+ after: |
+
+
+
+ after: |
+
+
+ 
+ Style adapted from: rstudio4edu-book (CC-BY 2.0)
diff --git a/style-sets/AnVIL/copy_to_assets/anvil_favicon.ico b/style-sets/AnVIL/copy_to_assets/anvil_favicon.ico new file mode 100755 index 0000000..f1eb1c4 Binary files /dev/null and b/style-sets/AnVIL/copy_to_assets/anvil_favicon.ico differ diff --git a/style-sets/AnVIL/copy_to_assets/big-image_anvil.html b/style-sets/AnVIL/copy_to_assets/big-image_anvil.html new file mode 100644 index 0000000..5724db5 --- /dev/null +++ b/style-sets/AnVIL/copy_to_assets/big-image_anvil.html @@ -0,0 +1,12 @@ + + + + + + + + + +
+ would */
+}
+
+.sourceCode pre {
+ margin: 0 !important; /* makes space above and below symmetrical*/
+}
+
+/* Footer */
+
+.footer {
+ font-family: "Lora", serif;
+ font-size: .85em;
+ color: #193a5c;
+}
\ No newline at end of file
diff --git a/style-sets/AnVIL/index.Rmd b/style-sets/AnVIL/index.Rmd
new file mode 100644
index 0000000..1803617
--- /dev/null
+++ b/style-sets/AnVIL/index.Rmd
@@ -0,0 +1,23 @@
+---
+title: "AnVIL Book Name "
+date: "`r format(Sys.time(), '%B %d, %Y')`"
+site: bookdown::bookdown_site
+documentclass: book
+bibliography: [book.bib, packages.bib]
+biblio-style: apalike
+link-citations: yes
+description: "Description about Course/Book."
+favicon: assets/anvil_favicon.ico
+---
+
+
+```{r include=FALSE}
+# automatically create a bib database for R packages
+knitr::write_bib(c(
+ .packages(), "bookdown", "knitr", "rmarkdown"
+), "packages.bib")
+```
+
+# About this Book {-}
+
+This book is part of a series of books for the Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL) of the National Human Genome Research Institute (NHGRI). Learn more about AnVIL by visiting `https://anvilproject.org` or reading the [preprint](https://www.biorxiv.org/content/10.1101/2021.04.22.436044v1).
diff --git a/style-sets/GDSCN/_output.yml b/style-sets/GDSCN/_output.yml
new file mode 100644
index 0000000..b950a3b
--- /dev/null
+++ b/style-sets/GDSCN/_output.yml
@@ -0,0 +1,16 @@
+bookdown::gitbook:
+ css: assets/style_gdscn.css
+ includes:
+ before_body: assets/big-image.html
+ after_body: assets/footer.html
+ highlight: tango
+ config:
+ toc:
+ collapse: section
+ before: |
+ Style adapted from: rstudio4edu-book (CC-BY 2.0) would */
+}
+
+.sourceCode pre {
+ margin: 0 !important; /* makes space above and below symmetrical*/
+}
+
+/* Footer */
+
+.footer {
+ font-family: "Lora", serif;
+ font-size: .85em;
+ color: #193a5c;
+}
\ No newline at end of file
diff --git a/style-sets/GDSCN/index.Rmd b/style-sets/GDSCN/index.Rmd
new file mode 100644
index 0000000..7717286
--- /dev/null
+++ b/style-sets/GDSCN/index.Rmd
@@ -0,0 +1,23 @@
+---
+title: "GDSCN: Course Name "
+date: "`r format(Sys.time(), '%B, %Y')`"
+site: bookdown::bookdown_site
+documentclass: book
+bibliography: [book.bib, packages.bib]
+biblio-style: apalike
+link-citations: yes
+description: "Description about Course/Book."
