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167 changes: 88 additions & 79 deletions docs/02-chapter_of_course.md
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Expand Up @@ -23,7 +23,7 @@ For this chapter, we'll need the following packages attached:
*Remember to add [any additional packages you need to your course's own docker image](https://github.com/jhudsl/OTTR_Template/wiki/Using-Docker#starting-a-new-docker-image).


```r
``` r
library(magrittr)
```

Expand All @@ -37,7 +37,7 @@ Here's a subheading and some text in this subsection!
You can demonstrate code like this:


```r
``` r
output_dir <- file.path("resources", "code_output")
if (!dir.exists(output_dir)) {
dir.create(output_dir)
Expand All @@ -47,7 +47,7 @@ if (!dir.exists(output_dir)) {
And make plots too:


```r
``` r
hist_plot <- hist(iris$Sepal.Length)
```

Expand All @@ -56,7 +56,7 @@ hist_plot <- hist(iris$Sepal.Length)
You can also save these plots to file:


```r
``` r
png(file.path(output_dir, "test_plot.png"))
hist_plot
```
Expand Down Expand Up @@ -85,7 +85,7 @@ hist_plot
## [1] "histogram"
```

```r
``` r
dev.off()
```

Expand All @@ -98,7 +98,7 @@ dev.off()

How to include a Google slide. It's simplest to use the `ottrpal` package:

<img src="resources/images/02-chapter_of_course_files/figure-html//1YmwKdIy9BeQ3EShgZhvtb3MgR8P6iDX4DfFD65W_gdQ_gcc4fbee202_0_141.png" title="Major point!! example image" alt="Major point!! example image" width="480" style="display: block; margin: auto;" />
<img src="resources/images/02-chapter_of_course_files/figure-html//1YmwKdIy9BeQ3EShgZhvtb3MgR8P6iDX4DfFD65W_gdQ_gcc4fbee202_0_141.png" alt="Major point!! example image" width="480" style="display: block; margin: auto;" />

But if you have the slide or some other image locally downloaded you can also use html like this:

Expand All @@ -114,7 +114,7 @@ Alternatively, you can use `knitr::include_url()` like this:
Note that we are using `echo=FALSE` in the code chunk because we don't want the code part of this to show up.
If you are unfamiliar with [how R Markdown code chunks work, read this](https://rmarkdown.rstudio.com/lesson-3.html).

<iframe src="https://www.youtube.com/embed/VOCYL-FNbr0" width="672" height="400px"></iframe>
<iframe src="https://www.youtube.com/embed/VOCYL-FNbr0" width="672" height="400px" data-external="1"></iframe>

OR this works:

Expand All @@ -124,23 +124,23 @@ OR this works:

This works:

<iframe src="https://www.bgsu.edu/content/dam/BGSU/center-for-faculty-excellence/docs/TLGuides/TLGuide-Learning-Objectives.pdf" width="672" height="800px"></iframe>
<iframe src="https://www.bgsu.edu/content/dam/BGSU/center-for-faculty-excellence/docs/TLGuides/TLGuide-Learning-Objectives.pdf" width="672" height="800px" data-external="1"></iframe>

Or this:

[This works](https://www.bgsu.edu/content/dam/BGSU/center-for-faculty-excellence/docs/TLGuides/TLGuide-Learning-Objectives.pdf).
[This works](https://genetics-gsa.org/education/genetics-learning-framework/).

Or this:

<iframe src="https://www.bgsu.edu/content/dam/BGSU/center-for-faculty-excellence/docs/TLGuides/TLGuide-Learning-Objectives.pdf" width="672" height="800px"></iframe>
<iframe src="https://genetics-gsa.org/education/genetics-learning-framework/" width="672" height="800px"></iframe>

### Links to websites

Examples of including a website link.

This works:

<iframe src="https://yihui.org" width="672" height="400px"></iframe>
<iframe src="https://yihui.org" width="672" height="400px" data-external="1"></iframe>

OR this:

Expand Down Expand Up @@ -210,81 +210,90 @@ Here's more words that are hidden.
You should print out session info when you have code for [reproducibility purposes](https://jhudatascience.org/Reproducibility_in_Cancer_Informatics/managing-package-versions.html).


