0;border-bottom-left-radius:0%;border-bottom-right-radius:0%}.code-with-filename div.sourceCode,.reveal .code-with-filename div.sourceCode{margin-top:0;border-top-left-radius:0%;border-top-right-radius:0%}.code-with-filename .code-with-filename-file pre{margin-bottom:0}.code-with-filename .code-with-filename-file{background-color:rgba(219,219,219,.8)}.quarto-dark .code-with-filename .code-with-filename-file{background-color:#555}.code-with-filename .code-with-filename-file strong{font-weight:400}.reveal.center .slide aside,.reveal.center .slide div.aside{position:initial}section.has-light-background,section.has-light-background h1,section.has-light-background h2,section.has-light-background h3,section.has-light-background h4,section.has-light-background h5,section.has-light-background h6{color:#222}section.has-light-background a,section.has-light-background a:hover{color:#2a76dd}section.has-light-background code{color:#4758ab}section.has-dark-background,section.has-dark-background h1,section.has-dark-background h2,section.has-dark-background h3,section.has-dark-background h4,section.has-dark-background h5,section.has-dark-background h6{color:#fff}section.has-dark-background a,section.has-dark-background a:hover{color:#42affa}section.has-dark-background code{color:#ffa07a}#title-slide,div.reveal div.slides section.quarto-title-block{text-align:center}#title-slide .subtitle,div.reveal div.slides section.quarto-title-block .subtitle{margin-bottom:2.5rem}.reveal .slides{text-align:left}.reveal .title-slide h1{font-size:1.6em}.reveal[data-navigation-mode=linear] .title-slide h1{font-size:2.5em}.reveal div.sourceCode{border:1px solid #fff;border-radius:4px}.reveal pre{width:100%;box-shadow:none;background-color:#001c48;border:none;margin:0;font-size:.55em}.reveal .code-with-filename .code-with-filename-file pre{background-color:unset}.reveal code{color:#e2e9eb;background-color:#001c48;white-space:pre-wrap}.reveal pre.sourceCode code{background-color:#001c48;padding:6px 9px;max-height:500px;white-space:pre}.reveal pre code{background-color:#1e5288;color:#e2e9eb}.reveal .column-output-location{display:flex;align-items:stretch}.reveal .column-output-location .column:first-of-type div.sourceCode{height:100%;background-color:#001c48}.reveal blockquote{display:block;position:relative;color:#fff;width:unset;margin:var(--r-block-margin) auto;padding:.625rem 1.75rem;border-left:.25rem solid #fff;font-style:normal;background:none;box-shadow:none}.reveal blockquote p:first-child,.reveal blockquote p:last-child{display:block}.reveal .slide aside,.reveal .slide div.aside{position:absolute;bottom:20px;font-size:0.7em;color:#fff}.reveal .slide sup{font-size:0.7em}.reveal .slide.scrollable aside,.reveal .slide.scrollable div.aside{position:relative;margin-top:1em}.reveal .slide aside .aside-footnotes{margin-bottom:0}.reveal .slide aside .aside-footnotes li:first-of-type{margin-top:0}.reveal .layout-sidebar{display:flex;width:100%;margin-top:.8em}.reveal .layout-sidebar .panel-sidebar{width:270px}.reveal .layout-sidebar-left .panel-sidebar{margin-right:calc(0.5em*2)}.reveal .layout-sidebar-right .panel-sidebar{margin-left:calc(0.5em*2)}.reveal .layout-sidebar .panel-fill,.reveal .layout-sidebar .panel-center,.reveal .layout-sidebar .panel-tabset{flex:1}.reveal .panel-input,.reveal .panel-sidebar{font-size:.5em;padding:.5em;border-style:solid;border-color:#fff;border-width:1px;border-radius:4px;background-color:#f8f9fa}.reveal .panel-sidebar :first-child,.reveal .panel-fill :first-child{margin-top:0}.reveal .panel-sidebar :last-child,.reveal .panel-fill :last-child{margin-bottom:0}.panel-input>div,.panel-input>div>div{vertical-align:middle;padding-right:1em}.reveal p,.reveal .slides section,.reveal .slides section>section{line-height:1.3}.reveal.smaller .slides section,.reveal .slides section.smaller,.reveal .slides section .callout{font-size:0.7em}.reveal.smaller .slides section section{font-size:inherit}.reveal.smaller .slides h1,.reveal .slides section.smaller h1{font-size:calc(2.5em/0.7)}.reveal.smaller .slides h2,.reveal .slides section.smaller h2{font-size:calc(1.6em/0.7)}.reveal.smaller .slides h3,.reveal .slides section.smaller h3{font-size:calc(1.3em/0.7)}.reveal .columns>.column>:not(ul,ol){margin-left:.25em;margin-right:.25em}.reveal .columns>.column:first-child>:not(ul,ol){margin-right:.5em;margin-left:0}.reveal .columns>.column:last-child>:not(ul,ol){margin-right:0;margin-left:.5em}.reveal .slide-number{color:#f36f80;background-color:#1e5288}.reveal .footer{color:#fff}.reveal .footer a{color:#ef4056}.reveal .footer.has-dark-background{color:#fff}.reveal .footer.has-dark-background a{color:#7bc6fa}.reveal .footer.has-light-background{color:#505050}.reveal .footer.has-light-background a{color:#6a9bdd}.reveal .slide-number{color:#fff}.reveal .slide-number.has-dark-background{color:#fff}.reveal .slide-number.has-light-background{color:#505050}.reveal .slide figure>figcaption,.reveal .slide img.stretch+p.caption,.reveal .slide img.r-stretch+p.caption{font-size:0.7em}@media screen and (min-width: 500px){.reveal .controls[data-controls-layout=edges] .navigate-left{left:.2em}.reveal .controls[data-controls-layout=edges] .navigate-right{right:.2em}.reveal .controls[data-controls-layout=edges] .navigate-up{top:.4em}.reveal .controls[data-controls-layout=edges] .navigate-down{bottom:2.3em}}.tippy-box[data-theme~=light-border]{background-color:#1e5288;color:#e2e9eb;border-radius:4px;border:solid 1px #fff;font-size:.6em}.tippy-box[data-theme~=light-border] .tippy-arrow{color:#fff}.tippy-box[data-placement^=bottom]>.tippy-content{padding:7px 10px;z-index:1}.reveal .callout.callout-style-simple .callout-body,.reveal .callout.callout-style-default .callout-body,.reveal .callout.callout-style-simple div.callout-title,.reveal .callout.callout-style-default div.callout-title{font-size:inherit}.reveal .callout.callout-style-default .callout-icon::before,.reveal .callout.callout-style-simple .callout-icon::before{height:2rem;width:2rem;background-size:2rem 2rem}.reveal .callout.callout-titled .callout-title p{margin-top:.5em}.reveal .callout.callout-titled .callout-icon::before{margin-top:1rem}.reveal .callout.callout-titled .callout-body>.callout-content>:last-child{margin-bottom:1rem}.reveal .panel-tabset [role=tab]{padding:.25em .7em}.reveal .slide-menu-button .fa-bars::before{background-image:url('data:image/svg+xml,')}.reveal .slide-chalkboard-buttons .fa-easel2::before{background-image:url('data:image/svg+xml,')}.reveal .slide-chalkboard-buttons .fa-brush::before{background-image:url('data:image/svg+xml,')}/*! dark */.reveal div.callout.callout-style-default .callout-title{color:#222}.reveal ol[type=a]{list-style-type:lower-alpha}.reveal ol[type=a s]{list-style-type:lower-alpha}.reveal ol[type=A s]{list-style-type:upper-alpha}.reveal ol[type=i]{list-style-type:lower-roman}.reveal ol[type=i s]{list-style-type:lower-roman}.reveal ol[type=I s]{list-style-type:upper-roman}.reveal ol[type="1"]{list-style-type:decimal}.reveal ul.task-list{list-style:none}.reveal ul.task-list li input[type=checkbox]{width:2em;height:2em;margin:0 1em .5em -1.6em;vertical-align:middle}div.cell-output-display div.pagedtable-wrapper table.table{font-size:.6em}.reveal .code-annotation-container-hidden{display:none}.reveal code.sourceCode button.code-annotation-anchor,.reveal code.sourceCode .code-annotation-anchor{font-family:Menlo,SFMono-Regular,Monaco,Consolas,Liberation Mono,Courier New,monospace;color:var(--quarto-hl-co-color);border:solid var(--quarto-hl-co-color) 1px;border-radius:50%;font-size:.7em;line-height:1.2em;margin-top:2px;user-select:none;-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none}.reveal code.sourceCode button.code-annotation-anchor{cursor:pointer}.reveal code.sourceCode a.code-annotation-anchor{text-align:center;vertical-align:middle;text-decoration:none;cursor:default;height:1.2em;width:1.2em}.reveal code.sourceCode.fragment a.code-annotation-anchor{left:auto}.reveal #code-annotation-line-highlight-gutter{width:100%;border-top:solid var(--quarto-hl-co-color) 1px;border-bottom:solid var(--quarto-hl-co-color) 1px;z-index:2}.reveal #code-annotation-line-highlight{margin-left:-8em;width:calc(100% + 4em);border-top:solid var(--quarto-hl-co-color) 1px;border-bottom:solid var(--quarto-hl-co-color) 1px;z-index:2;margin-bottom:-2px}.reveal code.sourceCode .code-annotation-anchor.code-annotation-active{background-color:var(--quarto-hl-normal-color, #aaaaaa);border:solid var(--quarto-hl-normal-color, #aaaaaa) 1px;color:#001c48;font-weight:bolder}.reveal pre.code-annotation-code{padding-top:0;padding-bottom:0}.reveal pre.code-annotation-code code{z-index:3;padding-left:0px}.reveal dl.code-annotation-container-grid{margin-left:.1em}.reveal dl.code-annotation-container-grid dt{margin-top:.65rem;font-family:Menlo,SFMono-Regular,Monaco,Consolas,Liberation Mono,Courier New,monospace;border:solid #e2e9eb 1px;border-radius:50%;height:1.3em;width:1.3em;line-height:1.3em;font-size:.5em;text-align:center;vertical-align:middle;text-decoration:none}.reveal dl.code-annotation-container-grid dd{margin-left:.25em}.reveal .scrollable ol li:first-child:nth-last-child(n+10),.reveal .scrollable ol li:first-child:nth-last-child(n+10)~li{margin-left:1em}html.print-pdf .reveal .slides .pdf-page:last-child{page-break-after:avoid}.reveal .quarto-title-block .quarto-title-authors{display:flex;justify-content:center}.reveal .quarto-title-block .quarto-title-authors .quarto-title-author{padding-left:.5em;padding-right:.5em}.reveal .quarto-title-block .quarto-title-authors .quarto-title-author a,.reveal .quarto-title-block .quarto-title-authors .quarto-title-author a:hover,.reveal .quarto-title-block .quarto-title-authors .quarto-title-author a:visited,.reveal .quarto-title-block .quarto-title-authors .quarto-title-author a:active{color:inherit;text-decoration:none}.reveal .quarto-title-block .quarto-title-authors .quarto-title-author .quarto-title-author-name{margin-bottom:.1rem}.reveal .quarto-title-block .quarto-title-authors .quarto-title-author .quarto-title-author-email{margin-top:0px;margin-bottom:.4em;font-size:.6em}.reveal .quarto-title-block .quarto-title-authors .quarto-title-author .quarto-title-author-orcid img{margin-bottom:4px}.reveal .quarto-title-block .quarto-title-authors .quarto-title-author .quarto-title-affiliation{font-size:.7em;margin-top:0px;margin-bottom:8px}.reveal .quarto-title-block .quarto-title-authors .quarto-title-author .quarto-title-affiliation:first{margin-top:12px}.reveal pre code{background-color:#001c48}.reveal p code{font-size:85%}.reveal div.sourceCode{margin-bottom:5px !important}.reveal div.cell-output{margin-bottom:10px !important}.reveal img.slide-logo{z-index:1}.reveal .slide-logo{max-height:3.5rem !important}blockquote{display:block !important;background:#e2e9eb !important;color:#555 !important;padding:15px 20px 15px 45px !important;margin:0 0 20px !important;position:relative !important;border-left:15px solid #ab0520 !important;border-right:2px solid #ab0520 !important;-moz-box-shadow:2px 2px 15px #102c49 !important;-webkit-box-shadow:2px 2px 15px #102c49 !important;box-shadow:2px 2px 15px #102c49 !important}blockquote::before{content:"“";font-size:75px;font-weight:bold;color:#aeaeae;position:absolute;left:10px;top:5px}blockquote::after{content:""}/*# sourceMappingURL=f95d2bded9c28492b788fe14c3e9f347.css.map */ +*/.ansi-black-fg{color:#3e424d}.ansi-black-bg{background-color:#3e424d}.ansi-black-intense-black,.ansi-bright-black-fg{color:#282c36}.ansi-black-intense-black,.ansi-bright-black-bg{background-color:#282c36}.ansi-red-fg{color:#e75c58}.ansi-red-bg{background-color:#e75c58}.ansi-red-intense-red,.ansi-bright-red-fg{color:#b22b31}.ansi-red-intense-red,.ansi-bright-red-bg{background-color:#b22b31}.ansi-green-fg{color:#00a250}.ansi-green-bg{background-color:#00a250}.ansi-green-intense-green,.ansi-bright-green-fg{color:#007427}.ansi-green-intense-green,.ansi-bright-green-bg{background-color:#007427}.ansi-yellow-fg{color:#ddb62b}.ansi-yellow-bg{background-color:#ddb62b}.ansi-yellow-intense-yellow,.ansi-bright-yellow-fg{color:#b27d12}.ansi-yellow-intense-yellow,.ansi-bright-yellow-bg{background-color:#b27d12}.ansi-blue-fg{color:#208ffb}.ansi-blue-bg{background-color:#208ffb}.ansi-blue-intense-blue,.ansi-bright-blue-fg{color:#0065ca}.ansi-blue-intense-blue,.ansi-bright-blue-bg{background-color:#0065ca}.ansi-magenta-fg{color:#d160c4}.ansi-magenta-bg{background-color:#d160c4}.ansi-magenta-intense-magenta,.ansi-bright-magenta-fg{color:#a03196}.ansi-magenta-intense-magenta,.ansi-bright-magenta-bg{background-color:#a03196}.ansi-cyan-fg{color:#60c6c8}.ansi-cyan-bg{background-color:#60c6c8}.ansi-cyan-intense-cyan,.ansi-bright-cyan-fg{color:#258f8f}.ansi-cyan-intense-cyan,.ansi-bright-cyan-bg{background-color:#258f8f}.ansi-white-fg{color:#c5c1b4}.ansi-white-bg{background-color:#c5c1b4}.ansi-white-intense-white,.ansi-bright-white-fg{color:#a1a6b2}.ansi-white-intense-white,.ansi-bright-white-bg{background-color:#a1a6b2}.ansi-default-inverse-fg{color:#fff}.ansi-default-inverse-bg{background-color:#000}.ansi-bold{font-weight:bold}.ansi-underline{text-decoration:underline}:root{--quarto-body-bg: #1E5288;--quarto-body-color: #E2E9EB;--quarto-text-muted: white;--quarto-border-color: white;--quarto-border-width: 1px;--quarto-border-radius: 4px}table.gt_table{color:var(--quarto-body-color);font-size:1em;width:100%;background-color:rgba(0,0,0,0);border-top-width:inherit;border-bottom-width:inherit;border-color:var(--quarto-border-color)}table.gt_table th.gt_column_spanner_outer{color:var(--quarto-body-color);background-color:rgba(0,0,0,0);border-top-width:inherit;border-bottom-width:inherit;border-color:var(--quarto-border-color)}table.gt_table th.gt_col_heading{color:var(--quarto-body-color);font-weight:bold;background-color:rgba(0,0,0,0)}table.gt_table thead.gt_col_headings{border-bottom:1px solid currentColor;border-top-width:inherit;border-top-color:var(--quarto-border-color)}table.gt_table thead.gt_col_headings:not(:first-child){border-top-width:1px;border-top-color:var(--quarto-border-color)}table.gt_table td.gt_row{border-bottom-width:1px;border-bottom-color:var(--quarto-border-color);border-top-width:0px}table.gt_table tbody.gt_table_body{border-top-width:1px;border-bottom-width:1px;border-bottom-color:var(--quarto-border-color);border-top-color:currentColor}div.columns{display:initial;gap:initial}div.column{display:inline-block;overflow-x:initial;vertical-align:top;width:50%}.code-annotation-tip-content{word-wrap:break-word}.code-annotation-container-hidden{display:none !important}dl.code-annotation-container-grid{display:grid;grid-template-columns:min-content auto}dl.code-annotation-container-grid dt{grid-column:1}dl.code-annotation-container-grid dd{grid-column:2}pre.sourceCode.code-annotation-code{padding-right:0}code.sourceCode .code-annotation-anchor{z-index:100;position:relative;float:right;background-color:rgba(0,0,0,0)}input[type=checkbox]{margin-right:.5ch}:root{--mermaid-bg-color: #1E5288;--mermaid-edge-color: #999;--mermaid-node-fg-color: #E2E9EB;--mermaid-fg-color: #000;--mermaid-fg-color--lighter: white;--mermaid-fg-color--lightest: white;--mermaid-font-family: Proxima Nova, Calibri, sans-serif;--mermaid-label-bg-color: #1E5288;--mermaid-label-fg-color: #468;--mermaid-node-bg-color: rgba(68, 102, 136, 0.1);--mermaid-node-fg-color: #E2E9EB}@media print{:root{font-size:11pt}#quarto-sidebar,#TOC,.nav-page{display:none}.page-columns .content{grid-column-start:page-start}.fixed-top{position:relative}.panel-caption,.figure-caption,figcaption{color:#666}}.code-copy-button{position:absolute;top:0;right:0;border:0;margin-top:5px;margin-right:5px;background-color:rgba(0,0,0,0);z-index:3}.code-copy-button:focus{outline:none}.code-copy-button-tooltip{font-size:.75em}pre.sourceCode:hover>.code-copy-button>.bi::before{display:inline-block;height:1rem;width:1rem;content:"";vertical-align:-0.125em;background-image:url('data:image/svg+xml,');background-repeat:no-repeat;background-size:1rem 1rem}pre.sourceCode:hover>.code-copy-button-checked>.bi::before{background-image:url('data:image/svg+xml,')}pre.sourceCode:hover>.code-copy-button:hover>.bi::before{background-image:url('data:image/svg+xml,')}pre.sourceCode:hover>.code-copy-button-checked:hover>.bi::before{background-image:url('data:image/svg+xml,')}.panel-tabset [role=tablist]{border-bottom:1px solid #e2e9eb;list-style:none;margin:0;padding:0;width:100%}.panel-tabset [role=tablist] *{-webkit-box-sizing:border-box;box-sizing:border-box}@media(min-width: 30em){.panel-tabset [role=tablist] li{display:inline-block}}.panel-tabset [role=tab]{border:1px solid rgba(0,0,0,0);border-top-color:#e2e9eb;display:block;padding:.5em 1em;text-decoration:none}@media(min-width: 30em){.panel-tabset [role=tab]{border-top-color:rgba(0,0,0,0);display:inline-block;margin-bottom:-1px}}.panel-tabset [role=tab][aria-selected=true]{background-color:#e2e9eb}@media(min-width: 30em){.panel-tabset [role=tab][aria-selected=true]{background-color:rgba(0,0,0,0);border:1px solid #e2e9eb;border-bottom-color:#1e5288}}@media(min-width: 30em){.panel-tabset [role=tab]:hover:not([aria-selected=true]){border:1px solid #e2e9eb}}.code-with-filename .code-with-filename-file{margin-bottom:0;padding-bottom:2px;padding-top:2px;padding-left:.7em;border:var(--quarto-border-width) solid var(--quarto-border-color);border-radius:var(--quarto-border-radius);border-bottom:0;border-bottom-left-radius:0%;border-bottom-right-radius:0%}.code-with-filename div.sourceCode,.reveal .code-with-filename div.sourceCode{margin-top:0;border-top-left-radius:0%;border-top-right-radius:0%}.code-with-filename .code-with-filename-file pre{margin-bottom:0}.code-with-filename .code-with-filename-file{background-color:rgba(219,219,219,.8)}.quarto-dark .code-with-filename .code-with-filename-file{background-color:#555}.code-with-filename .code-with-filename-file strong{font-weight:400}.reveal.center .slide aside,.reveal.center .slide div.aside{position:initial}section.has-light-background,section.has-light-background h1,section.has-light-background h2,section.has-light-background h3,section.has-light-background h4,section.has-light-background h5,section.has-light-background h6{color:#222}section.has-light-background a,section.has-light-background a:hover{color:#2a76dd}section.has-light-background code{color:#4758ab}section.has-dark-background,section.has-dark-background h1,section.has-dark-background h2,section.has-dark-background h3,section.has-dark-background h4,section.has-dark-background h5,section.has-dark-background h6{color:#fff}section.has-dark-background a,section.has-dark-background a:hover{color:#42affa}section.has-dark-background code{color:#ffa07a}#title-slide,div.reveal div.slides section.quarto-title-block{text-align:center}#title-slide .subtitle,div.reveal div.slides section.quarto-title-block .subtitle{margin-bottom:2.5rem}.reveal .slides{text-align:left}.reveal .title-slide h1{font-size:1.6em}.reveal[data-navigation-mode=linear] .title-slide h1{font-size:2.5em}.reveal div.sourceCode{border:1px solid #fff;border-radius:4px}.reveal pre{width:100%;box-shadow:none;background-color:#001c48;border:none;margin:0;font-size:.55em}.reveal .code-with-filename .code-with-filename-file pre{background-color:unset}.reveal code{color:#e2e9eb;background-color:#001c48;white-space:pre-wrap}.reveal pre.sourceCode code{background-color:#001c48;padding:6px 9px;max-height:500px;white-space:pre}.reveal pre code{background-color:#1e5288;color:#e2e9eb}.reveal .column-output-location{display:flex;align-items:stretch}.reveal .column-output-location .column:first-of-type div.sourceCode{height:100%;background-color:#001c48}.reveal blockquote{display:block;position:relative;color:#fff;width:unset;margin:var(--r-block-margin) auto;padding:.625rem 1.75rem;border-left:.25rem solid #fff;font-style:normal;background:none;box-shadow:none}.reveal blockquote p:first-child,.reveal blockquote p:last-child{display:block}.reveal .slide aside,.reveal .slide div.aside{position:absolute;bottom:20px;font-size:0.7em;color:#fff}.reveal .slide sup{font-size:0.7em}.reveal .slide.scrollable aside,.reveal .slide.scrollable div.aside{position:relative;margin-top:1em}.reveal .slide aside .aside-footnotes{margin-bottom:0}.reveal .slide aside .aside-footnotes li:first-of-type{margin-top:0}.reveal .layout-sidebar{display:flex;width:100%;margin-top:.8em}.reveal .layout-sidebar .panel-sidebar{width:270px}.reveal .layout-sidebar-left .panel-sidebar{margin-right:calc(0.5em*2)}.reveal .layout-sidebar-right .panel-sidebar{margin-left:calc(0.5em*2)}.reveal .layout-sidebar .panel-fill,.reveal .layout-sidebar .panel-center,.reveal .layout-sidebar .panel-tabset{flex:1}.reveal .panel-input,.reveal .panel-sidebar{font-size:.5em;padding:.5em;border-style:solid;border-color:#fff;border-width:1px;border-radius:4px;background-color:#f8f9fa}.reveal .panel-sidebar :first-child,.reveal .panel-fill :first-child{margin-top:0}.reveal .panel-sidebar :last-child,.reveal .panel-fill :last-child{margin-bottom:0}.panel-input>div,.panel-input>div>div{vertical-align:middle;padding-right:1em}.reveal p,.reveal .slides section,.reveal .slides section>section{line-height:1.3}.reveal.smaller .slides section,.reveal .slides section.smaller,.reveal .slides section .callout{font-size:0.7em}.reveal.smaller .slides section section{font-size:inherit}.reveal.smaller .slides h1,.reveal .slides section.smaller h1{font-size:calc(2.5em/0.7)}.reveal.smaller .slides h2,.reveal .slides section.smaller h2{font-size:calc(1.6em/0.7)}.reveal.smaller .slides h3,.reveal .slides section.smaller h3{font-size:calc(1.3em/0.7)}.reveal .columns>.column>:not(ul,ol){margin-left:.25em;margin-right:.25em}.reveal .columns>.column:first-child>:not(ul,ol){margin-right:.5em;margin-left:0}.reveal .columns>.column:last-child>:not(ul,ol){margin-right:0;margin-left:.5em}.reveal .slide-number{color:#f36f80;background-color:#1e5288}.reveal .footer{color:#fff}.reveal .footer a{color:#ef4056}.reveal .footer.has-dark-background{color:#fff}.reveal .footer.has-dark-background a{color:#7bc6fa}.reveal .footer.has-light-background{color:#505050}.reveal .footer.has-light-background a{color:#6a9bdd}.reveal .slide-number{color:#fff}.reveal .slide-number.has-dark-background{color:#fff}.reveal .slide-number.has-light-background{color:#505050}.reveal .slide figure>figcaption,.reveal .slide img.stretch+p.caption,.reveal .slide img.r-stretch+p.caption{font-size:0.7em}@media screen and (min-width: 500px){.reveal .controls[data-controls-layout=edges] .navigate-left{left:.2em}.reveal .controls[data-controls-layout=edges] .navigate-right{right:.2em}.reveal .controls[data-controls-layout=edges] .navigate-up{top:.4em}.reveal .controls[data-controls-layout=edges] .navigate-down{bottom:2.3em}}.tippy-box[data-theme~=light-border]{background-color:#1e5288;color:#e2e9eb;border-radius:4px;border:solid 1px #fff;font-size:.6em}.tippy-box[data-theme~=light-border] .tippy-arrow{color:#fff}.tippy-box[data-placement^=bottom]>.tippy-content{padding:7px 10px;z-index:1}.reveal .callout.callout-style-simple .callout-body,.reveal .callout.callout-style-default .callout-body,.reveal .callout.callout-style-simple div.callout-title,.reveal .callout.callout-style-default div.callout-title{font-size:inherit}.reveal .callout.callout-style-default .callout-icon::before,.reveal .callout.callout-style-simple .callout-icon::before{height:2rem;width:2rem;background-size:2rem 2rem}.reveal .callout.callout-titled .callout-title p{margin-top:.5em}.reveal .callout.callout-titled .callout-icon::before{margin-top:1rem}.reveal .callout.callout-titled .callout-body>.callout-content>:last-child{margin-bottom:1rem}.reveal .panel-tabset [role=tab]{padding:.25em .7em}.reveal .slide-menu-button .fa-bars::before{background-image:url('data:image/svg+xml,')}.reveal .slide-chalkboard-buttons .fa-easel2::before{background-image:url('data:image/svg+xml,')}.reveal .slide-chalkboard-buttons .fa-brush::before{background-image:url('data:image/svg+xml,')}/*! dark */.reveal div.callout.callout-style-default .callout-title{color:#222}.reveal ol[type=a]{list-style-type:lower-alpha}.reveal ol[type=a s]{list-style-type:lower-alpha}.reveal ol[type=A s]{list-style-type:upper-alpha}.reveal ol[type=i]{list-style-type:lower-roman}.reveal ol[type=i s]{list-style-type:lower-roman}.reveal ol[type=I s]{list-style-type:upper-roman}.reveal ol[type="1"]{list-style-type:decimal}.reveal ul.task-list{list-style:none}.reveal ul.task-list li input[type=checkbox]{width:2em;height:2em;margin:0 1em .5em -1.6em;vertical-align:middle}div.cell-output-display div.pagedtable-wrapper table.table{font-size:.6em}.reveal .code-annotation-container-hidden{display:none}.reveal code.sourceCode button.code-annotation-anchor,.reveal code.sourceCode .code-annotation-anchor{font-family:Menlo,SFMono-Regular,Monaco,Consolas,Liberation Mono,Courier New,monospace;color:var(--quarto-hl-co-color);border:solid var(--quarto-hl-co-color) 1px;border-radius:50%;font-size:.7em;line-height:1.2em;margin-top:2px;user-select:none;-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none}.reveal code.sourceCode button.code-annotation-anchor{cursor:pointer}.reveal code.sourceCode a.code-annotation-anchor{text-align:center;vertical-align:middle;text-decoration:none;cursor:default;height:1.2em;width:1.2em}.reveal code.sourceCode.fragment a.code-annotation-anchor{left:auto}.reveal #code-annotation-line-highlight-gutter{width:100%;border-top:solid var(--quarto-hl-co-color) 1px;border-bottom:solid var(--quarto-hl-co-color) 1px;z-index:2}.reveal #code-annotation-line-highlight{margin-left:-8em;width:calc(100% + 4em);border-top:solid var(--quarto-hl-co-color) 1px;border-bottom:solid var(--quarto-hl-co-color) 1px;z-index:2;margin-bottom:-2px}.reveal code.sourceCode .code-annotation-anchor.code-annotation-active{background-color:var(--quarto-hl-normal-color, #aaaaaa);border:solid var(--quarto-hl-normal-color, #aaaaaa) 1px;color:#001c48;font-weight:bolder}.reveal pre.code-annotation-code{padding-top:0;padding-bottom:0}.reveal pre.code-annotation-code code{z-index:3;padding-left:0px}.reveal dl.code-annotation-container-grid{margin-left:.1em}.reveal