+favicon: assets/gdscn_favicon.ico
+---
+
+
+```{r include=FALSE}
+# automatically create a bib database for R packages
+knitr::write_bib(c(
+ .packages(), "bookdown", "knitr", "rmarkdown"
+), "packages.bib")
+```
+
+# About this Course {-}
+
+This course is part of a series of courses for the [The Genomic Data Science Community Network (GDSCN)](https://www.gdscn.org/home) is a group of educators gathered with the aim to bring genomic data science education to students at diverse institutions.
diff --git a/style-sets/data-trail/_output.yml b/style-sets/data-trail/_output.yml
new file mode 100644
index 0000000..bf0596b
--- /dev/null
+++ b/style-sets/data-trail/_output.yml
@@ -0,0 +1,17 @@
+bookdown::gitbook:
+ css: assets/style_DataTrail.css
+ includes:
+ before_body: assets/big-image-DataTrail.html
+ after_body: assets/footer.html
+ highlight: tango
+ config:
+ toc:
+ collapse: section
+ before: |
+ would */
+}
+
+.sourceCode pre {
+ margin: 0 !important; /* makes space above and below symmetrical*/
+}
+
+/* Footer */
+
+.footer {
+ font-family: "Lora", serif;
+ font-size: .85em;
+ color: #193a5c;
+}
\ No newline at end of file
diff --git a/style-sets/data-trail/index.Rmd b/style-sets/data-trail/index.Rmd
new file mode 100644
index 0000000..34e0f3a
--- /dev/null
+++ b/style-sets/data-trail/index.Rmd
@@ -0,0 +1,38 @@
+---
+title: " Course Name "
+date: "`r format(Sys.time(), '%B, %Y')`"
+site: bookdown::bookdown_site
+documentclass: book
+bibliography: [book.bib, packages.bib]
+biblio-style: apalike
+link-citations: yes
+description: "Description about Course/Book."
+favicon: assets/DataTrail_favicon.ico
+---
+
+
+```{r include=FALSE}
+# automatically create a bib database for R packages
+knitr::write_bib(c(
+ .packages(), "bookdown", "knitr", "rmarkdown"
+), "packages.bib")
+```
+
+# About this Course {-}
+
+This course is part of a series of courses for [DataTrail](https://www.datatrail.org/). DataTrail is a no-cost, paid 14-week educational initiative for young-adult, high school and GED-graduates. DataTrail aims to equip members of underserved communities with the necessary skills and support required to work in the booming field of data science.
+
+DataTrail is a fresh take on workforce development that focuses on training both Black, Indigenous, and other people of color (BIPOC) interested in the data science industry and their potential employers.
+
+Offered by the Johns Hopkins Bloomberg School of Public Health, in partnership with local non-profits and Leanpub, DataTrail combines a mutually-intensive learning experience (MILE) with a whole-person ecosystem of support to allow aspiring data scientists and their employers to succeed.
+
+DataTrail uses mutually-intensive learning
+DataTrail joins aspiring data science scholars and expert-level data scientist mentors in a mutually-intensive learning experience (MILE).
+
+In the DataTrail MILE:
+
+Scholars engage in cutting-edge technical and soft skills training needed to enter the data science field.
+
+Mentors engage in anti-racism and mentorship training needed to be impactful mentors and informed colleagues on diverse data science teams.
+
+The social connections created along the way will fuel job opportunities for scholars and foster a more diverse, equitable, and inclusive climate at the mentors' institutions.
diff --git a/style-sets/itcr/_output.yml b/style-sets/itcr/_output.yml
new file mode 100644
index 0000000..87b4a01
--- /dev/null
+++ b/style-sets/itcr/_output.yml
@@ -0,0 +1,17 @@
+bookdown::gitbook:
+ css: assets/style_ITN.css
+ includes:
+ before_body: assets/big-image-itcr.html
+ after_body: assets/footer.html
+ highlight: tango
+ config:
+ toc:
+ collapse: section
+ before: |
+ would */
+}
+
+.sourceCode pre {
+ margin: 0 !important; /* makes space above and below symmetrical*/
+}
+
+/* Footer */
+
+.footer {
+ font-family: "Lora", serif;
+ font-size: .85em;
+ color: #193a5c;
+}
\ No newline at end of file
diff --git a/style-sets/itcr/index.Rmd b/style-sets/itcr/index.Rmd
new file mode 100644
index 0000000..33a998f
--- /dev/null
+++ b/style-sets/itcr/index.Rmd
@@ -0,0 +1,23 @@
+---
+title: "Informatics Technology for Cancer Research (ITCR): Course Name "
+date: "`r format(Sys.time(), '%B, %Y')`"
+site: bookdown::bookdown_site
+documentclass: book
+bibliography: [book.bib, packages.bib]
+biblio-style: apalike
+link-citations: yes
+description: "Description about Course/Book."