```r
``` r
devtools::session_info()
```

```
## ─ Session info ───────────────────────────────────────────────────────────────
## setting value
## version R version 4.0.2 (2020-06-22)
## os Ubuntu 20.04.5 LTS
## system x86_64, linux-gnu
## ui X11
## language (EN)
## collate en_US.UTF-8
## ctype en_US.UTF-8
## tz Etc/UTC
## date 2023-11-22
## setting value
## version R version 4.3.2 (2023-10-31)
## os Ubuntu 22.04.4 LTS
## system x86_64, linux-gnu
## ui X11
## language (EN)
## collate en_US.UTF-8
## ctype en_US.UTF-8
## tz Etc/UTC
## date 2024-08-05
## pandoc 3.1.1 @ /usr/local/bin/ (via rmarkdown)
##
## ─ Packages ───────────────────────────────────────────────────────────────────
## package * version date lib source
## assertthat 0.2.1 2019-03-21 [1] RSPM (R 4.0.5)
## bookdown 0.24 2023-03-28 [1] Github (rstudio/bookdown@88bc4ea)
## bslib 0.4.2 2022-12-16 [1] CRAN (R 4.0.2)
## cachem 1.0.7 2023-02-24 [1] CRAN (R 4.0.2)
## callr 3.5.0 2020-10-08 [1] RSPM (R 4.0.2)
## cli 3.6.1 2023-03-23 [1] CRAN (R 4.0.2)
## crayon 1.3.4 2017-09-16 [1] RSPM (R 4.0.0)
## curl 4.3 2019-12-02 [1] RSPM (R 4.0.3)
## desc 1.2.0 2018-05-01 [1] RSPM (R 4.0.3)
## devtools 2.3.2 2020-09-18 [1] RSPM (R 4.0.3)
## digest 0.6.25 2020-02-23 [1] RSPM (R 4.0.0)
## ellipsis 0.3.1 2020-05-15 [1] RSPM (R 4.0.3)
## evaluate 0.20 2023-01-17 [1] CRAN (R 4.0.2)
## fansi 0.4.1 2020-01-08 [1] RSPM (R 4.0.0)
## fastmap 1.1.1 2023-02-24 [1] CRAN (R 4.0.2)
## fs 1.5.0 2020-07-31 [1] RSPM (R 4.0.3)
## glue 1.4.2 2020-08-27 [1] RSPM (R 4.0.5)
## highr 0.8 2019-03-20 [1] RSPM (R 4.0.3)
## hms 0.5.3 2020-01-08 [1] RSPM (R 4.0.0)
## htmltools 0.5.5 2023-03-23 [1] CRAN (R 4.0.2)
## httr 1.4.2 2020-07-20 [1] RSPM (R 4.0.3)
## jquerylib 0.1.4 2021-04-26 [1] CRAN (R 4.0.2)
## jsonlite 1.7.1 2020-09-07 [1] RSPM (R 4.0.2)
## knitr 1.33 2023-03-28 [1] Github (yihui/knitr@a1052d1)
## lifecycle 1.0.3 2022-10-07 [1] CRAN (R 4.0.2)
## magrittr * 2.0.3 2022-03-30 [1] CRAN (R 4.0.2)
## memoise 2.0.1 2021-11-26 [1] CRAN (R 4.0.2)
## ottrpal 1.0.1 2023-03-28 [1] Github (jhudsl/ottrpal@151e412)
## pillar 1.9.0 2023-03-22 [1] CRAN (R 4.0.2)
## pkgbuild 1.1.0 2020-07-13 [1] RSPM (R 4.0.2)
## pkgconfig 2.0.3 2019-09-22 [1] RSPM (R 4.0.3)
## pkgload 1.1.0 2020-05-29 [1] RSPM (R 4.0.3)
## png 0.1-8 2022-11-29 [1] CRAN (R 4.0.2)
## prettyunits 1.1.1 2020-01-24 [1] RSPM (R 4.0.3)
## processx 3.4.4 2020-09-03 [1] RSPM (R 4.0.2)
## ps 1.4.0 2020-10-07 [1] RSPM (R 4.0.2)
## R6 2.4.1 2019-11-12 [1] RSPM (R 4.0.0)
## readr 1.4.0 2020-10-05 [1] RSPM (R 4.0.2)
## remotes 2.2.0 2020-07-21 [1] RSPM (R 4.0.3)
## rlang 1.1.0 2023-03-14 [1] CRAN (R 4.0.2)
## rmarkdown 2.10 2023-03-28 [1] Github (rstudio/rmarkdown@02d3c25)
## rprojroot 2.0.3 2022-04-02 [1] CRAN (R 4.0.2)
## sass 0.4.5 2023-01-24 [1] CRAN (R 4.0.2)
## sessioninfo 1.1.1 2018-11-05 [1] RSPM (R 4.0.3)
## stringi 1.5.3 2020-09-09 [1] RSPM (R 4.0.3)
## stringr 1.4.0 2019-02-10 [1] RSPM (R 4.0.3)
## testthat 3.0.1 2023-03-28 [1] Github (R-lib/testthat@e99155a)
## tibble 3.2.1 2023-03-20 [1] CRAN (R 4.0.2)
## usethis 1.6.3 2020-09-17 [1] RSPM (R 4.0.2)
## utf8 1.1.4 2018-05-24 [1] RSPM (R 4.0.3)
## vctrs 0.6.1 2023-03-22 [1] CRAN (R 4.0.2)
## withr 2.3.0 2020-09-22 [1] RSPM (R 4.0.2)
## xfun 