├── .gitignore ├── 03--Data_formatting.Rmd ├── 04--Markdown.Rmd ├── 05--RMarkdown.Rmd ├── 06--Git.Rmd ├── 07--Organization.Rmd ├── Extra_content---Advanced_RMarkdown.Rmd ├── Extra_content---The_Basics_of_R.Rmd ├── Getting_ready_to_use_R.html ├── Introduction.html ├── R-in-ten-minutes.R ├── README.md ├── Reproducible-science-in-R.Rproj ├── Setup.Rmd ├── _site.yml ├── bad_data ├── Fungicide Spread Sheet 2012.xls └── Temperature Spreadsheet 2012.xlsx ├── bibtexlib.bib ├── ex_data └── ComasOxapampa.csv ├── functions.R ├── header.html ├── images ├── blank_rmarkdown_file_screenshot.png ├── confirm_new_rmarkdown_file_screenshot.png ├── excel_date_error.jpg ├── git_branching.png ├── github.png ├── long_data.png ├── new_rmarkdown_file_screenshot.png ├── pinfestans_clone.png ├── pinfestans_fork.png ├── pinfestans_github.png ├── pinfestans_push.png ├── pressing_knit_down_arrow.png ├── pressing_knit_thumbnail_screenshot.png ├── r.png ├── rstudio-commit-confirm.png ├── rstudio-commit.png ├── rstudio-create.png ├── rstudio-empty.png ├── rstudio-git-add.png ├── rstudio-gitrepo.png ├── rstudio-history.png ├── rstudio-new.png ├── rstudio-rmd-add.png ├── rstudio-rmd-commit.png ├── rstudio-rmd.png ├── rstudio.png ├── two_column_data.png ├── two_sheet_data.png ├── ugly_data.png └── wide_data.png ├── index.Rmd ├── intro_presentation ├── .cache │ ├── __packages │ ├── simple-plot_91902e042121bfcfda489d5536b1648a.RData │ ├── simple-plot_91902e042121bfcfda489d5536b1648a.rdb │ ├── simple-plot_91902e042121bfcfda489d5536b1648a.rdx │ ├── unnamed-chunk-1_fb90a39790044ea355f08408c1f62625.RData │ ├── unnamed-chunk-1_fb90a39790044ea355f08408c1f62625.rdb │ └── unnamed-chunk-1_fb90a39790044ea355f08408c1f62625.rdx ├── assets │ ├── css │ │ ├── .gitkeep │ │ ├── custom.css │ │ ├── lists.css │ │ ├── quotes.css │ │ ├── ribbons.css │ │ ├── sizes.css │ │ ├── tables.css │ │ └── text.css │ ├── fig │ │ ├── simple-plot-1.png │ │ ├── unnamed-chunk-1-1.png │ │ └── unnamed-chunk-2-1.png │ ├── img │ │ └── .gitkeep │ ├── js │ │ └── .gitkeep │ ├── layouts │ │ └── .gitkeep │ └── libraries │ │ ├── frameworks │ │ └── io2012 │ │ │ ├── README.md │ │ │ ├── config.yml │ │ │ ├── css │ │ │ ├── default.css │ │ │ ├── fonts.css │ │ │ └── phone.css │ │ │ ├── images │ │ │ ├── google_developers_icon_128.png │ │ │ └── io2012_logo.png │ │ │ └── js │ │ │ ├── hammer.js │ │ │ ├── modernizr.custom.45394.js │ │ │ ├── order.js │ │ │ ├── polyfills │ │ │ ├── classList.min.js │ │ │ ├── dataset.min.js │ │ │ └── history.min.js │ │ │ ├── prettify │ │ │ ├── lang-apollo.js │ │ │ ├── lang-clj.js │ │ │ ├── lang-css.js │ │ │ ├── lang-go.js │ │ │ ├── lang-hs.js │ │ │ ├── lang-lisp.js │ │ │ ├── lang-lua.js │ │ │ ├── lang-ml.js │ │ │ ├── lang-n.js │ │ │ ├── lang-proto.js │ │ │ ├── lang-scala.js │ │ │ ├── lang-sql.js │ │ │ ├── lang-tex.js │ │ │ ├── lang-vb.js │ │ │ ├── lang-vhdl.js │ │ │ ├── lang-wiki.js │ │ │ ├── lang-xq.js │ │ │ ├── lang-yaml.js │ │ │ ├── prettify.css │ │ │ └── prettify.js │ │ │ ├── require-1.0.8.min.js │ │ │ ├── slide-controller.js │ │ │ ├── slide-deck.js │ │ │ ├── slide_config.js │ │ │ └── slides.js │ │ └── highlighters │ │ └── highlight.js │ │ ├── README.md │ │ ├── css │ │ ├── arta.css │ │ ├── ascetic.css │ │ ├── brown_paper.css │ │ ├── brown_papersq.png │ │ ├── dark.css │ │ ├── default.css │ │ ├── far.css │ │ ├── github.css │ │ ├── googlecode.css │ │ ├── hemisu-light.css │ │ ├── idea.css │ │ ├── ir_black.css │ │ ├── magula.css │ │ ├── monokai.css │ │ ├── pojoaque.css │ │ ├── pojoaque.jpg │ │ ├── school_book.css │ │ ├── school_book.png │ │ ├── solarized_dark.css │ │ ├── solarized_light.css │ │ ├── sunburst.css │ │ ├── tomorrow.css │ │ ├── tomorrow_night.css │ │ ├── vs.css │ │ ├── xcode.css │ │ └── zenburn.css │ │ └── highlight.pack.js ├── figure │ └── simple-plot-1.png ├── figures │ ├── Journal-of-Irrproducibe-Research.jpg │ ├── NatureSpecial.png │ ├── OSF.png │ ├── OSF2.png │ ├── Pubpeer1.png │ ├── Pubpeer2.png │ ├── Pubpeer3.png │ ├── Pubpeer4.png │ ├── RMarkdownOutputFormats.png │ ├── WashPost.png │ ├── docker.png │ └── docker.tiff ├── index.Rmd ├── index.md └── libraries │ ├── frameworks │ └── io2012 │ │ ├── README.md │ │ ├── config.yml │ │ ├── css │ │ ├── default.css │ │ ├── fonts.css │ │ ├── phone.css │ │ └── slidify.css │ │ ├── images │ │ ├── google_developers_icon_128.png │ │ └── io2012_logo.png │ │ └── js │ │ ├── hammer.js │ │ ├── modernizr.custom.45394.js │ │ ├── order.js │ │ ├── polyfills │ │ ├── classList.min.js │ │ ├── dataset.min.js │ │ └── history.min.js │ │ ├── prettify │ │ ├── lang-apollo.js │ │ ├── lang-clj.js │ │ ├── lang-css.js │ │ ├── lang-go.js │ │ ├── lang-hs.js │ │ ├── lang-lisp.js │ │ ├── lang-lua.js │ │ ├── lang-ml.js │ │ ├── lang-n.js │ │ ├── lang-proto.js │ │ ├── lang-scala.js │ │ ├── lang-sql.js │ │ ├── lang-tex.js │ │ ├── lang-vb.js │ │ ├── lang-vhdl.js │ │ ├── lang-wiki.js │ │ ├── lang-xq.js │ │ ├── lang-yaml.js │ │ ├── prettify.css │ │ └── prettify.js │ │ ├── require-1.0.8.min.js │ │ ├── slide-controller.js │ │ ├── slide-deck.js │ │ ├── slide_config.js │ │ └── slides.js │ └── highlighters │ └── highlight.js │ ├── README.md │ ├── css │ ├── arta.css │ ├── ascetic.css │ ├── brown_paper.css │ ├── brown_papersq.png │ ├── dark.css │ ├── default.css │ ├── far.css │ ├── github.css │ ├── googlecode.css │ ├── hemisu-light.css │ ├── idea.css │ ├── ir_black.css │ ├── magula.css │ ├── monokai.css │ ├── pojoaque.css │ ├── pojoaque.jpg │ ├── school_book.css │ ├── school_book.png │ ├── solarized_dark.css │ ├── solarized_light.css │ ├── sunburst.css │ ├── tomorrow.css │ ├── tomorrow_night.css │ ├── vs.css │ ├── xcode.css │ └── zenburn.css │ └── highlight.pack.js ├── make_gh_page.R ├── presentation_notes ├── markdown.Rmd └── rmarkdown.Rmd ├── quilt_config.yml └── tutorial.css /.gitignore: -------------------------------------------------------------------------------- 1 | .Rproj.user 2 | .Rhistory 3 | .RData 4 | **.html 5 | *_cache/** 6 | *_files/** 7 | *.cache/** 8 | site_libs/** 9 | !header.html 10 | -------------------------------------------------------------------------------- /07--Organization.Rmd: -------------------------------------------------------------------------------- 1 | --- 2 | title: Organization 3 | --- 4 | 5 | ```{r init, echo=FALSE} 6 | library(knitr) 7 | source("functions.R") 8 | ``` 9 | 10 | Although advanced tools like git and RMarkdown greatly enhance reproducibility, they are only useful if files and folders are organized in such a way that another person (or you 3 weeks/months/years later) can make sense of them. 11 | This can be surprisingly difficult and there is no universal solution that will work best for all people or projects. 12 | However, there are some tips that will help you arrive at a solution that fits your work style and the needs of your project. 13 | 14 | ## File/Folder naming 15 | 16 | Good file/folder naming is perhaps the easiest way to improve the understandably of the digital aspects of your project. 17 | Ideally, a file's name and the names of the folders it is in should be enough information to make a good guess at its contents. 18 | Note that this information need not all be in the file's name, which would lead to unreadably long file names; it should be distributed throughout the names of the folders it is in as well as the file's name. 19 | Below are a couple tips on file naming: 20 | 21 | - **Name files with a purpose.** Never use arbitrary names (e.g. `Document1.Rmd`, `asdafsa.Rmd`). If the file is unimportant or temporary, name it something like `temp.Rmd`, `scratch.Rmd`, or `random_gibberish.Rmd` so that you don't need to open it to know that it is unimportant. 22 | - **Only use letters, numbers, underscores, and dashes in file names.** Use underscores instead of spaces; file names with spaces are irritating to manipulate on the command line and are not well handled by UNIX-based operating systems. 23 | + One or more dashes make good delimiters if a file's name has multiple distinct components (e.g. `chapter_1--what_i_did_today.Rmd`). 24 | - **Avoid mixing upper and lower case letters.** Most operating systems are case-sensitive, so `file.Rmd` and `File.Rmd` would be considered different files yet they might be easily confused by people. If you use uppercase, use it for the whole file name (e.g. `README.txt`). 25 | - **Use YYYY-MM-DD for dates** If a file/folder pertains to a specific date, prefix the date in the YYYY-MM-DD format (e.g. "2016-03-23--wheat_audpc.Rmd"). Using YYYY-MM-DD instead of something like YYYY-DD-MM means that files are sorted by date correctly by default. Also, YYYY-MM-DD is the [ISO standard format for dates](http://www.iso.org/iso/home/standards/iso8601.htm). 26 | - **Order your analyses** If multiple files/folders have a logical order, prefix them with numbers, padding with leading zeros when needed (e.g. `002--DNA_extraction.Rmd`). The leading zeros make them ordered correctly by default. 27 | - **Use the correct extension** All files you create are, in essence, text files, but they don't all have to be labeled `.txt`. 28 | + If a text file has a table of comma-separated values, use `.csv` instead of `.txt`; if it is tab-separated, used `.tsv`. 29 | + If a text file contains markdown, use `.md`. 30 | 31 | ## Folder structure 32 | 33 | How to best construct a logical hierarchy of folders is less well defined than naming conventions since it will vary widely with project type and personal preference. 34 | Spend some time thinking about a system that will work for you and stick to it, at least within a single project. 35 | 36 | - **Use sub-folders.** Don't hesitate to use sub-folders to group similar files. A deep hierarchy with simple file names is better than a shallow hierarchy with long names. 37 | - **Keep things minimal.** Avoid large numbers of unrelated files/folders in a single folder. It should be easy to scan over file names to get a sense of what is in a folder. 38 | - **Use README files.** Add a "README.md" file to folders explaining their purpose and contents, especially if there are many files or files with un-intuitive names. 39 | - **Use a project-specific folder.** Avoid using default, operating-system-specific directories like "My Documents" since these often get cluttered by program-generated files and have properties that are not supported by other operating systems. Instead, make a single directory that contains all of your files, not including programs and operating system components. This makes it easy to backup your files and transfer them to other computers. 40 | 41 | 42 | ## Working habits 43 | 44 | Good organization takes time and work to create and maintain, but developing good habits can make the task less daunting and can make you more efficient in the long term. 45 | 46 | - **Be consistent.** Maintain a consistent organization style on all of the computers and projects you work on. 47 | - **Keep temporary files seperate.** Have a temporary folder for files that you might not keep or have not decided where to put yet. However, this must be kept clean to be useful. 48 | - **Use shortcuts.** Use shortcuts/links to access commonly used files/folders, especially if your project calls for a deep folder hierarchy. 49 | - **Back up early, Back up often.** Make routine backups stored in three different ways (e.g. An external hard drive stored at home, an online backup service, and code and text on GitHub). 50 | 51 | ## Additional resources 52 | 53 | - [howtogeek article on file/folder organization](http://www.howtogeek.com/howto/15677/zen-and-the-art-of-file-and-folder-organization/) 54 | - [presentation on organizing computational research](http://kbroman.org/Tools4RR/assets/lectures/06_org_eda_withnotes.pdf) by Karl Broman. 