+favicon: assets/ITN_favicon.ico
+---
+
+
+```{r include=FALSE}
+# automatically create a bib database for R packages
+knitr::write_bib(c(
+ .packages(), "bookdown", "knitr", "rmarkdown"
+), "packages.bib")
+```
+
+# About this Course {-}
+
+This course is part of a series of courses for the [Informatics Technology for Cancer Research (ITCR)](https://itcr.cancer.gov/) called the Informatics Technology for Cancer Research Education Resource. This material was created by the ITCR Training Network (ITN) which is a collaborative effort of researchers around the United States to support cancer informatics and data science training through resources, technology, and events. This initiative is funded by the following grant: [National Cancer Institute (NCI)](https://www.cancer.gov/) UE5 CA254170. Our courses feature tools developed by ITCR Investigators and make it easier for principal investigators, scientists, and analysts to integrate cancer informatics into their workflows. Please see our website at [www.itcrtraining.org](www.itcrtraining.org) for more information.
+ after: |
+
+
+
+ 
+ after: |
+
+
+
+
+
+
\ No newline at end of file
diff --git a/style-sets/data-trail/copy-to-assets/style_DataTrail.css b/style-sets/data-trail/copy-to-assets/style_DataTrail.css
new file mode 100644
index 0000000..e9f7115
--- /dev/null
+++ b/style-sets/data-trail/copy-to-assets/style_DataTrail.css
@@ -0,0 +1,458 @@
+@import url('https://fonts.googleapis.com/css?family=Abril+Fatface|Karla:400,400i,700,700i|Lora:400,400i,700,700i&display=swap');
+
+p.caption {
+ color: #777;
+ margin-top: 10px;
+}
+p code {
+ white-space: inherit;
+}
+pre {
+ word-break: normal;
+ word-wrap: normal;
+}
+pre code {
+ white-space: inherit;
+}
+
+/*---------------Hero Image------------------*/
+
+/* next 3 rules are for setting large image at top of each page and pushing down the book content to appear beneath the image */
+
+
+
+.hero-image-container {
+ position: absolute;
+ top: 0;
+ left: 0;
+ right: 0;
+ height: 200px;
+ background-color: #133454;
+}
+
+.hero-image {
+ width: 100%;
+ height: 200px;
+ object-fit: cover;
+}
+
+.page-inner {
+ padding-top: 210px !important;
+}
+/* ------------Links------------------ */
+
+.book .book-body .page-wrapper .page-inner section.normal a {
+ color: #1a9bc0;
+}
+
+
+/*------------- Body and header text---------------- */
+
+.book.font-family-1 {
+ font-family: 'Karla', arial, sans-serif;
+}
+
+h1, h2, h3, h4 {
+ font-family: 'Lora', arial, sans-serif;
+}
+
+
+.book .book-body .page-wrapper .page-inner section.normal h1,
+.book .book-body .page-wrapper .page-inner section.normal h2,
+.book .book-body .page-wrapper .page-inner section.normal h3,
+.book .book-body .page-wrapper .page-inner section.normal h4,
+.book .book-body .page-wrapper .page-inner section.normal h5,
+.book .book-body .page-wrapper .page-inner section.normal h6 {
+ margin-top: 2.275em;
+ margin-bottom: 1em;
+}
+
+.title {
+ font-family: 'Lora';
+ font-size: 4em !important;
+ color: #023e4c;
+ margin-top: 0.275em !important;
+ margin-bottom: 0.35em !important;
+}
+
+.subtitle {
+ font-family: 'Lora';
+ color: #0b8d96;
+}
+
+
+/*----------DROP CAPS--------------*/
+
+
+/*p:nth-child(2):first-letter { /* /* DROP-CAP FOR FIRST P BENEATH EACH H1 OR H2*/ /*
+ color: #3fb5bd;
+ float: left;
+ font-family: 'Abril Fatface', serif;
+ font-size: 7em;