0.26 2023-03-28 [1] Github (yihui/xfun@74c2a66)
## yaml 2.2.1 2020-02-01 [1] RSPM (R 4.0.3)
## package * version date (UTC) lib source
## askpass 1.2.0 2023-09-03 [1] RSPM (R 4.3.0)
## bookdown 0.39.1 2024-06-11 [1] Github (rstudio/bookdown@f244cf1)
## bslib 0.6.1 2023-11-28 [1] RSPM (R 4.3.0)
## cachem 1.0.8 2023-05-01 [1] RSPM (R 4.3.0)
## cli 3.6.2 2023-12-11 [1] RSPM (R 4.3.0)
## curl 5.2.0 2023-12-08 [1] RSPM (R 4.3.0)
## devtools 2.4.5 2022-10-11 [1] RSPM (R 4.3.0)
## digest 0.6.34 2024-01-11 [1] RSPM (R 4.3.0)
## ellipsis 0.3.2 2021-04-29 [1] RSPM (R 4.3.0)
## evaluate 0.23 2023-11-01 [1] RSPM (R 4.3.0)
## fansi 1.0.6 2023-12-08 [1] RSPM (R 4.3.0)
## fastmap 1.1.1 2023-02-24 [1] RSPM (R 4.3.0)
## fs 1.6.3 2023-07-20 [1] RSPM (R 4.3.0)
## glue 1.7.0 2024-01-09 [1] RSPM (R 4.3.0)
## highr 0.10 2022-12-22 [1] RSPM (R 4.3.0)
## hms 1.1.3 2023-03-21 [1] RSPM (R 4.3.0)
## htmltools 0.5.7 2023-11-03 [1] RSPM (R 4.3.0)
## htmlwidgets 1.6.4 2023-12-06 [1] RSPM (R 4.3.0)
## httpuv 1.6.14 2024-01-26 [1] RSPM (R 4.3.0)
## httr 1.4.7 2023-08-15 [1] RSPM (R 4.3.0)
## jquerylib 0.1.4 2021-04-26 [1] RSPM (R 4.3.0)
## jsonlite 1.8.8 2023-12-04 [1] RSPM (R 4.3.0)
## knitr 1.47.3 2024-06-11 [1] Github (yihui/knitr@e1edd34)
## later 1.3.2 2023-12-06 [1] RSPM (R 4.3.0)
## lifecycle 1.0.4 2023-11-07 [1] RSPM (R 4.3.0)
## magrittr * 2.0.3 2022-03-30 [1] RSPM (R 4.3.0)
## memoise 2.0.1 2021-11-26 [1] RSPM (R 4.3.0)
## mime 0.12 2021-09-28 [1] RSPM (R 4.3.0)
## miniUI 0.1.1.1 2018-05-18 [1] RSPM (R 4.3.0)
## openssl 2.1.1 2023-09-25 [1] RSPM (R 4.3.0)
## ottrpal 1.2.1 2024-06-11 [1] Github (jhudsl/ottrpal@828539f)
## pillar 1.9.0 2023-03-22 [1] RSPM (R 4.3.0)
## pkgbuild 1.4.3 2023-12-10 [1] RSPM (R 4.3.0)
## pkgconfig 2.0.3 2019-09-22 [1] RSPM (R 4.3.0)
## pkgload 1.3.4 2024-01-16 [1] RSPM (R 4.3.0)
## png 0.1-8 2022-11-29 [1] CRAN (R 4.3.2)
## profvis 0.3.8 2023-05-02 [1] RSPM (R 4.3.0)
## promises 1.2.1 2023-08-10 [1] RSPM (R 4.3.0)
## purrr 1.0.2 2023-08-10 [1] RSPM (R 4.3.0)
## R6 2.5.1 2021-08-19 [1] RSPM (R 4.3.0)
## Rcpp 1.0.12 2024-01-09 [1] RSPM (R 4.3.0)
## readr 2.1.5 2024-01-10 [1] RSPM (R 4.3.0)
## remotes 2.4.2.1 2023-07-18 [1] RSPM (R 4.3.0)
## rlang 1.1.4 2024-06-04 [1] CRAN (R 4.3.2)
## rmarkdown 2.27.1 2024-06-11 [1] Github (rstudio/rmarkdown@e1c93a9)
## sass 0.4.8 2023-12-06 [1] RSPM (R 4.3.0)
## sessioninfo 1.2.2 2021-12-06 [1] RSPM (R 4.3.0)
## shiny 1.8.0 2023-11-17 [1] RSPM (R 4.3.0)
## stringi 1.8.3 2023-12-11 [1] RSPM (R 4.3.0)
## stringr 1.5.1 2023-11-14 [1] RSPM (R 4.3.0)
## tibble 3.2.1 2023-03-20 [1] CRAN (R 4.3.2)
## tzdb 0.4.0 2023-05-12 [1] RSPM (R 4.3.0)
## urlchecker 1.0.1 2021-11-30 [1] RSPM (R 4.3.0)
## usethis 2.2.3 2024-02-19 [1] RSPM (R 4.3.0)
## utf8 1.2.4 2023-10-22 [1] RSPM (R 4.3.0)
## vctrs 0.6.5 2023-12-01 [1] RSPM (R 4.3.0)
## xfun 0.44.4 2024-06-11 [1] Github (yihui/xfun@9da62cc)
## xml2 1.3.6 2023-12-04 [1] RSPM (R 4.3.0)
## xtable 1.8-4 2019-04-21 [1] RSPM (R 4.3.0)
## yaml 2.3.8 2023-12-11 [1] RSPM (R 4.3.0)
##
## [1] /usr/local/lib/R/site-library
## [2] /usr/local/lib/R/library
##
## [1] /usr/local/lib/R/site-library
## [2] /usr/local/lib/R/library
## ──────────────────────────────────────────────────────────────────────────────
```