55 | - [Steps Toward Reproducible Research](http://kbroman.org/steps2rr/) Website accompanying the above lecture. -------------------------------------------------------------------------------- /Extra_content---Advanced_RMarkdown.Rmd: -------------------------------------------------------------------------------- 1 | --- 2 | title: Advanced **R**Markdown 3 | --- 4 | 5 | ```{r init, echo=FALSE} 6 | library(knitr) 7 | library(xtable) 8 | library(tools) 9 | library(ggplot2) 10 | source("functions.R") 11 | step <- make_step_counter_function() 12 | rmd_example <- make_markdown_example_function() 13 | opts_chunk$set(warning = FALSE, 14 | message = FALSE, 15 | echo = FALSE) 16 | 17 | ``` 18 | 19 | ```{r java, results='asis', echo = FALSE} 20 | # Add javascript to cause the iframes to be scrolled down all the way when the page loads. 21 | pre_scroll_iframe() 22 | ``` 23 | 24 | ## Animated figures 25 | 26 | If a chunk prints multiple graphs, the graphs can be converted into steps in an animation. 27 | This only works if ffmpeg is installed. 28 | 29 | `r step('Copy the text from the box below and paste it on to the end of your Markdown document and press "Knit HTML".')` 30 | 31 | ```{r animate_figure_example, results='asis', echo = FALSE, eval = TRUE} 32 | rmd_example(height = 500, render = system('ffmpeg -version') == 0, " 33 | ## Animated figures 34 | 35 | \`\`\`{r, fig.show='animate', fig.width=5, fig.height=4} 36 | library(ggplot2) 37 | for (count in 1:4) { 38 | n <- 10 ^ count 39 | x <- data.frame(var = rnorm(n)) 40 | print(ggplot(x) + 41 | geom_histogram(aes(x = var), binwidth = 0.2) + 42 | ggtitle(paste('n =', n))) 43 | } 44 | \`\`\` 45 | ") 46 | 47 | ``` 48 | 49 | 50 | ## Caching 51 | 52 | A potential downside of combining code used to analyse data and notes/interpretation is that every time you rerun the RMarkdown document to make a small change (e.g. add or update notes), all of the code is run again even if no changes to the code are made. 53 | For analyses that take a long time, this can make using RMarkdown impractical. 54 | Fortunately, there is a feature called caching that allows the results of each chunk to be saved independently and reused if no changes are made to that chunk. 55 | Setting the chunk option `cache` to `TRUE` will mean that after a code chunk is run for the first time it will not need to be run again unless it changes. 56 | 57 | Below is an example of code to draw a [Barnsley Fern](https://en.wikipedia.org/wiki/Barnsley_fern) borrowed from an [RPub by Kui-Ming Chen](https://rpubs.com/BenChen/fern_fractal). 58 | 59 | `r step('Copy the text from the box below and paste it on to the end of your Markdown document and press "Knit HTML". It should take at least a few seconds extra to draw the complicated graph. Once it is done, press "Knit HTML" again. It should take nearly the same amount of time as it had before adding the graph. Now, change the value of the "iter" variable on the first line to something else near 10000 and press "Knit HTML" again. Since the code has changed, it should once again take more time to remake the graph.')` 60 | 61 | ```{r caching_example, results='asis', echo = FALSE} 62 | rmd_example(height = NULL, " 63 | ## Caching 64 | 65 | \`\`\`{r, cache=TRUE} 66 | iter <- 10000 67 | p <- runif(iter) 68 | coord <- matrix(c(0, 0), ncol = 1) 69 | df <- rbind(data.frame(), t(coord)) 70 | for (i in 1:iter) { 71 | if (p[i] <= 0.05) { 72 | m <- matrix(c(0, 0, 0, 0.16), nrow = 2, ncol = 2) 73 | const <- matrix(c(0, 0), ncol = 1) 74 | } else if (p[i] > 0.05 && p[i] <= 0.86) { 75 | m <- matrix(c(0.85, -0.04, 0.04, 0.85), nrow = 2, ncol = 2) 76 | const <- matrix(c(0, 1.6), ncol = 1) 77 | } else if (p[i] > 0.86 && p[i] <= 0.93) { 78 | m <- matrix(c(0.2, 0.23, -0.26, 0.22), nrow = 2, ncol = 2) 79 | const <- matrix(c(0, 1.6), ncol = 1) 80 | 81 | } else { 82 | m <- matrix(c(-0.15, 0.26, 0.28, 0.24), nrow = 2, ncol = 2) 83 | const <- matrix(c(0, 0.44), ncol = 1) 84 | } 85 | coord <- m %*% coord + const 86 | df <- rbind(df, t(coord)) 87 | } 88 | 89 | plot(x = df[, 2], y = df[, 1], plt = c(0, 10, -5, 5), cex = 0.1, asp = 1) 90 | \`\`\` 91 | ") 92 | ``` 93 | 94 | There are subtle issues that can occur when mixing cached and uncached chunks that reference the same variables, so you should learn more about the details of how caching works before relying on it too heavily. 95 | 96 | -------------------------------------------------------------------------------- /R-in-ten-minutes.R: -------------------------------------------------------------------------------- 1 | ## ----calculate_good_times------------------------------------------------ 2 | 47 + 2 3 | 47 * 2 4 | 5 | ## ----its_magic----------------------------------------------------------- 6 | # 49 - 2 and 94/2 are both 47. It's magic! 7 | its <- 49 - 2 8 | magic <- 94 / 2 9 | 10 | ## ----vector_me_this------------------------------------------------------ 11 | some_numbers <- c(10.0, pi, 47.5362, 3.50, 1.1111) 12 | some_numbers 13 | 14 | some_integers <- c(NA, 1, 1, 2, 3) # NA is code for "missing" in R 15 | some_integers 16 | 17 | more_integers <- 1:5 # same as c(1, 2, 3, 4), but a lot easier to type! 18 | more_integers 19 | 20 | some_characters <- c("work it", "harder", "make it", "better", 21 | "do it", "faster", "makes us", "stronger") 22 | some_characters 23 | 24 | some_logic <- c(TRUE, FALSE, TRUE, TRUE, FALSE) 25 | some_logic 26 | 27 | ## ----v_add_o------------------------------------------------------------- 28 | some_integers ^ 2 29 | 30 | ## ----v_drag-------------------------------------------------------------- 31 | some_integers + some_numbers 32 | 33 | ## ----get_number---------------------------------------------------------- 34 | some_numbers[2] 35 | 36 | some_characters[c(1, 3, 5, 7)] 37 | 38 | some_logic[1:3] 39 | 40 | fib <- some_integers[-1] # remove the first element 41 | fib 42 | 43 | some_characters[fib] # you can also use other vectors! 44 | 45 | ## ----truth_and_consequences---------------------------------------------- 46 | some_numbers[some_logic] 47 | 48 | ## ----less_than_ten------------------------------------------------------- 49 | some_numbers # the first and second elements are not less than 10. 50 | some_numbers[some_numbers < 10] 51 | 52 | ## ------------------------------------------------------------------------ 53 | ComasOxapampa <- read.table("ex_data/ComasOxapampa.csv", sep = ",", head = TRUE) 54 | 55 | ## ------------------------------------------------------------------------ 56 | str(ComasOxapampa) 57 | 58 | ## ------------------------------------------------------------------------ 59 | ComasOxapampa$comas # vector of AUDPC values for Comas 60 | 61 | ## ------------------------------------------------------------------------ 62 | ComasOxapampa$difference <- ComasOxapampa$comas - ComasOxapampa$oxapampa 63 | head(ComasOxapampa) # Look at the top of the data (6 rows by default) 64 | 65 | ## ------------------------------------------------------------------------ 66 | nrow(ComasOxapampa) 67 | ncol(ComasOxapampa) 68 | 69 | ## ------------------------------------------------------------------------ 70 | length(unique(ComasOxapampa$cultivar)) 71 | 72 | ## ------------------------------------------------------------------------ 73 | region_t <- t.test(ComasOxapampa$comas, ComasOxapampa$oxapampa) 74 | region_t 75 | 76 | ## ----install_package, eval = FALSE--------------------------------------- 77 | install.packages("agricolae", repos = "https://cran.rstudio.org") 78 | 79 | ## ------------------------------------------------------------------------ 80 | library("agricolae") # The package with the audpc() function. 81 | ?audpc # open the R documentation of the function audpc() 82 | 83 | ## ---- eval = FALSE------------------------------------------------------- 84 | help(package = "agricolae") # Get help for a package. 85 | help("audpc") # Get help for the audpc function 86 | ?audpc # same as above 87 | ??disease # Search for help with the keyword 'disease' in all packages 88 | 89 | ## ------------------------------------------------------------------------ 90 | example("audpc", package = "agricolae") 91 | 92 | browseVignettes(package = "tidyr") # see vignettes from a specific package. 93 | 94 | ## ---- eval=FALSE--------------------------------------------------------- 95 | vignette('mlg') # Multilocus Genotype vignette from the poppr package 96 | 97 | 98 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # Reproducible science in R 2 | 3 | *Zachary S.L. Foster, Zhian N. Kamvar, and Niklaus J. Grünwald* 4 | 5 | Welcome! This primer provides a concise introduction to conducting reproducible science in R. While this primer does not require extensive knowledge of programming in R, the user is expected to install R and all packages required for this primer. 6 | 7 | # Chapters 8 | 9 | | Session | Length| Clock| 10 | |--------------------------------------------|-------|------| 11 | |Introduction (Nik) | 20min | 8:30| 12 | |Data formatting and read/write (Zhian) | 15min | 8:50| 13 | |Markdown (Zach) | 30min | 9:20| 14 | |Break | 20min | 9:40| 15 | |Intro to R (Zhian) | 10min | 10:00| 16 | |R markdown (Zach) | 50min | 10:10| 17 | |Git and github (Zhian) | 20min | 11:00| 18 | |Organizing Reproducible Research (Zach) | 10min | 11:20| 19 | |Wrapup Survey | 5min | 11:30| 20 | 21 | 22 | # Website 23 | 24 | You can find rendered vignettes on [our website](http://grunwaldlab.github.io/Reproducible-science-in-R/). 25 | 26 | ## Building the webite 27 | 28 | install the *git2r*, *knitcitations*, and *rmarkdown* packages: 29 | 30 | ```r 31 | devtools::install_github("rstudio/rmarkdown", "cboettig/knitcitations") 32 | install.packages("git2r") 33 | ``` 34 | 35 | To build the website locally: 36 | 37 | ```r 38 | rmarkdown::render_site() 39 | ``` 40 | 41 | To build the website on the `gh-pages` branch 42 | 43 | ```r 44 | source("make_gh_page.R", echo = TRUE) 45 | ``` 46 | 47 | You can then push your changes from the master and the gh-pages branch. 48 | 49 | It seems to work, but ¯\\_(ツ)_/¯ 50 | 51 | # Survey 52 | 53 | **http://goo.gl/forms/OCFxqPbXhsWMBQYT2** 54 | -------------------------------------------------------------------------------- /Reproducible-science-in-R.Rproj: -------------------------------------------------------------------------------- 1 | Version: 1.0 2 | 3 | RestoreWorkspace: Default 4 | SaveWorkspace: Default 5 | AlwaysSaveHistory: Default 6 | 7 | EnableCodeIndexing: Yes 8 | UseSpacesForTab: Yes 9 | NumSpacesForTab: 2 10 | Encoding: UTF-8 11 | 12 | RnwWeave: knitr 13 | LaTeX: pdfLaTeX 14 | -------------------------------------------------------------------------------- /_site.yml: -------------------------------------------------------------------------------- 1 | name: "Reproducible-science-in-R" 2 | output_dir: "." 