+ line-height: 65px;
+ padding-top: 4px;
+ padding-right: 8px;
+ padding-left: 3px;
+ margin-bottom: 9px;
+}
+*/
+
+.section.level1 > p:first-of-type:first-letter { /*drop cap for first p beneath level 1 headers only within class .section*/
+ color: #023e4c;
+ float: left;
+ font-family: 'Abril Fatface', serif;
+ font-size: 7em;
+ line-height: 65px;
+ padding-top: 4px;
+ padding-right: 8px;
+ padding-left: 3px;
+ margin-bottom: 9px;
+}
+
+/* add drop cap to first paragraph that follows the first 2nd level header*/
+/*
+.section.level2:first-of-type > p:first-of-type:first-letter {
+ color: #3fb5bd;
+ float: left;
+ font-family: 'Abril Fatface', serif;
+ font-size: 7em;
+ line-height: 65px;
+ padding-top: 4px;
+ padding-right: 8px;
+ padding-left: 3px;
+ margin-bottom: 9px;
+}
+*/
+
+
+
+/*------------ TOC --------------*/
+
+
+.book .book-summary {
+ background: white;
+ border-right: none;
+}
+
+/*---color of links in TOC----*/
+
+.book .book-summary a {
+color: #023e4c
+}
+
+.summary{
+ font-family: 'Karla', sans-serif;
+}
+
+/* all TOC list items, basically */
+.book .book-summary ul.summary li a,
+.book .book-summary ul.summary li span {
+ padding-top: 8px;
+ padding-bottom: 8px;
+ padding-left: 15px;
+ padding-right: 15px;
+ color: #023e4c;
+}
+
+.summary a:hover {
+ color: #1a9bc0 !important;
+}
+
+.book .book-summary ul.summary li.active>a { /*active TOC links*/
+ color: #1a9bc0 !important;
+ border-left: solid 4px;
+ border-color: #12af66;
+ padding-left: 11px !important;
+}
+
+.trapezoid {
+ width: 130px;
+ text-align: center;
+ height: 15;
+ position: relative;
+ border-right: 50px solid #023e4c;
+ border-bottom: 50px solid #e6e762;
+ border-left: 50px solid #023e4c;
+ box-sizing: content-box;
+}
+.trapezoid span {
+ position: absolute;
+ top: 5px;
+ bottom: 5px;
+ left: 5%;
+ color: #e6e762;
+}
+
+li.appendix span, li.part span { /* for TOC part names */
+ margin-top: 1em;
+ color: #000000;
+ opacity: .9 !important;
+ text-transform: uppercase;
+}
+
+.part + li[data-level=""] { /* grabs first .chapter immediately after .part...but only those ch without numbers */
+ text-transform: uppercase;
+}
+
+
+/* The next two rules make the horizontal line go straight across in top navbar */
+
+.summary > li:first-child {
+ height: 50px;
+ padding-top: 10px;
+ border-bottom: 1px solid rgba(0,0,0,.07);
+}
+
+.book .book-summary ul.summary li.divider {
+ height: 0px;
+}
+
+
+/*--- LOGO ---*/
+
+.toc-logo {
+ width: 200px !important;
+ object-fit: contain;
+ margin: 0 auto;
+}
+
+.toc-logo img {
+ max-width: 100%;
+ margin-bottom: 10px;
+}
+
+.summary > li:first-child {
+ height: auto !important;
+}
+
+/* --------------Two columns--------------- */
+
+.col2 {
+ columns: 2 200px; /* number of columns and width in pixels*/
+ -webkit-columns: 2 200px; /* chrome, safari */
+ -moz-columns: 2 200px; /* firefox */
+}
+
+
+.side-by-side {
+ display: flex;
+}
+
+.side1 {
+ width: 40%;
+}
+
+.side2 {
+ width: 58%;
+ margin-left: 1rem;
+}
+
+/* --------------Even split- two columns--------------- */
+
+.split {
+ display: flex;
+}
+
+.split1 {
+ width: 50%;
+ padding-right: 20px;
+}
+
+.split2 {
+ width: 50%;
+}
+
+
+/* Sidebar formating --------------------------------------------*/
+/* from r-pkgs.org*/
+
+div.rstudio-tip, div.tip, div.gotcha, div.design, div.hat{
+ border: 4px #aed6d963;
+ border-style: dashed solid;