10 changes: 5 additions & 5 deletions docs/03-AnVIL_modules.md
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Expand Up @@ -17,23 +17,23 @@ Here is an example of including the `_child_workspace_create.Rmd` with `cow::bor

1. In the drop-down menu on the left, navigate to "Workspaces". Click the triple bar in the top left corner to access the menu. Click "Workspaces".

<img src="03-AnVIL_modules_files/figure-html//1zyqZHITAthNhXeH2XQqA7FMOu2mek6wfgGEaje1KQsk_g117989bd49c_0_150.png" title="Screenshot of Terra drop-down menu. The &quot;hamburger&quot; button to extend the drop-down menu is highlighted, and the menu item &quot;Workspaces&quot; is highlighted." alt="Screenshot of Terra drop-down menu. The &quot;hamburger&quot; button to extend the drop-down menu is highlighted, and the menu item &quot;Workspaces&quot; is highlighted." width="480" />
<img src="03-AnVIL_modules_files/figure-html//1zyqZHITAthNhXeH2XQqA7FMOu2mek6wfgGEaje1KQsk_g117989bd49c_0_150.png" alt="Screenshot of Terra drop-down menu. The &quot;hamburger&quot; button to extend the drop-down menu is highlighted, and the menu item &quot;Workspaces&quot; is highlighted." width="480" />