3 | navbar: 4 | title: "Reproducible Science in R" 5 | href: index.html 6 | left: 7 | - text: "Setup" 8 | href: Setup.html 9 | - text: "Data formatting" 10 | href: 03--Data_formatting.html 11 | - text: "Markdown" 12 | href: 04--Markdown.html 13 | - text: "RMarkdown" 14 | href: 05--RMarkdown.html 15 | - text: "Git and GitHub" 16 | href: 06--Git.html 17 | - text: "Organization" 18 | href: 07--Organization.html 19 | - text: "Extra Content" 20 | menu: 21 | - text: "The Basics of R" 22 | href: Extra_content---The_Basics_of_R.html 23 | - text: "Advanced RMarkdown" 24 | href: Extra_content---Advanced_RMarkdown.html 25 | output: 26 | html_document: 27 | toc: true 28 | toc_float: 29 | collapsed: false 30 | toc_depth: 2 31 | theme: flatly 32 | css: tutorial.css 33 | includes: 34 | before_body: header.html -------------------------------------------------------------------------------- /bad_data/Fungicide Spread Sheet 2012.xls: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/grunwaldlab/Reproducible-science-in-R/0bb8e62689e0fb7c813051551342c046144f389b/bad_data/Fungicide Spread Sheet 2012.xls -------------------------------------------------------------------------------- /bad_data/Temperature Spreadsheet 2012.xlsx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/grunwaldlab/Reproducible-science-in-R/0bb8e62689e0fb7c813051551342c046144f389b/bad_data/Temperature Spreadsheet 2012.xlsx -------------------------------------------------------------------------------- /ex_data/ComasOxapampa.csv: -------------------------------------------------------------------------------- 1 | cultivar,replication,comas,oxapampa 2 | Amarilis-INIA,I,0.57,0.6 3 | Andinita,I,0.319,0.661 4 | Atahualpa,I,0.5,0.627 5 | Baseko,I,0.423,0.511 6 | BIRRIS,I,0.555,0.683 7 | C91-906-(Primavera),I,0.305,0.397 8 | Canchan-INIA,I,0.707,0.68 9 | Chagllina-INIA,I,0.602,0.618 10 | Chamak,I,0.655,0.723 11 | Chata-Roja,I,0.471,0.625 12 | Costanera,I,0.637,0.718 13 | CRUZA-148,I,0.148,0.61 14 | Dheera,I,0.524,0.693 15 | Enfula,I,0.245,0.629 16 | FLS-5-(Raniag),I,0.586,0.631 17 | Gikungu,I,0.087,0.509 18 | Heera,I,0.726,0.738 19 | ICA-Zipa,I,0.465,0.663 20 | Idiafrit,I,0.411,0.594 21 | IDIAP-92,I,0.309,0.362 22 | Ingabire,I,0.27,0.617 23 | INIA-301,I,0.268,0.664 24 | INIAP-FRIPAPA,I,0.341,0.619 25 | INIAPMargarita,I,0.133,0.666 26 | IRA-92,I,0.605,0.622 27 | Jubile,I,0.509,0.768 28 | Kigega,I,0.166,0.522 29 | Kinga,I,0.684,0.712 30 | Kinigi,I,0.195,0.6 31 | Kisoro,I,0.24,0.336 32 | Kori-INIA,I,0.251,0.598 33 | LB-(AWASH),I,0.547,0.72 34 | LB-III-(PRECODEPA),I,0.393,0.678 35 | LBr-40,I,0.03,0.019 36 | LB-VII-(Chaposa),I,0.37,0.575 37 | LT-5,I,0.5,0.27 38 | Maria-Bonita-INIA,I,0.405,0.397 39 | MariaHuanca,I,0.655,0.671 40 | Maria-Tambena,I,0.619,0.594 41 | MF-IxTPS-13(CIP-SURAJ),I,0.377,0.666 42 | Muruta,I,0.28,0.668 43 | Muziranzara,I,0.035,0.315 44 | P-9,I,0.303,0.615 45 | Perricholi,I,0.373,0.695 46 | PIMPERNEL,I,0.679,0.614 47 | REICHE,I,0.587,0.713 48 | Rukinzo,I,0.162,0.084 49 | SantaAna,I,0.534,0.609 50 | Tacna,I,0.669,0.74 51 | Tahuaquea,I,0.725,0.669 52 | TIBISAY,I,0.14,0.695 53 | Tubira,I,0.555,0.7 54 | UNICA,I,0.433,0.635 55 | Victoria,I,0.234,0.224 56 | Yana,I,0.564,0.728 57 | Yayla-Kizi,I,0.71,0.62 58 | Amarilis-INIA,II,0.596,0.652 59 | Andinita,II,0.357,0.688 60 | Atahualpa,II,0.498,0.63 61 | Baseko,II,0.334,0.598 62 | BIRRIS,II,0.499,0.68 63 | C91-906-(Primavera),II,0.236,0.435 64 | Canchan-INIA,II,0.646,0.694 65 | Chagllina-INIA,II,0.555,0.632 66 | Chamak,II,0.706,0.747 67 | Chata-Roja,II,0.42,0.642 68 | Costanera,II,0.706,0.724 69 | CRUZA-148,II,0.164,0.547 70 | Dheera,II,0.57,0.695 71 | Enfula,II,0.062,0.641 72 | FLS-5-(Raniag),II,0.663,0.611 73 | Gikungu,II,0.293,0.547 74 | Heera,II,0.734,0.743 75 | ICA-Zipa,II,0.489,0.676 76 | Idiafrit,II,0.39,0.618 77 | IDIAP-92,II,0.305,0.35 78 | Ingabire,II,0.346,0.612 79 | INIA-301,II,0.293,0.667 80 | INIAP-FRIPAPA,II,0.356,0.673 81 | INIAPMargarita,II,0.283,0.635 82 | IRA-92,II,0.541,0.632 83 | Jubile,II,0.537,0.725 84 | Kigega,II,0.162,0.582 85 | Kinga,II,0.67,0.724 86 | Kinigi,II,0.177,0.66 87 | Kisoro,II,0.269,0.261 88 | Kori-INIA,II,0.28,0.648 89 | LB-(AWASH),II,0.524,0.716 90 | LB-III-(PRECODEPA),II,0.353,0.717 91 | LBr-40,II,0.011,0.019 92 | LB-VII-(Chaposa),II,0.359,0.617 93 | LT-5,II,0.559,0.536 94 | Maria-Bonita-INIA,II,0.505,0.465 95 | MariaHuanca,II,0.729,0.656 96 | Maria-Tambena,II,0.557,0.575 97 | MF-IxTPS-13(CIP-SURAJ),II,0.5,0.62 98 | Muruta,II,0.445,0.649 99 | Muziranzara,II,0.035,0.259 100 | P-9,II,0.377,0.706 101 | Perricholi,II,0.541,0.728 102 | PIMPERNEL,II,0.583,0.679 103 | REICHE,II,0.596,0.786 104 | Rukinzo,II,0.328,0.118 105 | SantaAna,II,0.655,0.649 106 | Tacna,II,0.689,0.743 107 | Tahuaquea,II,0.704,0.719 108 | TIBISAY,II,0.203,0.68 109 | Tubira,II,0.642,0.679 110 | UNICA,II,0.515,0.644 111 | Victoria,II,0.461,0.241 112 | Yana,II,0.781,0.722 113 | Yayla-Kizi,II,0.725,0.722 114 | Amarilis-INIA,III,0.641,0.607 115 | Andinita,III,0.4,0.65 116 | Atahualpa,III,0.6,0.606 117 | Baseko,III,0.323,0.475 118 | BIRRIS,III,0.576,0.683 119 | C91-906-(Primavera),III,0.332,0.641 120 | Canchan-INIA,III,0.732,0.662 121 | Chagllina-INIA,III,0.57,0.588 122 | Chamak,III,0.711,0.682 123 | Chata-Roja,III,0.386,0.63 124 | Costanera,III,0.688,0.773 125 | CRUZA-148,III,0.194,0.524 126 | Dheera,III,0.62,0.652 127 | Enfula,III,0.202,0.598 128 | FLS-5-(Raniag),III,0.632,0.564 129 | Gikungu,III,0.271,0.516 130 | Heera,III,0.776,0.722 131 | ICA-Zipa,III,0.534,0.65 132 | Idiafrit,III,0.56,0.595 133 | IDIAP-92,III,0,0.244 134 | Ingabire,III,0.227,0.574 135 | INIA-301,III,0.345,0.627 136 | INIAP-FRIPAPA,III,0.507,0.594 137 | INIAPMargarita,III,0.326,0.621 138 | IRA-92,III,0.578,0.629 139 | Jubile,III,0.555,0.722 140 | Kigega,III,0.249,0.434 141 | Kinga,III,0.725,0.704 142 | Kinigi,III,0.285,0.595 143 | Kisoro,III,0.264,0.137 144 | Kori-INIA,III,0.248,0.615 145 | LB-(AWASH),III,0,0.684 146 | LB-III-(PRECODEPA),III,0.512,0.678 147 | LBr-40,III,0.011,0.031 148 | LB-VII-(Chaposa),III,0.328,0.54 149 | LT-5,III,0.64,0.207 150 | Maria-Bonita-INIA,III,0.505,0.437 151 | MariaHuanca,III,0.724,0.694 152 | Maria-Tambena,III,0.541,0.605 153 | MF-IxTPS-13(CIP-SURAJ),III,0.428,0.677 154 | Muruta,III,0.43,0.605 155 | Muziranzara,III,0.019,0.094 156 | P-9,III,0.364,0.623 157 | Perricholi,III,0,0.627 158 | PIMPERNEL,III,0.639,0.654 159 | REICHE,III,0.596,0.685 160 | Rukinzo,III,0.383,0.109 161 | SantaAna,III,0.56,0.602 162 | Tacna,III,0.641,0.722 163 | Tahuaquea,III,0.736,0.676 164 | TIBISAY,III,0.225,0.642 165 | Tubira,III,0.593,0.616 166 | UNICA,III,0.49,0.616 167 | Victoria,III,0.424,0.165 168 | Yana,III,0,0.744 169 | Yayla-Kizi,III,0.72,0.668 170 | -------------------------------------------------------------------------------- /functions.R: -------------------------------------------------------------------------------- 1 | #' Print step number 2 | #' 3 | #' Generates a closure (i.e. function with data) that prints a step header and increments the step number each time it is called. 4 | #' 5 | make_step_counter_function <- function() { 6 | step <- 0 7 | function(content) { 8 | step <<- step + 1 9 | paste0("**", " Step ", step, ") ", content, "**") 10 | } 11 | } 12 | 13 | 14 | 15 | #' Generate example HTML 16 | #' 17 | #' Generates a closure (i.e. function with data) that prints a peice of RMarkdown markup and the results of rendering it to HTML. 18 | #' The function generated can remember the information from previous calls and append content. 19 | #' 20 | #' @param content (\code{character} of lenght one) RMarkdown text to display and render. 21 | #' 22 | make_markdown_example_function <- function(content, horizontal = FALSE) { 23 | counter <- 0 24 | previous_content <- "" 25 | 26 | function(content, cumulative = FALSE, height = NULL, prefix = FALSE, show_knit_button = FALSE, render = TRUE) { 27 | # Set default figure height 28 | if (is.null(height)) { 29 | height <- (length(gregexpr("\\n", content)[[1]]) + 1) * 20 30 | } 31 | 32 | # increment counter so that file names can be unique 33 | counter <<- counter + 1 34 | 35 | # implement content saving 36 | currrent_content <- content 37 | if (cumulative) { 38 | if (prefix) { 39 | content <- paste0(content, previous_content) 40 | 41 | } else { 42 | content <- paste0(previous_content, content) 43 | } 44 | previous_content <<- content 45 | } 46 | 47 | 48 | # get input document information 49 | current_file_name <- knitr:::knit_concord$get("infile") 50 | current_folder <- normalizePath(knitr:::.knitEnv$input.dir) 51 | 52 | # Create source Rmd file 53 | source_path <- tempfile(pattern = "rmarkdown_example", fileext = ".Rmd", tmpdir = current_folder) 54 | cat(content, file = source_path) 55 | 56 | # Render source file to html 57 | current_knit_opts <- opts_chunk$get() # Save external knit parameters to restore later 58 | if (render) { 59 | output_path <- tempfile(pattern = "rmarkdown_example", fileext = ".html", tmpdir = current_folder) 60 | opts_chunk$restore() # Set knitr to use default chunk options 61 | rmarkdown::render(input = source_path, output_file = output_path, quiet = TRUE, output_format = "html_fragment") 62 | 63 | } 64 | 65 | # Generate html to display source 66 | source_html <- paste0("
", currrent_content, "
") 67 | 68 | # Generate html to display knit image 69 | img_path <- "./images/pressing_knit_down_arrow.png" 70 | image_html <- paste0("") 71 | 72 | # Rendered HTML 73 | if (render) { 74 | result_html <- readChar(output_path, file.info(output_path)$size) 75 | } 76 | 77 | on.exit({ 78 | do.call(opts_chunk$set, current_knit_opts) # Restore external knit parameters 79 | file.remove(source_path) 80 | if (render) { file.remove(output_path) } 81 | }) 82 | 83 | # Display result 84 | if (horizontal) { 85 | cat(paste0('
', 86 | '
', source_html, '
', 87 | ifelse(render, paste0('
', result_html, '
'), ""), 88 | '
')) 89 | } else { 90 | cat(paste0('
', 91 | '
', source_html, '
', 92 | ifelse(show_knit_button, image_html, ""), 93 | ifelse(render, paste0('
', result_html, '
'), ""), 94 | '
')) 95 | 96 | } 97 | } 98 | } 99 | 100 | 101 | 102 | #' Scrolls iframes 103 | #' 104 | #' Prints Javascript to make iframes scrolled down when page loads 105 | pre_scroll_iframe <- function() { 106 | cat(' 107 | 114 | ') 115 | } 116 | 117 | 118 | #' Glossary 119 | #' 120 | #' Handles the defining and printing of glossary terms. 121 | make_glossary_function <- function() { 122 | glossary <- list() 123 | function(term = NULL, description = NULL, display_glossary = FALSE) { 124 | if (display_glossary) { 125 | for (index in seq_along(glossary)) { 126 | glossary <<- glossary[order(names(glossary))] 127 | cat(paste0("", names(glossary)[index], ": ", glossary[[index]], "\n\n")) 128 | } 129 | } else { 130 | if (is.null(term) | is.null(description)) { 131 | stop("Glossary term and/or description required") 132 | } 133 | # Save term in glossary 134 | glossary[term] <<- description 135 | 136 | # Print formatted term 137 | rendered_term <- paste0("", term, "") 138 | return(rendered_term) 139 | } 140 | } 141 | } 142 | 143 | 144 | 145 | 146 | -------------------------------------------------------------------------------- /header.html: -------------------------------------------------------------------------------- 1 | 11 | -------------------------------------------------------------------------------- /images/blank_rmarkdown_file_screenshot.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/grunwaldlab/Reproducible-science-in-R/0bb8e62689e0fb7c813051551342c046144f389b/images/blank_rmarkdown_file_screenshot.png -------------------------------------------------------------------------------- /images/confirm_new_rmarkdown_file_screenshot.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/grunwaldlab/Reproducible-science-in-R/0bb8e62689e0fb7c813051551342c046144f389b/images/confirm_new_rmarkdown_file_screenshot.png 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provide the ability to replicate research results from a published study. This idea ultimately also includes the full computational environment comprising code and data to replicate the analysis `r citep("10.1126/science.1213847")`. 12 | 13 | Over recent years our research group has settled on using the R statistical and computing environment together with R studio, R markdown and latex with some or our own scripts and packages to conduct reproducible science. 14 | 15 | Why use R? 16 | ----- 17 | 18 | R provides a toolbox with its packages that 19 | allows analysis of most data conveniently without tedious reformatting on all 20 | major computing platforms including Microsoft Windows, Linux, and Apple's OS X. 21 | R is an open source statistical programming and graphing language that includes 22 | tools for statistical, epidemiological, population genetic, genomic, phylogenetic, and 23 | comparative genomic analyses. 