+ padding: 1em;
+ margin: 1em 0;
+ padding-left: 100px;
+ background-size: 70px;
+ background-repeat: no-repeat;
+ background-position: 15px center;
+ min-height: 120px;
+ color: #2ea8b3;
+ background-color: #fcfcfc;
+}
+
+
+div.rstudio-tip {
+ background-image: url("../images/divs/rstudio.png");
+}
+
+div.tip {
+ background-image: url("../images/divs/lightbulb.png");
+}
+
+div.gotcha {
+ background-image: url("../images/divs/gotcha_2.png");
+}
+
+div.design {
+ background-image: url("../images/divs/design.png");
+}
+
+div.hat {
+ background-image: url("../images/divs/hat.png");
+}
+
+/* for fancy bookdown cookbook */
+
+div.puzzle, div.fyi, div.demo, div.note {
+ padding: 1em;
+ margin: 1em 0;
+ padding-left: 100px;
+ background-size: 70px;
+ background-repeat: no-repeat;
+ background-position: 15px center;
+ min-height: 120px;
+ color: #1f5386;
+ background-color: #bed3ec;
+ border: solid 5px #dfedff;
+}
+
+div.puzzle {
+ background-image: url("../images/illos/Your-turn.png");
+}
+
+div.fyi {
+ background-image: url("../images/illos/fyi.png");
+}
+
+div.demo {
+ background-image: url("../images/illos/Live-code.png");
+}
+
+div.note {
+ background-image: url("../images/illos/lightbulb2.png");
+}
+
+
+/* .book .book-body .page-wrapper .page-inner section.normal is needed
+ to override the styles produced by gitbook, which are ridiculously
+ overspecified. Goal of the selectors is to ensure internal "margins"
+ controlled only by padding of container */
+
+.book .book-body .page-wrapper .page-inner section.normal div.rstudio-tip > :first-child,
+.book .book-body .page-wrapper .page-inner section.normal div.tip > :first-child {
+ margin-top: 0;
+}
+
+.book .book-body .page-wrapper .page-inner section.normal div.rstudio-tip > :last-child,
+.book .book-body .page-wrapper .page-inner section.normal div.tip > :last-child {
+ margin-bottom: 0;
+}
+
+iframe {
+ -moz-transform-origin: top left;
+ -webkit-transform-origin: top left;
+ -o-transform-origin: top left;
+ -ms-transform-origin: top left;
+ transform-origin: top left;
+}
+
+.iframe-container {
+ overflow: auto;
+ -webkit-overflow-scrolling: touch;
+ border: #ddd 2px solid;
+ box-shadow: #888 0px 5px 8px;
+ margin-bottom: 1em;
+}
+
+.iframe-container > iframe {
+ border: none;
+}
+
+
+/* -------Clipboard copy button --------- */
+.copy {
+ width: inherit;
+ background-color: #e2e2e2 ;
+ border: none;
+ border-radius: 2px;
+ float: right;
+ font-size: 60%;
+ padding: 4px 4px 4px 4px;
+}
+
+/* for new copy button */
+
+.hasCopyButton {
+ position: relative;
+}
+
+.btn-copy-ex {
+ position: absolute;
+ right: 0;
+ top: 0;
+ visibility: hidden;
+}
+
+.hasCopyButton:hover button.btn-copy-ex {
+ visibility: visible;
+}
+
+
+
+/* -----------Section anchors -------------*/
+
+.book .book-body .page-wrapper .page-inner section.normal {
+ overflow: visible !important; /*so anchor link doesn't get cut off */
+}
+
+a.anchor {
+ margin-left: -30px;
+ padding-right: 3px;
+ display:inline-block;
+ width: 30px;
+ height: 30px;
+ /*visibility: hidden;*/
+ background-image: url(https://image.flaticon.com/icons/svg/34/34735.svg) !important;
+ background-repeat: no-repeat !important;
+ background-size: 20px 20px !important;
+ background-position: center bottom !important;
+ opacity: 0;
+}
+
+
+.hasAnchor:hover a.anchor,
+a.anchor:hover {
+ /*visibility: visible;*/
+ opacity: 0.6;