dl.code-annotation-container-grid dt{margin-top:.65rem;font-family:Menlo,SFMono-Regular,Monaco,Consolas,Liberation Mono,Courier New,monospace;border:solid #e2e9eb 1px;border-radius:50%;height:1.3em;width:1.3em;line-height:1.3em;font-size:.5em;text-align:center;vertical-align:middle;text-decoration:none}.reveal dl.code-annotation-container-grid dd{margin-left:.25em}.reveal .scrollable ol li:first-child:nth-last-child(n+10),.reveal .scrollable ol li:first-child:nth-last-child(n+10)~li{margin-left:1em}html.print-pdf .reveal .slides .pdf-page:last-child{page-break-after:avoid}.reveal .quarto-title-block .quarto-title-authors{display:flex;justify-content:center}.reveal .quarto-title-block .quarto-title-authors .quarto-title-author{padding-left:.5em;padding-right:.5em}.reveal .quarto-title-block .quarto-title-authors .quarto-title-author a,.reveal .quarto-title-block .quarto-title-authors .quarto-title-author a:hover,.reveal .quarto-title-block .quarto-title-authors .quarto-title-author a:visited,.reveal .quarto-title-block .quarto-title-authors .quarto-title-author a:active{color:inherit;text-decoration:none}.reveal .quarto-title-block .quarto-title-authors .quarto-title-author .quarto-title-author-name{margin-bottom:.1rem}.reveal .quarto-title-block .quarto-title-authors .quarto-title-author .quarto-title-author-email{margin-top:0px;margin-bottom:.4em;font-size:.6em}.reveal .quarto-title-block .quarto-title-authors .quarto-title-author .quarto-title-author-orcid img{margin-bottom:4px}.reveal .quarto-title-block .quarto-title-authors .quarto-title-author .quarto-title-affiliation{font-size:.7em;margin-top:0px;margin-bottom:8px}.reveal .quarto-title-block .quarto-title-authors .quarto-title-author .quarto-title-affiliation:first{margin-top:12px}.reveal pre code{background-color:#001c48}.reveal p code{font-size:85%}.reveal div.sourceCode{margin-bottom:5px !important}.reveal div.cell-output{margin-bottom:10px !important}.reveal img.slide-logo{z-index:1}.reveal .slide-logo{max-height:3.5rem !important}blockquote{display:block !important;background:#e2e9eb !important;color:#555 !important;padding:15px 20px 15px 45px !important;margin:0 0 20px !important;position:relative !important;border-left:15px solid #ab0520 !important;border-right:2px solid #ab0520 !important;-moz-box-shadow:2px 2px 15px #102c49 !important;-webkit-box-shadow:2px 2px 15px #102c49 !important;box-shadow:2px 2px 15px #102c49 !important}blockquote::before{content:"“";font-size:75px;font-weight:bold;color:#aeaeae;position:absolute;left:10px;top:5px}blockquote::after{content:""}/*# sourceMappingURL=f95d2bded9c28492b788fe14c3e9f347.css.map */ diff --git a/colloquium.qmd b/colloquium.qmd new file mode 100644 index 0000000..28b86ae --- /dev/null +++ b/colloquium.qmd @@ -0,0 +1,39 @@ +--- +title: "Reproducibility Colloquium" +--- + +The [final session](index.qmd#schedule) of this workshop series is our ✨**Reproducibility Colloquium**✨, where you all get a chance to share what you've learned with each other and anyone you'd like to invite to attend. +You are invited to give a short (about 5min) talk with slides (about 5). +To make this as low stakes as possible, here is an outline you may follow when putting together your presentation. + +::: callout-important +For each slide, you don't need to address **all** of the bullet points—focus on what is relevant for the specific aspects of your project you focused on! +::: + +::: callout-note +Feel free to adapt this outline—add or remove slides as fits your project. +::: + +- Slide 1: Super short description of your project for a ***general audience.***[^1] +- Slide 2: Describe the data and code components of your project. + - What data types/sources do you work with? + - Hand-collected field data? A data compilation? Instrument data? + - Data type (e.g., numeric, survey responses, DNA sequences, geospatial)? + - File types and sizes? + - What computational tools are you using, and what are you using them for? + - e.g. Excel for data entry; R for data cleaning and analysis; Illustrator for polishing figures +- Slide 3: Which aspects of the project did you focus on improving? What was the state of the project before the "makeover"? + - e.g. "I focused on transitioning to using git for version control; previously, I was saving my scripts with a new name each time I worked on them." + - Screen shots of the "before" are encouraged as visuals +- Slide 4: What changes did you make as part of the "makeover"? + - Why did you focus on these? + - How did you implement the changes? + - Screen shots of the "after" are encouraged as visuals +- Slide 5: Reflections + - What are you most proud of about this? + - Did you run into any challenges? + - What do you see as the next steps? + +[^1]: This is a good opportunity to practice an elevator pitch! + Try to keep it to just a couple sentences—just enough background to give some context to your data and code. + The goal of the presentation is to focus on your project organization and reproducibility, *not* the details of your research topic. diff --git a/index.qmd b/index.qmd index 8417aee..8b686dc 100644 --- a/index.qmd +++ b/index.qmd @@ -12,8 +12,7 @@ Welcome to the syllabus for the CCT Data Science fall workshop series: **Reprodu We'll