24 | 25 | Note that the R user community is very active and that both R and its packages 26 | are regularly updated, critically modified, and noted as deprecated (no longer 27 | updated) as appropriate. 28 | 29 | > Any R user needs to make sure all components are up-to-date and that versions 30 | > are compatible. 31 | 32 | References 33 | ---------- 34 | ```{r, results = 'asis', echo=FALSE} 35 | bibliography() 36 | ``` 37 | 38 | -------------------------------------------------------------------------------- /intro_presentation/.cache/__packages: -------------------------------------------------------------------------------- 1 | base 2 | slidify 3 | ggplot2 4 | -------------------------------------------------------------------------------- /intro_presentation/.cache/simple-plot_91902e042121bfcfda489d5536b1648a.RData: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/grunwaldlab/Reproducible-science-in-R/0bb8e62689e0fb7c813051551342c046144f389b/intro_presentation/.cache/simple-plot_91902e042121bfcfda489d5536b1648a.RData -------------------------------------------------------------------------------- /intro_presentation/.cache/simple-plot_91902e042121bfcfda489d5536b1648a.rdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/grunwaldlab/Reproducible-science-in-R/0bb8e62689e0fb7c813051551342c046144f389b/intro_presentation/.cache/simple-plot_91902e042121bfcfda489d5536b1648a.rdb -------------------------------------------------------------------------------- /intro_presentation/.cache/simple-plot_91902e042121bfcfda489d5536b1648a.rdx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/grunwaldlab/Reproducible-science-in-R/0bb8e62689e0fb7c813051551342c046144f389b/intro_presentation/.cache/simple-plot_91902e042121bfcfda489d5536b1648a.rdx -------------------------------------------------------------------------------- /intro_presentation/.cache/unnamed-chunk-1_fb90a39790044ea355f08408c1f62625.RData: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/grunwaldlab/Reproducible-science-in-R/0bb8e62689e0fb7c813051551342c046144f389b/intro_presentation/.cache/unnamed-chunk-1_fb90a39790044ea355f08408c1f62625.RData -------------------------------------------------------------------------------- /intro_presentation/.cache/unnamed-chunk-1_fb90a39790044ea355f08408c1f62625.rdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/grunwaldlab/Reproducible-science-in-R/0bb8e62689e0fb7c813051551342c046144f389b/intro_presentation/.cache/unnamed-chunk-1_fb90a39790044ea355f08408c1f62625.rdb -------------------------------------------------------------------------------- /intro_presentation/.cache/unnamed-chunk-1_fb90a39790044ea355f08408c1f62625.rdx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/grunwaldlab/Reproducible-science-in-R/0bb8e62689e0fb7c813051551342c046144f389b/intro_presentation/.cache/unnamed-chunk-1_fb90a39790044ea355f08408c1f62625.rdx -------------------------------------------------------------------------------- /intro_presentation/assets/css/.gitkeep: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/grunwaldlab/Reproducible-science-in-R/0bb8e62689e0fb7c813051551342c046144f389b/intro_presentation/assets/css/.gitkeep -------------------------------------------------------------------------------- /intro_presentation/assets/css/custom.css: -------------------------------------------------------------------------------- 1 | /* Niks custom css for slidify */ 2 | 3 | .title-slide { 4 | background-color: #FFFFFF; 5 | /* background-color: #CBE7A5; #EDE0CF; ; #CA9F9D*/ 6 | /* background-image:url(http://goo.gl/EpXln); */ 7 | } 8 | 9 | .title-slide hgroup > h1{ 10 | font-family: 'Oswald', 'Helvetica', sanserif; 11 | } 12 | 13 | .title-slide hgroup > h1, 14 | .title-slide hgroup > h2 { 15 | color: #4c4c4c ; /* #535E43; #EF5150*/ 16 | } 17 | 18 | slide:not(.segue) h2{ 19 | font-family: "Open Sans Condensed"; 20 | font-weight: 700; 21 | color: #0864cc; /* darkslategray; */ 22 | } 23 | -------------------------------------------------------------------------------- /intro_presentation/assets/css/lists.css: -------------------------------------------------------------------------------- 1 | /* Styling for Ordered Lists (only for io2012) */ 2 | ol { 3 | margin-left: 2em; 4 | margin-bottom: 1em; 5 | position: relative; 6 | } 7 | 8 | ol li { 9 | margin-bottom: 0.5em; 10 | } 11 | 12 | ol li ol { 13 | margin-left: 2em; 14 | margin-bottom: 0; 15 | } 16 | 17 | ol ul { 18 | margin-top: .5em; 19 | } 20 | 21 | ol { 22 | list-style-type: decimal; 23 | } 24 | 25 | -------------------------------------------------------------------------------- /intro_presentation/assets/css/quotes.css: -------------------------------------------------------------------------------- 1 | /* Quotes and Shout (for io2012, custom) */ 2 | article q { 3 | font-family: 'Crimson Text', sans-serif; 4 | } 5 | 6 | q { 7 | display: block; 8 | font-size: 44px; 9 | line-height: 56px; 10 | margin-left: 50px; 11 | margin-top: 100px; 12 | margin-right: 150px; 13 | } 14 | 15 | q::before { 16 | content: '“'; 17 | position: absolute; 18 | display: inline-block; 19 | margin-left: -2.1em; 20 | width: 2em; 21 | text-align: right; 22 | font-size: 90px; 23 | color: silver; 24 | } 25 | 26 | q::after { 27 | content: '”'; 28 | position: absolute; 29 | margin-left: .1em; 30 | font-size: 90px; 31 | color: silver; 32 | } 33 | 34 | div.author { 35 | text-align: right; 36 | font-size: 40px; 37 | margin-top: 20px; 38 | margin-right: 150px; 39 | } 40 | 41 | div.author::before { 42 | content: '—'; 43 | } 44 | 45 | q.shout:before { 46 | content: ''; 47 | position: absolute; 48 | margin-left: -0.5em; 49 | } 50 | 51 | q.shout:after { 52 | content: ''; 53 | position: absolute; 54 | margin-left: 0.1em; 55 | } 56 | -------------------------------------------------------------------------------- /intro_presentation/assets/css/ribbons.css: -------------------------------------------------------------------------------- 1 | /*Github Ribbon Test*/ 2 | /* Source: https://github.com/dciccale/css3-github-ribbon */ 3 | /* Define classes for example, definition, problem etc. */ 4 | /* Choose meaningful colors for background and text */ 5 | 6 | .example { 7 | background-color: #121621; 8 | top: 1.2em; 9 | right: -3.2em; 10 | -webkit-transform: rotate(45deg); 11 | -moz-transform: rotate(45deg); 12 | transform: rotate(45deg); 13 | -webkit-box-shadow: 0 0 0 1px #1d212e inset,0 0 2px 1px #fff inset,0 0 1em #888; 14 | -moz-box-shadow: 0 0 0 1px #1d212e inset,0 0 2px 1px #fff inset,0 0 1em #888; 15 | box-shadow: 0 0 0 1px #1d212e inset,0 0 2px 1px #fff inset,0 0 1em #888; 16 | color: #FF0; 17 | display: block; 18 | padding: .6em 3.5em; 19 | position: absolute; 20 | font: bold .82em sans-serif; 21 | text-align: center; 22 | text-decoration: none; 23 | text-shadow: 1px -1px 8px rgba(0,0,0,0.60); 24 | -webkit-user-select: none; 25 | -moz-user-select: none; 26 | user-select: none; 27 | } 28 | 29 | .definition { 30 | background-color: #a00; 31 | top: 1.2em; 32 | right: -3.2em; 33 | -webkit-transform: rotate(45deg); 34 | -moz-transform: rotate(45deg); 35 | transform: rotate(45deg); 36 | -webkit-box-shadow: 0 0 0 1px #1d212e inset,0 0 2px 1px #fff inset,0 0 1em #888; 37 | -moz-box-shadow: 0 0 0 1px #1d212e inset,0 0 2px 1px #fff inset,0 0 1em #888; 38 | box-shadow: 0 0 0 1px #1d212e inset,0 0 2px 1px #fff inset,0 0 1em #888; 39 | color: #FFF; 40 | display: block; 41 | padding: .6em 3.5em; 42 | position: absolute; 43 | font: bold .82em sans-serif; 44 | text-align: center; 45 | text-decoration: none; 46 | text-shadow: 1px -1px 8px rgba(0,0,0,0.60); 47 | -webkit-user-select: none; 48 | -moz-user-select: none; 49 | user-select: none; 50 | } 51 | -------------------------------------------------------------------------------- /intro_presentation/assets/css/sizes.css: -------------------------------------------------------------------------------- 1 | /* Slide Classes */ 2 | 3 | slide.smaller li{ 4 | font-size: 0.8em; 5 | line-height: 1.3em; 6 | } 7 | 8 | slide.smaller p{ 9 | font-size: 0.8em; 10 | line-height: 1.3em; 11 | } 12 | 13 | slide.large p, li{ 14 | font-size: 1.2em; 15 | } -------------------------------------------------------------------------------- /intro_presentation/assets/css/tables.css: -------------------------------------------------------------------------------- 1 | /* Tables */ 2 | table caption{ 3 | margin-top: 20pt; 4 | font-weight: normal; 5 | font-family: "Trebuchet MS", Garuda, sans-serif; 6 | } 7 | 8 | table th { 9 | text-transform: capitalize; 10 | } 11 | 12 | table { 13 | border: none; 14 | width: 100%; 15 | border-collapse: collapse; 16 | font-size: 24px; 17 | line-height: 32px; 18 | font-family: 'Trebuchet MS'; 19 | font-weight: bolder; 20 | color: rgb(102, 102, 102); 21 | } 22 | table thead { 23 | border-top: 1px solid #BFBEAD; 24 | border-bottom: 1px solid #BFBEAD; 25 | } 26 | table th, table td, table caption { 27 | margin: 0; 28 | padding: 2pt 6pt; 29 | text-align: left; 30 | vertical-align: top; 31 | } 32 | table th { 33 | background: #CFCEBD; 34 | color: #575400; 35 | text-transform: uppercase; 36 | } 37 | table td { 38 | border-bottom: 1px solid #CFCEBD; 39 | } 40 | table tr:nth-child(2n+1) { 41 | /* background: #E8F2FF; */ 42 | background: #EFEEDD; 43 | } 44 | 45 | 46 | 47 | -------------------------------------------------------------------------------- /intro_presentation/assets/css/text.css: -------------------------------------------------------------------------------- 1 | @import url(http://fonts.googleapis.com/css?family=Permanent+Marker); 2 | @import url(http://fonts.googleapis.com/css?family=Crimson+Text); 3 | @import url(http://fonts.googleapis.com/css?family=The+Girl+Next+Door); 4 | @import url(http://fonts.googleapis.com/css?family=Quattrocento+Sans); 5 | @import url(http://fonts.googleapis.com/css?family=Yanone+Kaffeesatz:700); 6 | @import url(http://fonts.googleapis.com/css?family=Vollkorn); 7 | @import url(http://fonts.googleapis.com/css?family=Oswald); 8 | @import url(captions.css); 9 | @import url(http://fonts.googleapis.com/css?family=Architects+Daughter); 10 | @import url(http://fonts.googleapis.com/css?family=Hammersmith+One); 11 | @import url(http://fonts.googleapis.com/css?family=Signika+Negative:400,600); 12 | @import url(http://fonts.googleapis.com/css?family=Open+Sans:400,700,600); 13 | @import url(http://fonts.googleapis.com/css?family=Droid+Sans+Mono); 14 | @import url(http://fonts.googleapis.com/css?family=Droid+Serif); 15 | @import url(http://fonts.googleapis.com/css?family=Source+Code+Pro:600); 16 | @import url(http://fonts.googleapis.com/css?family=Quattrocento+Sans:700); 17 | 18 | @import url(../fonts/stylesheet.css); 19 | 20 | /* Modifications to Bootstrap by Ramnath Vaidyanathan*/ 21 | div.alert p { 22 | font-family: 'Arial', 'Helvetica Neue'; 23 | font-size: 16px; 24 | line-height: 24px; 25 | text-align: justify; 26 | color: inherit; 27 | } 28 | 29 | /* Reduce Space between Title and Body */ 30 | slides > slide > hgroup + article { 31 | margin-top: 15px; 32 | } 33 | 34 | /* Remove Border, Margins and Padding from iframe */ 35 | iframe { 36 | border: none; 37 | margin: 0; 38 | padding: 0; 39 | } 40 | 41 | /* Code and Pre Blocks */ 42 | pre { 43 | font-family: 'Monaco', 'Consolas', sans-serif; 44 | font-size: 18px; 45 | line-height: 27px; 46 | white-space: pre-wrap; /* css-3 */ 47 | white-space: -moz-pre-wrap; /* Mozilla, since 1999 */ 48 | white-space: -pre-wrap; /* Opera 4-6 */ 49 | white-space: -o-pre-wrap; /* Opera 7 */ 50 | word-wrap: break-word; /* Internet Explorer 5.5+ */ 51 | } 52 | 53 | /* Nik changed */ 54 | code { 55 | font-family: 'Monaco', monospace; 56 | font-size: 28px; /* default : 18px;*/ 57 | line-height: 27px; 58 | /* font-weight: 600; */ 59 | color: #800000; 60 | color: green; 61 | text-align: left; /* Nik added */ 62 | } 63 | 64 | /* Knitr Images */ 65 | .rimage.left { 66 | text-align: left; 67 | } 68 | .rimage.right { 69 | text-align: right; 70 | } 71 | .rimage.center { 72 | text-align: center; 73 | } 74 | 75 | /* Rounded Pill around em Element */ 76 | /* Usage: Text */ 77 | em.rounded { 78 | font-style:normal; 79 | -moz-border-radius:20px; 80 | -webkit-border-radius:20px; 81 | border-radius:20px; 82 | padding:1px 10px; 83 | background:#f0f0f0; 84 | -moz-box-shadow: 1px 1px rgba(0,0,0,0.2); 85 | -webkit-box-shadow: 1px 1px rgba(0,0,0,0.2); 86 | box-shadow: 1px 1px rgba(0,0,0,0.2); 87 | } 88 | 89 | /* Redefine Fonts for Labels and Badges */ 90 | .label, .badge { 91 | font-size:14px; 92 | text-transform:uppercase; 93 | font-family: Helvetica, sans-serif; 94 | margin: 2px; 95 | } 96 | 97 | .key { 98 | color: white; 99 | display: inline-block; 100 | padding: 5px 6px 2px 5px; 101 | /*font-size: 25px;*/ 102 | line-height: 16px; 103 | text-shadow: none; 104 | letter-spacing: 0; 105 | bottom: 3px; 106 | position: relative; 107 | border-radius: 6px; 108 | -moz-border-radius: 6px; 109 | -webkit-border-radius: 6px; 110 | background: #BEBEBE; 111 | } 112 | 113 | /* Styles for Title Slide */ 114 | .title-slide hgroup > h1{ 115 | font-family: 'Oswald', sans-serif; 116 | } 117 | 118 | .title-slide hgroup > h2{ 119 | font-family: 'Signika Negative', 'Calibri', sans-serif; 120 | } 121 | 122 | /* Nik changed */ 123 | section p, section li, 124 | article p, article li, article li.build{ 125 | font-family: 'Helvetica', 'Crimson Text', 'Garamond', 'Palatino', sans-serif; 126 | text-align: justify; 127 | font-size:28px; /* default : 22px;*/ 128 | line-height: 1.0em; /* default : 1.5em;*/ 129 | } 130 | 131 | article > p, article li, article li.build { 132 | /* color: #565b62;*/ 133 | color: #000000; 134 | } 135 | 136 | slide.segue:not(.title-slide) h2{ 137 | font-family: 'Yanone Kaffeesatz', sans-serif; 138 | font-size: 3.5em; 139 | color: #F56702; 140 | } 141 | 142 | slide:not(.segue) h2 { 143 | font-family: 'Oswald', 'Yanone Kaffeesatz', 'Calibri', 'Arial', 'Helvetica', sans-serif; 144 | font-size:2em; 145 | color: #004D5D; /*color: #495961;*/ 146 | color: #262b31; 147 | line-height:1em; 148 | letter-spacing: 4px; 149 | } 150 | 151 | slide:not(.segue) h2{ 152 | font-family: 'Signika Negative', 'Calibri', Arial, sans-serif; 153 | font-size: 52px; 154 | font-style: normal; 155 | font-weight: bold; 156 | text-transform: normal; 157 | letter-spacing: -2px; 158 | line-height: 1.2em; 159 | /* color: #193441;*/ 160 | /* color: #02574D;*/ 161 | color: #0864cc; /* #CC2904; default changed - Nik */ 162 | } 163 | 164 | slide.fill h2{ 165 | color: black; 166 | background: rgba(255, 255, 255, .75); 167 | padding-top: .2em; 168 | padding-bottom: .3em; 169 | margin-top: -.2em; 170 | margin-left: -60px; 171 | padding-left: 60px; 172 | margin-right: -1000px; 173 | padding-right: 60px; 174 | } 175 | 176 | /*slide.segue h2{ 177 | font-size: 4em; 178 | font-size: inherit; 179 | color: inherit; 180 | }*/ 181 | 182 | em.answer { 183 | font-weight: bolder; 184 | color: #0A8787; 185 | } 186 | 187 | /* Nik changed */ 188 | .source { 189 | font-size: 14px; /* default : 14px;*/ 190 | color: #a9a9a9; 191 | position: absolute; 192 | bottom: 30px; 193 | left: 60px; 194 | } 195 | -------------------------------------------------------------------------------- /intro_presentation/assets/fig/simple-plot-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/grunwaldlab/Reproducible-science-in-R/0bb8e62689e0fb7c813051551342c046144f389b/intro_presentation/assets/fig/simple-plot-1.png -------------------------------------------------------------------------------- /intro_presentation/assets/fig/unnamed-chunk-1-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/grunwaldlab/Reproducible-science-in-R/0bb8e62689e0fb7c813051551342c046144f389b/intro_presentation/assets/fig/unnamed-chunk-1-1.png -------------------------------------------------------------------------------- /intro_presentation/assets/fig/unnamed-chunk-2-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/grunwaldlab/Reproducible-science-in-R/0bb8e62689e0fb7c813051551342c046144f389b/intro_presentation/assets/fig/unnamed-chunk-2-1.png -------------------------------------------------------------------------------- /intro_presentation/assets/img/.gitkeep: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/grunwaldlab/Reproducible-science-in-R/0bb8e62689e0fb7c813051551342c046144f389b/intro_presentation/assets/img/.gitkeep -------------------------------------------------------------------------------- /intro_presentation/assets/js/.gitkeep: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/grunwaldlab/Reproducible-science-in-R/0bb8e62689e0fb7c813051551342c046144f389b/intro_presentation/assets/js/.gitkeep -------------------------------------------------------------------------------- /intro_presentation/assets/layouts/.gitkeep: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/grunwaldlab/Reproducible-science-in-R/0bb8e62689e0fb7c813051551342c046144f389b/intro_presentation/assets/layouts/.gitkeep -------------------------------------------------------------------------------- /intro_presentation/assets/libraries/frameworks/io2012/README.md: -------------------------------------------------------------------------------- 1 | ## Google IO 2012 HTML5 Slides 2 | 3 | Authors: 4 | Eric Bidelman 5 | Luke Mahé 6 | 7 | Modified By: 8 | Ramnath Vaidyanathan 9 | 10 | URL: https://code.google.com/p/io-2012-slides 11 | 12 | LICENSE: Apache 2.0 13 | -------------------------------------------------------------------------------- /intro_presentation/assets/libraries/frameworks/io2012/config.yml: -------------------------------------------------------------------------------- 1 | io2012: 2 | theme: NULL 3 | layout: default 4 | -------------------------------------------------------------------------------- /intro_presentation/assets/libraries/frameworks/io2012/css/fonts.css: -------------------------------------------------------------------------------- 1 | @font-face { 2 | font-family: 'Open Sans'; 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12 | height: $slide-height !important; 13 | margin-left: -$slide-width / 2 !important; 14 | margin-top: -$slide-height / 2 !important; 15 | */ 16 | -webkit-transition: none !important; 17 | -webkit-transition: none !important; 18 | -moz-transition: none !important; 19 | -ms-transition: none !important; 20 | -o-transition: none !important; 21 | transition: none !important; 22 | } 23 | 24 | /* iPhone 4 ----------- */ 25 | @media only screen and (-webkit-min-device-pixel-ratio : 1.5), only screen and (min-device-pixel-ratio : 1.5) { 26 | /* Styles */ 27 | } 28 | -------------------------------------------------------------------------------- /intro_presentation/assets/libraries/frameworks/io2012/images/google_developers_icon_128.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/grunwaldlab/Reproducible-science-in-R/0bb8e62689e0fb7c813051551342c046144f389b/intro_presentation/assets/libraries/frameworks/io2012/images/google_developers_icon_128.png -------------------------------------------------------------------------------- /intro_presentation/assets/libraries/frameworks/io2012/images/io2012_logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/grunwaldlab/Reproducible-science-in-R/0bb8e62689e0fb7c813051551342c046144f389b/intro_presentation/assets/libraries/frameworks/io2012/images/io2012_logo.png -------------------------------------------------------------------------------- /intro_presentation/assets/libraries/frameworks/io2012/js/order.js: -------------------------------------------------------------------------------- 1 | /* 2 | RequireJS order 1.0.5 Copyright (c) 2010-2011, The Dojo Foundation All Rights Reserved. 3 | Available via the MIT or new BSD license. 4 | see: http://github.com/jrburke/requirejs for details 5 | */ 6 | (function(){function k(a){var b=a.currentTarget||a.srcElement,c;if(a.type==="load"||l.test(b.readyState)){a=b.getAttribute("data-requiremodule");j[a]=!0;for(a=0;c=g[a];a++)if(j[c.name])c.req([c.name],c.onLoad);else break;a>0&&g.splice(0,a);setTimeout(function(){b.parentNode.removeChild(b)},15)}}function m(a){var b,c;a.setAttribute("data-orderloaded","loaded");for(a=0;c=h[a];a++)if((b=i[c])&&b.getAttribute("data-orderloaded")==="loaded")delete i[c],require.addScriptToDom(b);else break;a>0&&h.splice(0, 7 | a)}var f=typeof document!=="undefined"&&typeof window!=="undefined"&&document.createElement("script"),n=f&&(f.async||window.opera&&Object.prototype.toString.call(window.opera)==="[object Opera]"||"MozAppearance"in document.documentElement.style),o=f&&f.readyState==="uninitialized",l=/^(complete|loaded)$/,g=[],j={},i={},h=[],f=null;define({version:"1.0.5",load:function(a,b,c,e){var d;b.nameToUrl?(d=b.nameToUrl(a,null),require.s.skipAsync[d]=!0,n||e.isBuild?b([a],c):o?(e=require.s.contexts._,!e.urlFetched[d]&& 8 | !e.loaded[a]&&(e.urlFetched[d]=!0,require.resourcesReady(!1),e.scriptCount+=1,d=require.attach(d,e,a,null,null,m),i[a]=d,h.push(a)),b([a],c)):b.specified(a)?b([a],c):(g.push({name:a,req:b,onLoad:c}),require.attach(d,null,a,k,"script/cache"))):b([a],c)}})})(); 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2 | PR.registerLangHandler(PR.createSimpleLexer([["pun",/^[:>?|]+/,a,":|>?"],["dec",/^%(?:YAML|TAG)[^\n\r#]+/,a,"%"],["typ",/^&\S+/,a,"&"],["typ",/^!\S*/,a,"!"],["str",/^"(?:[^"\\]|\\.)*(?:"|$)/,a,'"'],["str",/^'(?:[^']|'')*(?:'|$)/,a,"'"],["com",/^#[^\n\r]*/,a,"#"],["pln",/^\s+/,a," \t\r\n"]],[["dec",/^(?:---|\.\.\.)(?:[\n\r]|$)/],["pun",/^-/],["kwd",/^\w+:[\n\r ]/],["pln",/^\w+/]]),["yaml","yml"]); 3 | -------------------------------------------------------------------------------- /intro_presentation/assets/libraries/frameworks/io2012/js/prettify/prettify.css: -------------------------------------------------------------------------------- 1 | .pln{color:#000}@media screen{.str{color:#080}.kwd{color:#008}.com{color:#800}.typ{color:#606}.lit{color:#066}.pun,.opn,.clo{color:#660}.tag{color:#008}.atn{color:#606}.atv{color:#080}.dec,.var{color:#606}.fun{color:red}}@media print,projection{.str{color:#060}.kwd{color:#006;font-weight:bold}.com{color:#600;font-style:italic}.typ{color:#404;font-weight:bold}.lit{color:#044}.pun,.opn,.clo{color:#440}.tag{color:#006;font-weight:bold}.atn{color:#404}.atv{color:#060}}pre.prettyprint{padding:2px;border:1px solid #888}ol.linenums{margin-top:0;margin-bottom:0}li.L0,li.L1,li.L2,li.L3,li.L5,li.L6,li.L7,li.L8{list-style-type:none}li.L1,li.L3,li.L5,li.L7,li.L9{background:#eee} -------------------------------------------------------------------------------- /intro_presentation/assets/libraries/frameworks/io2012/js/slide-controller.js: -------------------------------------------------------------------------------- 1 | (function(window) { 2 | 3 | var ORIGIN_ = location.protocol + '//' + location.host; 4 | 5 | function SlideController() { 6 | this.popup = null; 7 | this.isPopup = window.opener; 8 | 9 | if (this.setupDone()) { 10 | window.addEventListener('message', this.onMessage_.bind(this), false); 11 | 12 | // Close popups if we reload the main window. 13 | window.addEventListener('beforeunload', function(e) { 14 | if (this.popup) { 15 | this.popup.close(); 16 | } 17 | }.bind(this), false); 18 | } 19 | } 20 | 21 | SlideController.PRESENTER_MODE_PARAM = 'presentme'; 22 | 23 | SlideController.prototype.setupDone = function() { 24 | var params = location.search.substring(1).split('&').map(function(el) { 25 | return el.split('='); 26 | }); 27 | 28 | var presentMe = null; 29 | for (var i = 0, param; param = params[i]; ++i) { 30 | if (param[0].toLowerCase() == SlideController.PRESENTER_MODE_PARAM) { 31 | presentMe = param[1] == 'true'; 32 | break; 33 | } 34 | } 35 | 36 | if (presentMe !