+}
+
+/* disable anchors for headers with "no-anchor" class */
+.no-anchor .hasAnchor:hover a.anchor,
+.no-anchor a.anchor:hover {
+ opacity: 0 !important;
+}
+
+@media (max-width: 1144px) { /* don't show anchor link on small screens */
+ .hasAnchor:hover a.anchor {
+ visibility: hidden;
+ }
+}
+
+
+/*____Code Chunks____*/
+
+.sourceCode {
+ margin-bottom: 0.85em; /* adds same amount of margin as a 
+
+ after: |
+
+
+
+
+
+
\ No newline at end of file
diff --git a/style-sets/itcr/copy-to-assets/itcr_main_image.png b/style-sets/itcr/copy-to-assets/itcr_main_image.png
new file mode 100644
index 0000000..db2c053
Binary files /dev/null and b/style-sets/itcr/copy-to-assets/itcr_main_image.png differ
diff --git a/style-sets/itcr/copy-to-assets/style_ITN.css b/style-sets/itcr/copy-to-assets/style_ITN.css
new file mode 100644
index 0000000..6f005a2
--- /dev/null
+++ b/style-sets/itcr/copy-to-assets/style_ITN.css
@@ -0,0 +1,463 @@
+@import url('https://fonts.googleapis.com/css?family=Abril+Fatface|Karla:400,400i,700,700i|Lora:400,400i,700,700i&display=swap');
+
+p.caption {
+ color: #777;
+ margin-top: 10px;
+}
+p code {
+ white-space: inherit;
+}
+pre {
+ word-break: normal;
+ word-wrap: normal;
+}
+pre code {
+ white-space: inherit;
+}
+
+/*---------------Hero Image------------------*/
+
+/* next 3 rules are for setting large image at top of each page and pushing down the book content to appear beneath the image */
+
+.hero-image-container {
+ position: absolute;
+ top: 0;
+ left: 0;
+ right: 0;
+ height: 200px;
+ /*background-image: url("images/books.jpg");*/
+ /*background-color: #193a5c;*/
+}
+
+.hero-image {
+ width: 100%;
+ height: 80%;
+ /*object-fit: cover;*/
+}
+
+.page-inner {
+ padding-top: 140px !important;
+}
+
+
+/* ------------Links------------------ */
+
+.book .book-body .page-wrapper .page-inner section.normal a {
+ color: #e0471c;
+}
+
+
+/*------------- Body and header text---------------- */
+
+.book.font-family-1 {
+ font-family: 'Karla', arial, sans-serif;
+}
+
+h1, h2, h3, h4 {
+ font-family: 'Lora', arial, sans-serif;
+}
+
+
+.book .book-body .page-wrapper .page-inner section.normal h1,
+.book .book-body .page-wrapper .page-inner section.normal h2,
+.book .book-body .page-wrapper .page-inner section.normal h3,
+.book .book-body .page-wrapper .page-inner section.normal h4,
+.book .book-body .page-wrapper .page-inner section.normal h5,
+.book .book-body .page-wrapper .page-inner section.normal h6 {
+ margin-top: 2.275em;
+ margin-bottom: 1em;
+}
+
+.title {
+ font-family: 'Lora';
+ font-size: 4em !important;
+ color: #193a5c;
+ margin-top: 0.275em !important;
+ margin-bottom: 0.35em !important;
+}
+
+.subtitle {
+ font-family: 'Lora';
+ color: #0b8d96;
+}
+
+
+/*----------DROP CAPS--------------*/
+
+
+/*p:nth-child(2):first-letter { /* /* DROP-CAP FOR FIRST P BENEATH EACH H1 OR H2*/ /*
+ color: #3fb5bd;
+ float: left;
+ font-family: 'Abril Fatface', serif;
+ font-size: 7em;
+ line-height: 65px;
+ padding-top: 4px;
+ padding-right: 8px;
+ padding-left: 3px;
+ margin-bottom: 9px;
+}
+*/
+
+.section.level1 > p:first-of-type:first-letter { /*drop cap for first p beneath level 1 headers only within class .section*/
+ color: #193a5c;
+ float: left;
+ font-family: 'Abril Fatface', serif;
+ font-size: 7em;
+ line-height: 65px;
+ padding-top: 4px;
+ padding-right: 8px;
+ padding-left: 3px;