meet on Tuesdays and Thursdays from 11am to 1pm via Zoom (link pinned in Slack channel) - - + ```{r} #| echo: false diff --git a/lessons/1-project-management/notes.qmd b/lessons/1-project-management/notes.qmd index 0387ddd..b107f4d 100644 --- a/lessons/1-project-management/notes.qmd +++ b/lessons/1-project-management/notes.qmd @@ -1,6 +1,8 @@ --- title: "Project Management and Documentation" -format: html +format: + html: default + typst: default --- ## Objective diff --git a/lessons/10-get-credit/notes.qmd b/lessons/10-get-credit/notes.qmd index 2ce59cf..3cd99a9 100644 --- a/lessons/10-get-credit/notes.qmd +++ b/lessons/10-get-credit/notes.qmd @@ -1,6 +1,8 @@ --- title: "Getting Credit For Your Hard Work" -format: html +format: + html: default + typst: default bibliography: references.bib --- diff --git a/lessons/11-getting-help/notes.qmd b/lessons/11-getting-help/notes.qmd index ab3cde4..0f7e742 100644 --- a/lessons/11-getting-help/notes.qmd +++ b/lessons/11-getting-help/notes.qmd @@ -1,6 +1,8 @@ --- title: "Getting help" -format: html +format: + html: default + typst: default --- [Slides](slides.qmd) diff --git a/lessons/12-drop-in/notes.qmd b/lessons/12-drop-in/notes.qmd index 09213b8..8bc6663 100644 --- a/lessons/12-drop-in/notes.qmd +++ b/lessons/12-drop-in/notes.qmd @@ -1,5 +1,8 @@ --- title: "Drop-in / Q&A" +format: + html: default + typst: default --- We asked learners to vote on the following topics for a mini-lesson for the last session before the show-and-tell session: diff --git a/lessons/2-markdown-quarto/notes.qmd b/lessons/2-markdown-quarto/notes.qmd index 327ec8a..5258ec8 100644 --- a/lessons/2-markdown-quarto/notes.qmd +++ b/lessons/2-markdown-quarto/notes.qmd @@ -1,6 +1,8 @@ --- title: "Documentation and Literate Programming" -format: html +format: + html: default + typst: default --- ## Objective diff --git a/lessons/3-shell/notes.qmd b/lessons/3-shell/notes.qmd index ed8f256..ae71054 100644 --- a/lessons/3-shell/notes.qmd +++ b/lessons/3-shell/notes.qmd @@ -1,6 +1,8 @@ --- title: "Using the Shell" -format: html +format: + html: default + typst: default --- ## Objectives diff --git a/lessons/4-git/notes.qmd b/lessons/4-git/notes.qmd index 62dca93..3dbd31d 100644 --- a/lessons/4-git/notes.qmd +++ b/lessons/4-git/notes.qmd @@ -1,6 +1,8 @@ --- title: "Version control with git" -format: html +format: + html: default + typst: default --- ## Objective @@ -24,10 +26,10 @@ format: html - SW Carpentry Git lesson 2 https://swcarpentry.github.io/git-novice/02-setup - Setting up git using git config - Make sure participants use their GH email/intended GH email - - `git` `verb` `options` - - `git config --global core.editor "vim"` - - `git` `verb` `--help` -- Live coding: git init + - `git` `verb` `options` + - `git config --global core.editor "vim"` + - `git` `verb` `--help` +- Live coding: git init - SW Carpentry Git lesson 3 https://swcarpentry.github.io/git-novice/03-create.html - Introduce the concept of a repository - Go over 3 ways to init a git repo and when to use each @@ -49,8 +51,8 @@ format: html - Live coding: `.gitignore` - SW Carpentry Git lesson 6https://swcarpentry.github.io/git-novice/06-ignore - .gitignore: - - `DS_Store` - - Create a file and then ignore it. + - `DS_Store` + - Create a file and then ignore it. - (Time permitting): SW Carpentry Git lesson 5 - https://swcarpentry.github.io/git-novice/05-history - Navigating git history @@ -67,6 +69,7 @@ format: html 5. [Software Carpentry Version Control with Git episode #6](https://swcarpentry.github.io/git-novice/06-ignore) 6. (optional) [Software Carpentry Version Control with Git episode #5](https://swcarpentry.github.io/git-novice/05-history) +```{=html} \ No newline at end of file +---> +``` diff --git a/lessons/5-github-basics/notes.qmd b/lessons/5-github-basics/notes.qmd index 56a9ae3..603af4e 100644 --- a/lessons/5-github-basics/notes.qmd +++ b/lessons/5-github-basics/notes.qmd @@ -1,6 +1,8 @@ --- title: "Developing Code on Github" -format: html +format: + html: default + typst: default --- ## Objective diff --git a/lessons/5-github-basics/slides.qmd b/lessons/5-github-basics/slides.qmd index eafacc7..1aa8077 100644 --- a/lessons/5-github-basics/slides.qmd +++ b/lessons/5-github-basics/slides.qmd @@ -36,6 +36,10 @@ bibliography: references.bib The most common git commands can be used with the RStudio GUI. +::: notes +Demo save, add, commit cycle with Git pane AND git menu in RStudio +::: + ## Sharing with GitHub ![](github-diagram-bryan.png){fig-align="center" width="671"} @@ -57,11 +61,25 @@ Figure 2 from [@bryan2018] - Connect your local git repo to a remote GitHub repo with `use_github()` - Explore the GitHub interface +::: notes +Demo "starting from scratch" by running `gitcreds::gitcreds_delete()`. +Remember to delete the PAT you create and show on camera.