== null) { 37 | localStorage.ENABLE_PRESENTOR_MODE = presentMe; 38 | // TODO: use window.history.pushState to update URL instead of the redirect. 39 | if (window.history.replaceState) { 40 | window.history.replaceState({}, '', location.pathname); 41 | } else { 42 | location.replace(location.pathname); 43 | return false; 44 | } 45 | } 46 | 47 | var enablePresenterMode = localStorage.getItem('ENABLE_PRESENTOR_MODE'); 48 | if (enablePresenterMode && JSON.parse(enablePresenterMode)) { 49 | // Only open popup from main deck. Don't want recursive popup opening! 50 | if (!this.isPopup) { 51 | var opts = 'menubar=no,location=yes,resizable=yes,scrollbars=no,status=no'; 52 | this.popup = window.open(location.href, 'mywindow', opts); 53 | 54 | // Loading in the popup? Trigger the hotkey for turning presenter mode on. 55 | this.popup.addEventListener('load', function(e) { 56 | var evt = this.popup.document.createEvent('Event'); 57 | evt.initEvent('keydown', true, true); 58 | evt.keyCode = 'P'.charCodeAt(0); 59 | this.popup.document.dispatchEvent(evt); 60 | // this.popup.document.body.classList.add('with-notes'); 61 | // document.body.classList.add('popup'); 62 | }.bind(this), false); 63 | } 64 | } 65 | 66 | return true; 67 | } 68 | 69 | SlideController.prototype.onMessage_ = function(e) { 70 | var data = e.data; 71 | 72 | // Restrict messages to being from this origin. Allow local developmet 73 | // from file:// though. 74 | // TODO: It would be dope if FF implemented location.origin! 75 | if (e.origin != ORIGIN_ && ORIGIN_.indexOf('file://') != 0) { 76 | alert('Someone tried to postMessage from an unknown origin'); 77 | return; 78 | } 79 | 80 | // if (e.source.location.hostname != 'localhost') { 81 | // alert('Someone tried to postMessage from an unknown origin'); 82 | // return; 83 | // } 84 | 85 | if ('keyCode' in data) { 86 | var evt = document.createEvent('Event'); 87 | evt.initEvent('keydown', true, true); 88 | evt.keyCode = data.keyCode; 89 | document.dispatchEvent(evt); 90 | } 91 | }; 92 | 93 | SlideController.prototype.sendMsg = function(msg) { 94 | // // Send message to popup window. 95 | // if (this.popup) { 96 | // this.popup.postMessage(msg, ORIGIN_); 97 | // } 98 | 99 | // Send message to main window. 100 | if (this.isPopup) { 101 | // TODO: It would be dope if FF implemented location.origin. 102 | window.opener.postMessage(msg, '*'); 103 | } 104 | }; 105 | 106 | window.SlideController = SlideController; 107 | 108 | })(window); 109 | 110 | -------------------------------------------------------------------------------- /intro_presentation/assets/libraries/frameworks/io2012/js/slide_config.js: -------------------------------------------------------------------------------- 1 | var SLIDE_CONFIG = { 2 | // Slide settings 3 | settings: { 4 | useBuilds: true, // Default: true. False will turn off slide animation builds. 5 | usePrettify: false, // Default: true 6 | enableSlideAreas: false, // Default: true. False turns off the click areas on either slide of the slides. 7 | enableTouch: true, // Default: true. If touch support should enabled. Note: the device must support touch. 8 | //analytics: 'UA-XXXXXXXX-1', // TODO: Using this breaks GA for some reason (probably requirejs). Update your tracking code in template.html instead. 9 | favIcon: false, 10 | fonts: [ 11 | 'Open Sans:regular,semibold,italic,italicsemibold', 12 | 'Inconsolata' 13 | ], 14 | //theme: ['mytheme'], // Add your own custom themes or styles in /theme/css. Leave off the .css extension. 15 | }, 16 | }; -------------------------------------------------------------------------------- /intro_presentation/assets/libraries/frameworks/io2012/js/slides.js: -------------------------------------------------------------------------------- 1 | require(['order!slide_config','order!modernizr.custom.45394', 'order!hammer', 2 | 'order!slide-controller', 'order!slide-deck'], function(someModule) { 3 | }); 4 | -------------------------------------------------------------------------------- /intro_presentation/assets/libraries/highlighters/highlight.js/css/arta.css: -------------------------------------------------------------------------------- 1 | /* 2 | Date: 17.V.2011 3 | Author: pumbur 4 | */ 5 | 6 | pre code 7 | { 8 | display: block; padding: 0.5em; 9 | background: #222; 10 | } 11 | 12 | pre .profile .header *, 13 | pre .ini .title 14 | { 15 | color: #fff; 16 | } 17 | 18 | pre .comment, 19 | pre .javadoc, 20 | pre .preprocessor, 21 | pre .preprocessor .title, 22 | pre .shebang, 23 | pre .profile .summary, 24 | pre .diff, 25 | pre .pi, 26 | pre .doctype, 27 | pre .tag, 28 | pre .template_comment, 29 | pre .css .rules, 30 | pre .tex .special 31 | { 32 | color: #444; 33 | } 34 | 35 | pre .string, 36 | pre .symbol, 37 | pre .diff .change, 38 | pre .regexp, 39 | pre .xml .attribute, 40 | pre .smalltalk .char, 41 | pre .xml .value, 42 | pre .ini .value 43 | { 44 | color: #ffcc33; 45 | } 46 | 47 | pre .number, 48 | pre .addition 49 | { 50 | color: #00cc66; 51 | } 52 | 53 | pre .built_in, 54 | pre .literal, 55 | pre .vhdl .typename, 56 | pre .go .constant, 57 | pre .go .typename, 58 | pre .ini .keyword, 59 | pre .lua .title, 60 | pre .perl .variable, 61 | pre .php .variable, 62 | pre .mel .variable, 63 | pre .django .variable, 64 | pre .css .funtion, 65 | pre .smalltalk .method, 66 | pre .hexcolor, 67 | pre .important, 68 | pre .flow, 69 | pre .inheritance, 70 | pre .parser3 .variable 71 | { 72 | color: #32AAEE; 73 | } 74 | 75 | pre .keyword, 76 | pre .tag .title, 77 | pre .css .tag, 78 | pre .css .class, 79 | pre .css .id, 80 | pre .css .pseudo, 81 | pre .css .attr_selector, 82 | pre .lisp .title, 83 | pre .winutils, 84 | pre .tex .command, 85 | pre .request, 86 | pre .status 87 | { 88 | color: #6644aa; 89 | } 90 | 91 | pre .title, 92 | pre .ruby .constant, 93 | pre .vala .constant, 94 | pre .parent, 95 | pre .deletion, 96 | pre .template_tag, 97 | pre .css .keyword, 98 | pre .objectivec .class .id, 99 | pre .smalltalk .class, 100 | pre .lisp .keyword, 101 | pre .apache .tag, 102 | pre .nginx .variable, 103 | pre .envvar, 104 | pre .bash .variable, 105 | pre .go .built_in, 106 | pre .vbscript .built_in, 107 | pre .lua .built_in, 108 | pre .rsl .built_in, 109 | pre .tail, 110 | pre .avrasm .label, 111 | pre .tex .formula, 112 | pre .tex .formula * 113 | { 114 | color: #bb1166; 115 | } 116 | 117 | pre .yardoctag, 118 | pre .phpdoc, 119 | pre .profile .header, 120 | pre .ini .title, 121 | pre .apache .tag, 122 | pre .parser3 .title 123 | { 124 | font-weight: bold; 125 | } 126 | 127 | pre .coffeescript .javascript, 128 | pre .xml .javascript, 129 | pre .xml .css, 130 | pre .xml .cdata 131 | { 132 | opacity: 0.6; 133 | } 134 | 135 | pre code, 136 | pre .javascript, 137 | pre .css, 138 | pre .xml, 139 | pre .subst, 140 | pre .diff .chunk, 141 | pre .css .value, 142 | pre .css .attribute, 143 | pre .lisp .string, 144 | pre .lisp .number, 145 | pre .tail .params, 146 | pre .container, 147 | pre .haskell *, 148 | pre .erlang *, 149 | pre .erlang_repl * 150 | { 151 | color: #aaa; 152 | } 153 | -------------------------------------------------------------------------------- /intro_presentation/assets/libraries/highlighters/highlight.js/css/ascetic.css: -------------------------------------------------------------------------------- 1 | /* 2 | 3 | Original style from softwaremaniacs.org (c) Ivan Sagalaev 4 | 5 | */ 6 | 7 | pre code { 8 | display: block; padding: 0.5em; 9 | background: white; color: black; 10 | } 11 | 12 | pre .string, 13 | pre .tag .value, 14 | pre .filter .argument, 15 | pre .addition, 16 | pre .change, 17 | pre .apache .tag, 18 | pre .apache .cbracket, 19 | pre .nginx .built_in, 20 | pre .tex .formula { 21 | color: #888; 22 | } 23 | 24 | pre .comment, 25 | pre .template_comment, 26 | pre .shebang, 27 | pre .doctype, 28 | pre .pi, 29 | pre .javadoc, 30 | pre .deletion, 31 | pre .apache .sqbracket { 32 | color: #CCC; 33 | } 34 | 35 | pre .keyword, 36 | pre .tag .title, 37 | pre .css .tag, 38 | pre .ini .title, 39 | pre .winutils, 40 | pre .flow, 41 | pre .lisp .title, 42 | pre .apache .tag, 43 | pre .tex .command, 44 | pre .http .title, 45 | pre .request, 46 | pre .status { 47 | font-weight: bold; 48 | } 49 | -------------------------------------------------------------------------------- /intro_presentation/assets/libraries/highlighters/highlight.js/css/brown_paper.css: -------------------------------------------------------------------------------- 1 | /* 2 | 3 | Brown Paper style from goldblog.com.ua (c) Zaripov Yura 4 | 5 | */ 6 | 7 | pre code { 8 | display: block; padding: 0.5em; 9 | background:#b7a68e url(./brown_papersq.png); 10 | } 11 | 12 | pre .keyword, 13 | pre .literal, 14 | pre .change, 15 | pre .winutils, 16 | pre .flow, 17 | pre .lisp .title, 18 | pre .tex .special, 19 | pre .request, 20 | pre .status { 21 | color:#005599; 22 | font-weight:bold; 23 | } 24 | 25 | pre code, 26 | pre .ruby .subst, 27 | pre .tag .keyword { 28 | color: #363C69; 29 | } 30 | 31 | pre .string, 32 | pre .title, 33 | pre .haskell .type, 34 | pre .tag .value, 35 | pre .css .rules .value, 36 | pre .preprocessor, 37 | pre .ruby .symbol, 38 | pre .ruby .symbol .string, 39 | pre .ruby .symbol .keyword, 40 | pre .ruby .symbol .keymethods, 41 | pre .ruby .instancevar, 42 | pre .ruby .class .parent, 43 | pre .built_in, 44 | pre .sql .aggregate, 45 | pre .django .template_tag, 46 | pre .django .variable, 47 | pre .smalltalk .class, 48 | pre .javadoc, 49 | pre .ruby .string, 50 | pre .django .filter .argument, 51 | pre .smalltalk .localvars, 52 | pre .smalltalk .array, 53 | pre .attr_selector, 54 | pre .pseudo, 55 | pre .addition, 56 | pre .stream, 57 | pre .envvar, 58 | pre .apache .tag, 59 | pre .apache .cbracket, 60 | pre .tex .number { 61 | color: #2C009F; 62 | } 63 | 64 | pre .comment, 65 | pre .java .annotation, 66 | pre .python .decorator, 67 | pre .template_comment, 68 | pre .pi, 69 | pre .doctype, 70 | pre .deletion, 71 | pre .shebang, 72 | pre .apache .sqbracket, 73 | pre .nginx .built_in, 74 | pre .tex .formula { 75 | color: #802022; 76 | } 77 | 78 | pre .keyword, 79 | pre .literal, 80 | pre .css .id, 81 | pre .phpdoc, 82 | pre .title, 83 | pre .haskell .type, 84 | pre .vbscript .built_in, 85 | pre .sql .aggregate, 86 | pre .rsl .built_in, 87 | pre .smalltalk .class, 88 | pre .diff .header, 89 | pre .chunk, 90 | pre .winutils, 91 | pre .bash .variable, 92 | pre .apache .tag, 93 | pre .tex .command { 94 | font-weight: bold; 95 | } 96 | 97 | pre .coffeescript .javascript, 98 | pre .xml .css, 99 | pre .xml .javascript, 100 | pre .xml .vbscript, 101 | pre .tex .formula { 102 | opacity: 0.8; 103 | } 104 | -------------------------------------------------------------------------------- /intro_presentation/assets/libraries/highlighters/highlight.js/css/brown_papersq.