+ margin-bottom: 9px;
+}
+
+/* add drop cap to first paragraph that follows the first 2nd level header*/
+/*
+.section.level2:first-of-type > p:first-of-type:first-letter {
+ color: #3fb5bd;
+ float: left;
+ font-family: 'Abril Fatface', serif;
+ font-size: 7em;
+ line-height: 65px;
+ padding-top: 4px;
+ padding-right: 8px;
+ padding-left: 3px;
+ margin-bottom: 9px;
+}
+*/
+
+
+
+/*------------ TOC --------------*/
+
+
+.book .book-summary {
+ background: white;
+ border-right: none;
+}
+
+/*---color of links in TOC----*/
+
+.book .book-summary a {
+color: #193a5c
+}
+
+.summary{
+ font-family: 'Karla', sans-serif;
+}
+
+/* all TOC list items, basically */
+.book .book-summary ul.summary li a,
+.book .book-summary ul.summary li span {
+ padding-top: 8px;
+ padding-bottom: 8px;
+ padding-left: 15px;
+ padding-right: 15px;
+ color: #193a5c;
+}
+
+.summary a:hover {
+ color: #e0471c !important;
+}
+
+.book .book-summary ul.summary li.active>a { /*active TOC links*/
+ color: #e0471c !important;
+ border-left: solid 4px;
+ border-color: #e0471c;
+ padding-left: 11px !important;
+}
+
+.trapezoid {
+ width: 130px;
+ text-align: center;
+ height: 15;
+ position: relative;
+ border-right: 50px solid transparent;
+ border-bottom: 50px solid #dbdbdb;
+ border-left: 50px solid transparent;
+ box-sizing: content-box;
+}
+.trapezoid span {
+ position: absolute;
+ top: 5px;
+ bottom: 5px;
+ left: 5%;
+ color: #fff;
+}
+
+
+
+
+li.appendix span, li.part span { /* for TOC part names */
+ margin-top: 1em;
+ color: #000000;
+ opacity: .9 !important;
+ text-transform: uppercase;
+}
+
+.part + li[data-level=""] { /* grabs first .chapter immediately after .part...but only those ch without numbers */
+ text-transform: uppercase;
+}
+
+
+/* The next two rules make the horizontal line go straight across in top navbar */
+
+.summary > li:first-child {
+ height: 50px;
+ padding-top: 10px;
+ border-bottom: 1px solid rgba(0,0,0,.07);
+}
+
+.book .book-summary ul.summary li.divider {
+ height: 0px;
+}
+
+
+
+/*--- LOGO ---*/
+
+.toc-logo {
+ width: 200px !important;
+ object-fit: contain;
+ margin: 0 auto;
+}
+
+.toc-logo img {
+ max-width: 100%;
+ margin-bottom: 10px;
+}
+
+.summary > li:first-child {
+ height: auto !important;
+}
+
+/* --------------Two columns--------------- */
+
+.col2 {
+ columns: 2 200px; /* number of columns and width in pixels*/
+ -webkit-columns: 2 200px; /* chrome, safari */
+ -moz-columns: 2 200px; /* firefox */
+}
+
+
+.side-by-side {
+ display: flex;
+}
+
+.side1 {
+ width: 40%;
+}
+
+.side2 {
+ width: 58%;
+ margin-left: 1rem;
+}
+
+/* --------------Even split- two columns--------------- */
+
+.split {
+ display: flex;
+}
+
+.split1 {
+ width: 50%;
+ padding-right: 20px;
+}
+
+.split2 {
+ width: 50%;
+}
+
+
+/* Sidebar formating --------------------------------------------*/
+/* from r-pkgs.org*/
+
+div.rstudio-tip, div.tip, div.gotcha, div.design, div.hat{
+ border: 4px #aed6d963;
+ border-style: dashed solid;
+ padding: 1em;
+ margin: 1em 0;
+ padding-left: 100px;
+ background-size: 70px;
+ background-repeat: no-repeat;
+ background-position: 15px center;
+ min-height: 120px;
+ color: #2ea8b3;
+ background-color: #fcfcfc;
+}
+
+
+div.rstudio-tip {
+ background-image: url("../images/divs/rstudio.png");
+}
+
+div.tip {
+ background-image: url("../images/divs/lightbulb.png");
+}
+
+div.gotcha {