1. Click on the **plus icon** near the top of left of the page.

<img src="03-AnVIL_modules_files/figure-html//1zyqZHITAthNhXeH2XQqA7FMOu2mek6wfgGEaje1KQsk_g117989bd49c_0_733.png" title="Screenshot of Terra Workspaces page. The &quot;+&quot; is highlighted." alt="Screenshot of Terra Workspaces page. The &quot;+&quot; is highlighted." width="480" />
<img src="03-AnVIL_modules_files/figure-html//1zyqZHITAthNhXeH2XQqA7FMOu2mek6wfgGEaje1KQsk_g117989bd49c_0_733.png" alt="Screenshot of Terra Workspaces page. The &quot;+&quot; is highlighted." width="480" />

1. Name your Workspace and select the appropriate Billing Project. **All activity in the Workspace will be charged to this Billing Project** (regardless of who conducted it).

<img src="03-AnVIL_modules_files/figure-html//1zyqZHITAthNhXeH2XQqA7FMOu2mek6wfgGEaje1KQsk_g117989bd49c_0_877.png" title="Screenshot of Terra dialog box for creating a new Workspace. The text box labeled &quot;Workspace name&quot; and the drop-down menu labeled &quot;Billing project&quot; are highlighted." alt="Screenshot of Terra dialog box for creating a new Workspace. The text box labeled &quot;Workspace name&quot; and the drop-down menu labeled &quot;Billing project&quot; are highlighted." width="480" />
<img src="03-AnVIL_modules_files/figure-html//1zyqZHITAthNhXeH2XQqA7FMOu2mek6wfgGEaje1KQsk_g117989bd49c_0_877.png" alt="Screenshot of Terra dialog box for creating a new Workspace. The text box labeled &quot;Workspace name&quot; and the drop-down menu labeled &quot;Billing project&quot; are highlighted." width="480" />

1. If you are working with protected data, you can set the **Authorization Domain** to limit who can be added to your Workspace. Note that the Authorization Domain cannot be changed after the Workspace is created (i.e. there is no way to make this Workspace shareable with a larger audience in the future). Workspaces by default are only visible to people you specifically share them with. Authorization domains add an extra layer of enforcement over privacy, but by nature make sharing more complicated. We recommend using Authorization Domains in cases where it is extremely important and/or legally required that the data be kept private (e.g. protected patient data, industry data). For data you would merely prefer not be shared with the world, we recommend relying on standard Workspace sharing permissions rather than Authorization Domains, as Authorization Domains can make future collaborations, publications, or other sharing complicated.

<img src="03-AnVIL_modules_files/figure-html//1zyqZHITAthNhXeH2XQqA7FMOu2mek6wfgGEaje1KQsk_g117989bd49c_0_1022.png" title="Screenshot of Terra dialog box for creating a new Workspace. The drop-down menu labeled &quot;Authorization domain&quot; is highlighted." alt="Screenshot of Terra dialog box for creating a new Workspace. The drop-down menu labeled &quot;Authorization domain&quot; is highlighted." width="480" />
<img src="03-AnVIL_modules_files/figure-html//1zyqZHITAthNhXeH2XQqA7FMOu2mek6wfgGEaje1KQsk_g117989bd49c_0_1022.png" alt="Screenshot of Terra dialog box for creating a new Workspace. The drop-down menu labeled &quot;Authorization domain&quot; is highlighted." width="480" />

1. Click "CREATE WORKSPACE". The new Workspace should now show up under your Workspaces.

<img src="03-AnVIL_modules_files/figure-html//1zyqZHITAthNhXeH2XQqA7FMOu2mek6wfgGEaje1KQsk_g117989bd49c_0_1166.png" title="Screenshot of Terra dialog box for creating a new Workspace. The &quot;Create Workspace&quot; button is highlighted." alt="Screenshot of Terra dialog box for creating a new Workspace. The &quot;Create Workspace&quot; button is highlighted." width="480" />
<img src="03-AnVIL_modules_files/figure-html//1zyqZHITAthNhXeH2XQqA7FMOu2mek6wfgGEaje1KQsk_g117989bd49c_0_1166.png" alt="Screenshot of Terra dialog box for creating a new Workspace. The &quot;Create Workspace&quot; button is highlighted." width="480" />

## Background Highlighting for Borrowed Chapters

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