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/grunwaldlab/Reproducible-science-in-R/0bb8e62689e0fb7c813051551342c046144f389b/intro_presentation/assets/libraries/highlighters/highlight.js/css/brown_papersq.png -------------------------------------------------------------------------------- /intro_presentation/assets/libraries/highlighters/highlight.js/css/dark.css: -------------------------------------------------------------------------------- 1 | /* 2 | 3 | Dark style from softwaremaniacs.org (c) Ivan Sagalaev 4 | 5 | */ 6 | 7 | pre code { 8 | display: block; padding: 0.5em; 9 | background: #444; 10 | } 11 | 12 | pre .keyword, 13 | pre .literal, 14 | pre .change, 15 | pre .winutils, 16 | pre .flow, 17 | pre .lisp .title, 18 | pre .tex .special { 19 | color: white; 20 | } 21 | 22 | pre code, 23 | pre .ruby .subst { 24 | color: #DDD; 25 | } 26 | 27 | pre .string, 28 | pre .title, 29 | pre .haskell .type, 30 | pre .ini .title, 31 | pre .tag .value, 32 | pre .css .rules .value, 33 | pre .preprocessor, 34 | pre .ruby .symbol, 35 | pre .ruby .symbol .string, 36 | pre .ruby .symbol .keyword, 37 | pre .ruby .symbol .keymethods, 38 | pre .ruby .instancevar, 39 | pre .ruby .class .parent, 40 | pre .built_in, 41 | pre .sql .aggregate, 42 | pre .django .template_tag, 43 | pre .django .variable, 44 | pre .smalltalk .class, 45 | pre .javadoc, 46 | pre .ruby .string, 47 | pre .django .filter .argument, 48 | pre .smalltalk .localvars, 49 | pre .smalltalk .array, 50 | pre .attr_selector, 51 | pre .pseudo, 52 | pre .addition, 53 | pre .stream, 54 | pre .envvar, 55 | pre .apache .tag, 56 | pre .apache .cbracket, 57 | pre .tex .command, 58 | pre .input_number { 59 | color: #D88; 60 | } 61 | 62 | pre .comment, 63 | pre .java .annotation, 64 | pre .python .decorator, 65 | pre .template_comment, 66 | pre .pi, 67 | pre .doctype, 68 | pre .deletion, 69 | pre .shebang, 70 | pre .apache .sqbracket, 71 | pre .tex .formula { 72 | color: #777; 73 | } 74 | 75 | pre .keyword, 76 | pre .literal, 77 | pre .title, 78 | pre .css .id, 79 | pre .phpdoc, 80 | pre .haskell .type, 81 | pre .vbscript .built_in, 82 | pre .sql .aggregate, 83 | pre .rsl .built_in, 84 | pre .smalltalk .class, 85 | pre .diff .header, 86 | pre .chunk, 87 | pre .winutils, 88 | pre .bash .variable, 89 | pre .apache .tag, 90 | pre .tex .special, 91 | pre .request, 92 | pre .status { 93 | font-weight: bold; 94 | } 95 | 96 | pre .coffeescript .javascript, 97 | pre .xml .css, 98 | pre .xml .javascript, 99 | pre .xml .vbscript, 100 | pre .tex .formula { 101 | opacity: 0.5; 102 | } 103 | -------------------------------------------------------------------------------- /intro_presentation/assets/libraries/highlighters/highlight.js/css/default.css: -------------------------------------------------------------------------------- 1 | /* 2 | 3 | Original style from softwaremaniacs.org (c) Ivan Sagalaev 4 | 5 | */ 6 | 7 | pre code { 8 | display: block; padding: 0.5em; 9 | background: #F0F0F0; 10 | } 11 | 12 | pre code, 13 | pre .ruby .subst, 14 | pre .tag .title, 15 | pre .lisp .title { 16 | color: black; 17 | } 18 | 19 | pre .string, 20 | pre .title, 21 | pre .constant, 22 | pre .parent, 23 | pre .tag .value, 24 | pre .rules .value, 25 | pre .rules .value .number, 26 | pre .preprocessor, 27 | pre .ruby .symbol, 28 | pre .ruby .symbol .string, 29 | pre .ruby .symbol .keyword, 30 | pre .ruby .symbol .keymethods, 31 | pre .instancevar, 32 | pre .aggregate, 33 | pre .template_tag, 34 | pre .django .variable, 35 | pre .smalltalk .class, 36 | pre .addition, 37 | pre .flow, 38 | 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-------------------------------------------------------------------------------- /intro_presentation/assets/libraries/highlighters/highlight.js/css/far.css: -------------------------------------------------------------------------------- 1 | /* 2 | 3 | FAR Style (c) MajestiC 4 | 5 | */ 6 | 7 | pre code { 8 | display: block; padding: 0.5em; 9 | background: #000080; 10 | } 11 | 12 | pre code, 13 | .ruby .subst { 14 | color: #0FF; 15 | } 16 | 17 | pre .string, 18 | pre .ruby .string, 19 | pre .haskell .type, 20 | pre .tag .value, 21 | pre .css .rules .value, 22 | pre .css .rules .value .number, 23 | pre .preprocessor, 24 | pre .ruby .symbol, 25 | pre .ruby .symbol .string, 26 | pre .ruby .symbol .keyword, 27 | pre .ruby .symbol .keymethods, 28 | pre .built_in, 29 | pre .sql .aggregate, 30 | pre .django .template_tag, 31 | pre .django .variable, 32 | pre .smalltalk .class, 33 | pre .addition, 34 | pre .apache .tag, 35 | pre .apache .cbracket, 36 | pre .tex .command { 37 | color: #FF0; 38 | } 39 | 40 | pre .keyword, 41 | pre .css .id, 42 | pre .title, 43 | pre .haskell .type, 44 | pre .vbscript .built_in, 45 | pre .sql .aggregate, 46 | pre .rsl .built_in, 47 | pre .smalltalk .class, 48 | pre .xml .tag .title, 49 | pre .winutils, 50 | pre .flow, 51 | pre .change, 52 | pre .envvar, 53 | pre .bash .variable, 54 | pre .tex .special { 55 | color: #FFF; 56 | } 57 | 58 | pre .comment, 59 | pre .phpdoc, 60 | pre .javadoc, 61 | pre .java .annotation, 62 | pre .template_comment, 63 | pre .deletion, 64 | pre .apache .sqbracket, 65 | pre .tex .formula { 66 | color: #888; 67 | } 68 | 69 | pre .number, 70 | pre .date, 71 | pre .regexp, 72 | pre .literal, 73 | pre .smalltalk .symbol, 74 | pre .smalltalk .char { 75 | color: #0F0; 76 | } 77 | 78 | pre .python .decorator, 79 | pre .django .filter .argument, 80 | pre .smalltalk .localvars, 81 | pre .smalltalk .array, 82 | pre .attr_selector, 83 | pre .pseudo, 84 | pre .xml .pi, 85 | pre .diff .header, 86 | pre .chunk, 87 | pre .shebang, 88 | pre .nginx .built_in, 89 | pre .input_number { 90 | color: #008080; 91 | } 92 | 93 | pre .keyword, 94 | pre .css .id, 95 | pre .title, 96 | pre .haskell .type, 97 | pre .vbscript .built_in, 98 | pre .sql .aggregate, 99 | pre .rsl .built_in, 100 | pre .smalltalk .class, 101 | pre .winutils, 102 | pre .flow, 103 | pre .apache .tag, 104 | pre .nginx .built_in, 105 | pre .tex .command, 106 | pre .tex .special, 107 | pre .request, 108 | pre .status { 109 | font-weight: bold; 110 | } 111 | -------------------------------------------------------------------------------- /intro_presentation/assets/libraries/highlighters/highlight.js/css/github.css: -------------------------------------------------------------------------------- 1 | /* 2 | 3 | github.com style (c) Vasily Polovnyov 4 | 5 | */ 6 | 7 | pre code { 8 | display: block; padding: 0.5em; 9 | color: #000; 10 | background: #f8f8ff 11 | } 12 | 13 | pre .comment, 14 | pre .template_comment, 15 | pre .diff .header, 16 | pre .javadoc { 17 | color: #998; 18 | font-style: italic 19 | } 20 | 21 | pre .keyword, 22 | pre .css .rule .keyword, 23 | pre .winutils, 24 | pre .javascript .title, 25 | pre .lisp .title, 26 | pre .subst, 27 | pre .request, 28 | pre .status { 29 | color: #000; 30 | font-weight: bold 31 | } 32 | 33 | pre .number, 34 | pre .hexcolor { 35 | color: #40a070 36 | } 37 | 38 | pre .string, 39 | pre .tag .value, 40 | pre .phpdoc, 41 | pre .tex .formula { 42 | color: #d14 43 | } 44 | 45 | pre .title, 46 | pre .id { 47 | color: #900; 48 | font-weight: bold 49 | } 50 | 51 | pre .javascript .title, 52 | pre .lisp .title, 53 | pre .subst { 54 | font-weight: normal 55 | } 56 | 57 | pre .class .title, 58 | pre .haskell .type, 59 | pre .vhdl .literal, 60 | pre .tex .command { 61 | color: #458; 62 | font-weight: bold 63 | } 64 | 65 | pre .tag, 66 | pre .tag .title, 67 | pre .rules .property, 68 | pre .django .tag .keyword { 69 | color: #000080; 70 | font-weight: normal 71 | } 72 | 73 | pre .attribute, 74 | pre .variable, 75 | pre .instancevar, 76 | pre .lisp .body { 77 | color: #008080 78 | } 79 | 80 | pre .regexp { 81 | color: #009926 82 | } 83 | 84 | pre .class { 85 | color: #458; 86 | font-weight: bold 87 | } 88 | 89 | pre .symbol, 90 | pre .ruby .symbol .string, 91 | pre .ruby .symbol .keyword, 92 | pre .ruby .symbol .keymethods, 93 | pre .lisp .keyword, 94 | pre .tex .special, 95 | pre .input_number { 96 | color: #990073 97 | } 98 | 99 | pre .builtin, 100 | pre .built_in, 101 | pre .lisp .title { 102 | color: #0086b3 103 | } 104 | 105 | pre .preprocessor, 106 | pre .pi, 107 | pre .doctype, 108 | pre .shebang, 109 | pre .cdata { 110 | color: #999; 111 | font-weight: bold 112 | } 113 | 114 | pre .deletion { 115 | background: #fdd 116 | } 117 | 118 | pre .addition { 119 | background: #dfd 120 | } 121 | 122 | pre .diff .change { 123 | background: #0086b3 124 | } 125 | 126 | pre .chunk { 127 | color: #aaa 128 | } 129 | 130 | pre .tex .formula { 131 | opacity: 0.5; 132 | } 133 | -------------------------------------------------------------------------------- /intro_presentation/assets/libraries/highlighters/highlight.js/css/googlecode.css: -------------------------------------------------------------------------------- 1 | /* 2 | 3 | Google Code style (c) Aahan Krish 4 | 5 | */ 6 | 7 | pre code { 8 | display: block; padding: 0.5em; 9 | background: white; color: black; 10 | } 11 | 12 | pre .comment, 13 | pre .template_comment, 14 | pre .javadoc, 15 | pre .comment * { 16 | color: #800; 17 | } 18 | 19 | pre .keyword, 20 | pre .method, 21 | pre .list .title, 22 | pre .tag .title, 23 | pre .setting .value, 24 | pre .winutils, 25 | pre .tex .command, 26 | pre .http .title, 27 | pre .request, 28 | pre .status { 29 | color: #008; 30 | } 31 | 32 | pre .envvar, 33 | pre .tex .special { 34 | color: #660; 35 | } 36 | 37 | pre .string, 38 | pre .tag .value, 39 | pre .cdata, 40 | pre .filter .argument, 41 | pre .attr_selector, 42 | pre .apache .cbracket, 43 | pre .date, 44 | pre .regexp { 45 | color: #080; 46 | } 47 | 48 | pre .sub .identifier, 49 | pre .pi, 50 | pre .tag, 51 | pre .tag .keyword, 52 | pre .decorator, 53 | pre .ini .title, 54 | pre .shebang, 55 | pre .input_number, 56 | pre .hexcolor, 57 | pre .rules .value, 58 | pre .css .value .number, 59 | pre .literal, 60 | pre .symbol, 61 | pre .ruby .symbol .string, 62 | pre .ruby .symbol .keyword, 63 | pre .ruby .symbol .keymethods, 64 | pre .number, 65 | pre .css .function { 66 | color: #066; 67 | } 68 | 69 | pre .class .title, 70 | pre .haskell .type, 71 | pre .smalltalk .class, 72 | pre .javadoctag, 73 | pre .yardoctag, 74 | pre .phpdoc, 75 | pre .typename, 76 | pre .tag .attribute, 77 | pre .doctype, 78 | pre .class .id, 79 | pre .built_in, 80 | pre .setting, 81 | pre .params, 82 | pre .variable { 83 | color: #606; 84 | } 85 | 86 | pre .css .tag, 87 | pre .rules .property, 88 | pre .pseudo, 89 | pre .subst { 90 | color: #000; 91 | } 92 | 93 | pre .css .class, pre .css .id { 94 | color: #9B703F; 95 | } 96 | 97 | pre .value .important { 98 | color: #ff7700; 99 | font-weight: bold; 100 | } 101 | 102 | pre .rules .keyword { 103 | color: #C5AF75; 104 | } 105 | 106 | pre .annotation, 107 | pre .apache .sqbracket, 108 | pre .nginx .built_in { 109 | color: #9B859D; 110 | } 111 | 112 | pre .preprocessor, 113 | pre .preprocessor * { 114 | color: #444; 115 | } 116 | 117 | pre .tex .formula { 118 | background-color: #EEE; 119 | font-style: italic; 120 | } 121 | 122 | pre .diff .header, 123 | pre .chunk { 124 | color: #808080; 125 | font-weight: bold; 126 | } 127 | 128 | pre .diff .change { 129 | background-color: #BCCFF9; 130 | } 131 | 132 | pre .addition { 133 | background-color: #BAEEBA; 134 | } 135 | 136 | pre .deletion { 137 | background-color: #FFC8BD; 138 | } 139 | 140 | pre .comment .yardoctag { 141 | font-weight: bold; 142 | } 143 | -------------------------------------------------------------------------------- /intro_presentation/assets/libraries/highlighters/highlight.js/css/hemisu-light.css: -------------------------------------------------------------------------------- 1 | /* Hemisu Light */ 2 | /* http://jmblog.github.com/color-themes-for-google-code-highlightjs */ 3 | /* Original theme - http://noahfrederick.com/vim-color-scheme-hemisu/ */ 4 | /* http://jmblog.github.com/color-themes-for-google-code-highlightjs */ 5 | .hemisu-comment, pre .comment, pre .xml .doctype, pre .html .doctype { 6 | color: #999999; 7 | } 8 | 9 | .hemisu-accent1, pre .number, pre .ruby .keyword { 10 | color: #538192; 11 | } 12 | 13 | .hemisu-accent2, pre .string, pre .regexp, pre .xml .value, pre .html .value { 14 | color: #739200; 15 | } 16 | 17 | .hemisu-accent3, pre .keyword, pre .title, pre .constant, pre .xml .tag, pre .html .tag, pre .css .rules .attribute { 18 | color: #ff0055; 19 | } 20 | 21 | .hemisu-accent4 { 22 | color: #503d15; 23 | } 24 | 25 | pre code { 26 | display: block; 27 | background: white; 28 | color: #111111; 29 | font-family: Menlo, Monaco, Consolas, monospace; 30 | line-height: 1.5; 31 | border: 1px solid #ccc; 32 | padding: 10px; 33 | } 34 | pre .xml .tag .title { 35 | color: #111111; 36 | } 37 | pre .html .tag .title { 