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.notice{
+ border: 4px #193a5c;
+ border-style: solid;
+ padding: 1em;
+ margin: 1em 0;
+ padding-left: 100px;
+ background-size: 70px;
+ background-repeat: no-repeat;
+ background-position: 15px center;
+ min-height: 120px;
+ background-color: #e8ebee;
+}
+
+div.notice{
+ background-image: url("../assets/box_images/note.png");
+}
+
+div.warning{
+ border: 4px #e0471c;
+ border-style: solid;
+ padding: 1em;
+ margin: 1em 0;
+ padding-left: 100px;
+ background-size: 70px;
+ background-repeat: no-repeat;
+ background-position: 15px center;
+ min-height: 120px;
+ background-color: #e8ebee;
+}
+
+div.warning{
+ background-image: url("../assets/box_images/warning.png");
+}
+
+
+
+div.github{
+ border: 4px #000000;
+ border-style: solid;
+ padding: 1em;
+ margin: 1em 0;
+ padding-left: 100px;
+ background-size: 70px;
+ background-repeat: no-repeat;
+ background-position: 15px center;
+ min-height: 120px;
+ background-color: #e8ebee;
+}
+
+div.github{
+ background-image: url("../assets/box_images/github.png");
+}
+
+div.dictionary{
+ border: 4px #193a5c;
+ border-style: solid;
+ padding: 1em;
+ margin: 1em 0;
+ padding-left: 100px;
+ background-size: 70px;
+ background-repeat: no-repeat;
+ background-position: 15px center;
+ min-height: 120px;
+ background-color: #e8ebee;
+}
+
+div.dictionary{
+ background-image: url("../assets/box_images/dictionary.png");
+}
+
+div.reflection{
+ border: 4px #193a5c;
+ border-style: solid;
+ padding: 1em;
+ margin: 1em 0;
+ padding-left: 100px;
+ background-size: 90px;
+ background-repeat: no-repeat;
+ background-position: 15px center;
+ min-height: 120px;
+ background-color: #e8ebee;
+}
+
+div.reflection{
+ background-image: url("../assets/box_images/thinking_face.png");
+}
+
+
+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 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/index.Rmd b/index.Rmd
index 79614a5..33a998f 100644
--- a/index.Rmd
+++ b/index.Rmd
@@ -1,26 +1,23 @@
---
-title: "Course Name"
+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]
+bibliography: [book.bib, packages.bib]
biblio-style: apalike
link-citations: yes
description: "Description about Course/Book."
-favicon: assets/dasl_favicon.ico
-output:
- bookdown::word_document2:
- toc: true
+favicon: assets/ITN_favicon.ico
---
-# About this Course {-}
-
-## Available course formats
+```{r include=FALSE}
+# automatically create a bib database for R packages
+knitr::write_bib(c(
+ .packages(), "bookdown", "knitr", "rmarkdown"
+), "packages.bib")
+```
-This course is available in multiple formats which allows you to take it in the way that best suites your needs. You can take it for certificate which can be for free or fee.
+# About this Course {-}
-- The material for this course can be viewed without login requirement on this [Bookdown website](LINK HERE). This format might be most appropriate for you if you rely on screen-reader technology.
-- This course can be taken for [free certification through Leanpub](LINK HERE).
-- This course can be taken on [Coursera for certification here](LINK HERE) (but it is not available for free on Coursera).
-- Our courses are open source, you can find the [source material for this course on GitHub](LINK HERE).
+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: |
+ 
+