+ background-image: url("../images/divs/gotcha_2.png");
+}
+
+div.design {
+ background-image: url("../images/divs/design.png");
+}
+
+div.hat {
+ background-image: url("../images/divs/hat.png");
+}
+
+/* for fancy bookdown cookbook */
+
+div.puzzle, div.fyi, div.demo, div.note {
+ padding: 1em;
+ margin: 1em 0;
+ padding-left: 100px;
+ background-size: 70px;
+ background-repeat: no-repeat;
+ background-position: 15px center;
+ min-height: 120px;
+ color: #1f5386;
+ background-color: #bed3ec;
+ border: solid 5px #dfedff;
+}
+
+div.puzzle {
+ background-image: url("../images/illos/Your-turn.png");
+}
+
+div.fyi {
+ background-image: url("../images/illos/fyi.png");
+}
+
+div.demo {
+ background-image: url("../images/illos/Live-code.png");
+}
+
+div.note {
+ background-image: url("../images/illos/lightbulb2.png");
+}
+
+
+/* .book .book-body .page-wrapper .page-inner section.normal is needed
+ to override the styles produced by gitbook, which are ridiculously
+ overspecified. Goal of the selectors is to ensure internal "margins"
+ controlled only by padding of container */
+
+.book .book-body .page-wrapper .page-inner section.normal div.rstudio-tip > :first-child,
+.book .book-body .page-wrapper .page-inner section.normal div.tip > :first-child {
+ margin-top: 0;
+}
+
+.book .book-body .page-wrapper .page-inner section.normal div.rstudio-tip > :last-child,
+.book .book-body .page-wrapper .page-inner section.normal div.tip > :last-child {
+ margin-bottom: 0;
+}
+
+iframe {
+ -moz-transform-origin: top left;
+ -webkit-transform-origin: top left;
+ -o-transform-origin: top left;
+ -ms-transform-origin: top left;
+ transform-origin: top left;
+}
+
+.iframe-container {
+ overflow: auto;
+ -webkit-overflow-scrolling: touch;
+ border: #ddd 2px solid;
+ box-shadow: #888 0px 5px 8px;
+ margin-bottom: 1em;
+}
+
+.iframe-container > iframe {
+ border: none;
+}
+
+
+/* -------Clipboard copy button --------- */
+.copy {
+ width: inherit;
+ background-color: #e2e2e2 ;
+ border: none;
+ border-radius: 2px;
+ float: right;
+ font-size: 60%;
+ padding: 4px 4px 4px 4px;
+}
+
+/* for new copy button */
+
+.hasCopyButton {
+ position: relative;
+}
+
+.btn-copy-ex {
+ position: absolute;
+ right: 0;
+ top: 0;
+ visibility: hidden;
+}
+
+.hasCopyButton:hover button.btn-copy-ex {
+ visibility: visible;
+}
+
+
+
+/* -----------Section anchors -------------*/
+
+.book .book-body .page-wrapper .page-inner section.normal {
+ overflow: visible !important; /*so anchor link doesn't get cut off */
+}
+
+a.anchor {
+ margin-left: -30px;
+ padding-right: 3px;
+ display:inline-block;
+ width: 30px;
+ height: 30px;
+ /*visibility: hidden;*/
+ background-image: url(https://image.flaticon.com/icons/svg/34/34735.svg) !important;
+ background-repeat: no-repeat !important;
+ background-size: 20px 20px !important;
+ background-position: center bottom !important;
+ opacity: 0;
+}
+
+
+.hasAnchor:hover a.anchor,
+a.anchor:hover {
+ /*visibility: visible;*/
+ opacity: 0.6;
+}
+
+/* disable anchors for headers with "no-anchor" class */
+.no-anchor .hasAnchor:hover a.anchor,
+.no-anchor a.anchor:hover {
+ opacity: 0 !important;
+}
+
+@media (max-width: 1144px) { /* don't show anchor link on small screens */
+ .hasAnchor:hover a.anchor {
+ visibility: hidden;
+ }
+}
+
+
+/*____Code Chunks____*/
+
+.sourceCode {
+ margin-bottom: 0.85em; /* adds same amount of margin as a 
+