\ + +\ +Remind learners that repos can be private. +`use_github(private = TRUE)` +::: + ## Work With RStudio and GitHub (Live Coding) - Push local changes to GitHub - Pull GitHub changes to local +::: notes +Demo save, add, commit, push and check GitHub for changes. +Then, edit README on github and pull changes. +::: + ## Ignoring files {.smaller} ::: incremental @@ -91,6 +109,10 @@ Can use .gitkeep to get git to track an empty folder. - Put your research compendium on GitHub (e.g. with `use_github()`) and share the link in our Slack channel (if it can be made public) - Explore other research compendia shared in Slack +::: notes +If there is extra time, encourage learners to use it to practice these new skills with a *real* project repo while you're all still there to help troubleshoot. +::: + ## References ::: refs diff --git a/lessons/6-github-collab/notes.qmd b/lessons/6-github-collab/notes.qmd index 8f0c8b8..6a44e87 100644 --- a/lessons/6-github-collab/notes.qmd +++ b/lessons/6-github-collab/notes.qmd @@ -1,6 +1,9 @@ --- title: "Collaborating with GitHub" -format: html +format: + typst: + output-file: "lesson-6-notes.pdf" + html: default --- ## Objective diff --git a/lessons/6-github-collab/slides.qmd b/lessons/6-github-collab/slides.qmd index 5335e2a..20455c9 100644 --- a/lessons/6-github-collab/slides.qmd +++ b/lessons/6-github-collab/slides.qmd @@ -52,7 +52,7 @@ Ask for a volunteer and give them permission to push to a repo ## Example repo -- Everyone practice cloning this example repo as a new RStudio project: [^1] +- Everyone practice cloning this example repo as a new RStudio project: [^1] - Need **one** volunteer to edit the README.md and practice commit + push @@ -92,11 +92,11 @@ git config --global pull.rebase false ![](merge_conflict.png) -- Resolve the conflict however you want (i.e. keep one of the two sections) +1. Resolve the conflict however you want (i.e. keep one of the two sections) -- Delete all lines with `<<<<<<<`, `>>>>>>>`, or `=======` +2. Delete all lines with `<<<<<<<`, `>>>>>>>`, or `=======` -- Save and commit +3. Save and commit ::: notes Let's have a round of applause for our volunteer! @@ -104,7 +104,7 @@ Let's have a round of applause for our volunteer! ## Avoid merge conflicts by working on branches -Each person works on a "branch"---an independent series of commits that can be merged back into the "main" branch. +Each person works on a "branch"—an independent series of commits that can be merged back into the "main" branch. ```{mermaid} gitGraph @@ -129,10 +129,25 @@ gitGraph - Make a new branch using RStudio's Git pane (for this demo, use your name) -- Commit changes and push to your branch +- Make some edits (e.g. to README.md), save, add, commit. + +- You can go back to the "main" version of your project at any time. + +::: notes +Demonstrate how switching branches changes the files on their computer. +Hammer home that this is why it is a bad idea to use git for projects on shared drives. +::: + +## Working on a Branch + +- Push your branch to GitHub - View changes on GitHub +::: notes +Show how to look at different branches on GitHub +::: + ## Pull Requests A request to merge changes into the main branch @@ -187,7 +202,7 @@ Learn more, including handy `usethis` shortcuts: .\ Make a new branch, make commits, and make a pull request to the upstream repo. ::: diff --git a/lessons/7-data-manipulation/lesson_script.R b/lessons/7-data-manipulation/lesson_script.R index 3d166fa..6bf302a 100644 --- a/lessons/7-data-manipulation/lesson_script.R +++ b/lessons/7-data-manipulation/lesson_script.R @@ -25,7 +25,7 @@ penguins_data <- penguins write.csv( penguins_data, - "lessons/7-data-manipulation/data_raw/penguins_data_raw.csv", + "penguins_data_raw.csv", row.names = F ) @@ -142,7 +142,7 @@ ggplot(penguins_coords, aes(longitude, body_mass_g, color = species)) + #### Modify - add - commit #### -# adds penguins + penguins_long to repo +# adds penguins_data_raw repo # commit and push #### Palmer penguins citation #### diff --git a/lessons/7-data-manipulation/notes.qmd b/lessons/7-data-manipulation/notes.qmd index daa28dd..f41a7f9 100644 --- a/lessons/7-data-manipulation/notes.qmd +++ b/lessons/7-data-manipulation/notes.qmd @@ -1,6 +1,8 @@ --- title: "Data manipulation" -format: html +format: + html: default + typst: default --- ## Objective diff --git a/lessons/8-intermediate-r-1/notes.qmd b/lessons/8-intermediate-r-1/notes.qmd index 130598c..2c1173e 100644 --- a/lessons/8-intermediate-r-1/notes.qmd +++ b/lessons/8-intermediate-r-1/notes.qmd @@ -1,6 +1,8 @@ --- title: "Intermediate R programming I" -format: html +format: + html: default + typst: default --- ## Objective diff --git a/lessons/9-intermediate-r-2/notes.qmd b/lessons/9-intermediate-r-2/notes.qmd index b1d1e2f..6ea97e3 100644 --- a/lessons/9-intermediate-r-2/notes.qmd +++ b/lessons/9-intermediate-r-2/notes.qmd @@ -1,6 +1,8 @@ --- title: "Intermediate R programming II" -format: html +format: + html: default + typst: default --- ## Objective diff --git a/schedule.csv b/schedule.csv index 6201ee8..bf16b9f 100644 --- a/schedule.csv +++ b/schedule.csv @@ -10,4 +10,4 @@ Lesson,Date,Theme,Topic,Links,Notes 9,2024-10-01,Repeat & Reproduce,Intermediate R programming II,,iteration (and anonymous functions) 10,2024-10-03,Document & Publish,Getting credit for your hard work,,"renv, LICENSE, CITATION.cff, Zenodo, GitHub releases" 11,2024-10-08,Review,Drop-in co-working,, -12,2024-10-10,Reproducibility Colloquium,An opportunity for you to show off what you've learned,, +12,2024-10-10,Reproducibility Colloquium,An opportunity for you to show off what you've learned,[guidelines](colloquium.html),