38 | color: #111111; 39 | } -------------------------------------------------------------------------------- /intro_presentation/assets/libraries/highlighters/highlight.js/css/idea.css: -------------------------------------------------------------------------------- 1 | /* 2 | 3 | Intellij Idea-like styling (c) Vasily Polovnyov 4 | 5 | */ 6 | 7 | pre code { 8 | display: block; padding: 0.5em; 9 | color: #000; 10 | background: #fff; 11 | } 12 | 13 | pre .subst, 14 | pre .title { 15 | font-weight: normal; 16 | color: #000; 17 | } 18 | 19 | pre .comment, 20 | pre .template_comment, 21 | pre .javadoc, 22 | pre .diff .header { 23 | color: #808080; 24 | font-style: italic; 25 | } 26 | 27 | pre .annotation, 28 | pre .decorator, 29 | pre .preprocessor, 30 | pre .doctype, 31 | pre .pi, 32 | pre .chunk, 33 | pre .shebang, 34 | pre .apache .cbracket, 35 | pre .input_number, 36 | pre .http .title { 37 | color: #808000; 38 | } 39 | 40 | pre .tag, 41 | pre .pi { 42 | background: #efefef; 43 | } 44 | 45 | pre .tag .title, 46 | pre .id, 47 | pre .attr_selector, 48 | pre .pseudo, 49 | pre .literal, 50 | pre .keyword, 51 | pre .hexcolor, 52 | pre .css .function, 53 | pre .ini .title, 54 | pre .css .class, 55 | pre .list .title, 56 | pre .tex .command, 57 | pre .request, 58 | pre .status { 59 | font-weight: bold; 60 | color: #000080; 61 | } 62 | 63 | pre .attribute, 64 | pre .rules .keyword, 65 | pre .number, 66 | pre .date, 67 | pre .regexp, 68 | pre .tex .special { 69 | font-weight: bold; 70 | color: #0000ff; 71 | } 72 | 73 | pre .number, 74 | pre .regexp { 75 | font-weight: normal; 76 | } 77 | 78 | pre .string, 79 | pre .value, 80 | pre .filter .argument, 81 | pre .css .function .params, 82 | pre .apache .tag { 83 | color: #008000; 84 | font-weight: bold; 85 | } 86 | 87 | pre .symbol, 88 | pre .ruby .symbol .string, 89 | pre .ruby .symbol .keyword, 90 | pre .ruby .symbol .keymethods, 91 | pre .char, 92 | pre .tex .formula { 93 | color: #000; 94 | background: #d0eded; 95 | font-style: italic; 96 | } 97 | 98 | pre .phpdoc, 99 | pre .yardoctag, 100 | pre .javadoctag { 101 | text-decoration: underline; 102 | } 103 | 104 | pre .variable, 105 | pre .envvar, 106 | pre .apache .sqbracket, 107 | pre .nginx .built_in { 108 | color: #660e7a; 109 | } 110 | 111 | pre .addition { 112 | background: #baeeba; 113 | } 114 | 115 | pre .deletion { 116 | background: #ffc8bd; 117 | } 118 | 119 | pre .diff .change { 120 | background: #bccff9; 121 | } 122 | -------------------------------------------------------------------------------- /intro_presentation/assets/libraries/highlighters/highlight.js/css/ir_black.css: -------------------------------------------------------------------------------- 1 | /* 2 | IR_Black style (c) Vasily Mikhailitchenko 3 | */ 4 | 5 | pre code { 6 | display: block; padding: 0.5em; 7 | background: #000; color: #f8f8f8; 8 | } 9 | 10 | pre .shebang, 11 | pre .comment, 12 | pre .template_comment, 13 | pre .javadoc { 14 | color: #7c7c7c; 15 | } 16 | 17 | pre .keyword, 18 | pre .tag, 19 | pre .tex .command, 20 | pre .request, 21 | pre .status { 22 | color: #96CBFE; 23 | } 24 | 25 | pre .sub .keyword, 26 | pre .method, 27 | pre .list .title { 28 | color: #FFFFB6; 29 | } 30 | 31 | pre .string, 32 | pre .tag .value, 33 | pre .cdata, 34 | pre .filter .argument, 35 | pre .attr_selector, 36 | pre .apache .cbracket, 37 | pre .date { 38 | color: #A8FF60; 39 | } 40 | 41 | pre .subst { 42 | color: #DAEFA3; 43 | } 44 | 45 | pre .regexp { 46 | color: #E9C062; 47 | } 48 | 49 | pre .title, 50 | pre .sub .identifier, 51 | pre .pi, 52 | pre .decorator, 53 | pre .tex .special, 54 | pre .haskell .type, 55 | pre .constant, 56 | pre .smalltalk .class, 57 | pre .javadoctag, 58 | pre .yardoctag, 59 | pre .phpdoc, 60 | pre .nginx .built_in { 61 | color: #FFFFB6; 62 | } 63 | 64 | pre .symbol, 65 | pre .ruby .symbol .string, 66 | pre .ruby .symbol .keyword, 67 | pre .ruby .symbol .keymethods, 68 | pre .number, 69 | pre .variable, 70 | pre .vbscript, 71 | pre .literal { 72 | color: #C6C5FE; 73 | } 74 | 75 | pre .css .tag { 76 | color: #96CBFE; 77 | } 78 | 79 | pre .css .rules .property, 80 | pre .css .id { 81 | color: #FFFFB6; 82 | } 83 | 84 | pre .css .class { 85 | color: #FFF; 86 | } 87 | 88 | pre .hexcolor { 89 | color: #C6C5FE; 90 | } 91 | 92 | pre .number { 93 | color:#FF73FD; 94 | } 95 | 96 | pre .tex .formula { 97 | opacity: 0.7; 98 | } 99 | -------------------------------------------------------------------------------- /intro_presentation/assets/libraries/highlighters/highlight.js/css/magula.css: -------------------------------------------------------------------------------- 1 | /* 2 | Description: Magula style for highligh.js 3 | Author: Ruslan Keba 4 | Website: http://rukeba.com/ 5 | Version: 1.0 6 | Date: 2009-01-03 7 | Music: Aphex Twin / Xtal 8 | */ 9 | 10 | pre code { 11 | display: block; padding: 0.5em; 12 | background-color: #f4f4f4; 13 | } 14 | 15 | pre code, 16 | pre .ruby .subst, 17 | pre .lisp .title { 18 | color: black; 19 | } 20 | 21 | pre .string, 22 | pre .title, 23 | pre .parent, 24 | pre .tag .value, 25 | pre .rules .value, 26 | pre .rules .value .number, 27 | pre .preprocessor, 28 | pre .ruby .symbol, 29 | pre .ruby .symbol .string, 30 | pre .ruby .symbol .keyword, 31 | pre .ruby .symbol .keymethods, 32 | pre .instancevar, 33 | pre .aggregate, 34 | pre .template_tag, 35 | pre .django .variable, 36 | pre .smalltalk .class, 37 | pre .addition, 38 | pre .flow, 39 | pre .stream, 40 | pre .bash .variable, 41 | pre .apache .cbracket { 42 | color: #050; 43 | } 44 | 45 | pre .comment, 46 | pre .annotation, 47 | pre .template_comment, 48 | pre .diff .header, 49 | pre .chunk { 50 | color: #777; 51 | } 52 | 53 | pre .number, 54 | pre .date, 55 | pre .regexp, 56 | pre .literal, 57 | pre .smalltalk .symbol, 58 | pre .smalltalk .char, 59 | pre .change, 60 | pre .tex .special { 61 | color: #800; 62 | } 63 | 64 | pre .label, 65 | pre .javadoc, 66 | pre .ruby .string, 67 | pre .decorator, 68 | pre .filter .argument, 69 | pre .localvars, 70 | pre .array, 71 | pre .attr_selector, 72 | pre .pseudo, 73 | pre .pi, 74 | pre .doctype, 75 | pre .deletion, 76 | pre .envvar, 77 | pre .shebang, 78 | pre .apache .sqbracket, 79 | pre .nginx .built_in, 80 | pre .tex .formula, 81 | pre .input_number { 82 | color: #00e; 83 | } 84 | 85 | pre .keyword, 86 | pre .id, 87 | pre .phpdoc, 88 | pre .title, 89 | pre .built_in, 90 | pre .aggregate, 91 | pre .smalltalk .class, 92 | pre .winutils, 93 | pre .bash .variable, 94 | pre .apache .tag, 95 | pre .xml .tag, 96 | pre .tex .command, 97 | pre .request, 98 | pre .status { 99 | font-weight: bold; 100 | color: navy; 101 | } 102 | 103 | pre .nginx .built_in { 104 | font-weight: normal; 105 | } 106 | 107 | pre .coffeescript .javascript, 108 | pre .xml .css, 109 | pre .xml .javascript, 110 | pre .xml .vbscript, 111 | pre .tex .formula { 112 | opacity: 0.5; 113 | } 114 | 115 | /* --- */ 116 | pre .apache .tag { 117 | font-weight: bold; 118 | color: blue; 119 | } 120 | 121 | -------------------------------------------------------------------------------- /intro_presentation/assets/libraries/highlighters/highlight.js/css/monokai.css: -------------------------------------------------------------------------------- 1 | /* 2 | Monokai style - ported by Luigi Maselli - http://grigio.org 3 | */ 4 | 5 | pre code { 6 | display: block; padding: 0.5em; 7 | background: #272822; 8 | } 9 | 10 | pre .params .identifier .keymethods { 11 | color: #FD971F; 12 | } 13 | 14 | pre .tag, 15 | pre .tag .title, 16 | pre .keyword, 17 | pre .literal, 18 | pre .change, 19 | pre .winutils, 20 | pre .flow, 21 | pre .lisp .title, 22 | pre .tex .special { 23 | color: #F92672; 24 | } 25 | 26 | pre code { 27 | color: #DDD; 28 | } 29 | 30 | pre code .constant { 31 | color: #66D9EF; 32 | } 33 | 34 | pre .class .title { 35 | color: white; 36 | } 37 | 38 | pre .attribute, 39 | pre .symbol, 40 | pre .value, 41 | pre .regexp { 42 | color: #BF79DB; 43 | } 44 | 45 | pre .tag .value, 46 | pre .string, 47 | pre .ruby .subst, 48 | pre .title, 49 | pre .haskell .type, 50 | pre .preprocessor, 51 | pre .ruby .instancevar, 52 | pre .ruby .class .parent, 53 | pre .built_in, 54 | pre .sql .aggregate, 55 | pre .django .template_tag, 56 | pre .django .variable, 57 | pre .smalltalk .class, 58 | pre .javadoc, 59 | pre .ruby .string, 60 | pre .django .filter .argument, 61 | pre .smalltalk .localvars, 62 | pre .smalltalk .array, 63 | pre .attr_selector, 64 | pre .pseudo, 65 | pre .addition, 66 | pre .stream, 67 | pre .envvar, 68 | pre .apache .tag, 69 | pre .apache .cbracket, 70 | pre .tex .command, 71 | pre .input_number { 72 | color: #A6E22E; 73 | } 74 | 75 | pre .comment, 76 | pre .java .annotation, 77 | pre .python .decorator, 78 | pre .template_comment, 79 | pre .pi, 80 | pre .doctype, 81 | pre .deletion, 82 | pre .shebang, 83 | pre .apache .sqbracket, 84 | pre .tex .formula { 85 | color: #75715E; 86 | } 87 | 88 | pre .keyword, 89 | pre .literal, 90 | pre .css .id, 91 | pre .phpdoc, 92 | pre .title, 93 | pre .haskell .type, 94 | pre .vbscript .built_in, 95 | pre .sql .aggregate, 96 | pre .rsl .built_in, 97 | pre .smalltalk .class, 98 | pre .diff .header, 99 | pre .chunk, 100 | pre .winutils, 101 | pre .bash .variable, 102 | pre .apache .tag, 103 | pre .tex .special, 104 | pre .request, 105 | pre .status { 106 | font-weight: bold; 107 | } 108 | 109 | pre .coffeescript .javascript, 110 | pre .xml .css, 111 | pre .xml .javascript, 112 | pre .xml .vbscript, 113 | pre .tex .formula { 114 | opacity: 0.5; 115 | } 116 | -------------------------------------------------------------------------------- /intro_presentation/assets/libraries/highlighters/highlight.js/css/pojoaque.css: -------------------------------------------------------------------------------- 1 | /* 2 | 3 | Pojoaque Style by Jason Tate 4 | http://web-cms-designs.com/ftopict-10-pojoaque-style-for-highlight-js-code-highlighter.html 5 | Based on Solarized Style from http://ethanschoonover.com/solarized 6 | 7 | */ 8 | 9 | pre code { 10 | display: block; padding: 0.5em; 11 | color: #DCCF8F; 12 | background: url(./pojoaque.jpg) repeat scroll left top #181914; 13 | } 14 | 15 | pre .comment, 16 | pre .template_comment, 17 | pre .diff .header, 18 | pre .doctype, 19 | pre .lisp .string, 20 | pre .javadoc { 21 | color: #586e75; 22 | font-style: italic; 23 | } 24 | 25 | pre .keyword, 26 | pre .css .rule .keyword, 27 | pre .winutils, 28 | pre .javascript .title, 29 | pre .method, 30 | pre .addition, 31 | pre .css .tag, 32 | pre .lisp .title { 33 | color: #B64926; 34 | } 35 | 36 | pre .number, 37 | pre .command, 38 | pre .string, 39 | pre .tag .value, 40 | pre .phpdoc, 41 | pre .tex .formula, 42 | pre .regexp, 43 | pre .hexcolor { 44 | color: #468966; 45 | } 46 | 47 | pre .title, 48 | pre .localvars, 49 | pre .function .title, 50 | pre .chunk, 51 | pre .decorator, 52 | pre .builtin, 53 | pre .built_in, 54 | pre .lisp .title, 55 | pre .identifier, 56 | pre .title .keymethods, 57 | pre .id { 58 | color: #FFB03B; 59 | } 60 | 61 | pre .attribute, 62 | pre .variable, 63 | pre .instancevar, 64 | pre .lisp .body, 65 | pre .smalltalk .number, 66 | pre .constant, 67 | pre .class .title, 68 | pre .parent, 69 | pre .haskell .type { 70 | color: #b58900; 71 | } 72 | 73 | pre .css .attribute { 74 | color: #b89859; 75 | } 76 | 77 | pre .css .number,pre .css .hexcolor{ 78 | color: #DCCF8F; 79 | } 80 | 81 | pre .css .class { 82 | color: #d3a60c; 83 | } 84 | 85 | pre .preprocessor, 86 | pre .pi, 87 | pre .shebang, 88 | pre .symbol, 89 | pre .diff .change, 90 | pre .special, 91 | pre .keymethods, 92 | pre .attr_selector, 93 | pre .important, 94 | pre .subst, 95 | pre .cdata { 96 | color: #cb4b16; 97 | } 98 | 99 | pre .deletion { 100 | color: #dc322f; 101 | } 102 | 103 | pre .tex .formula { 104 | background: #073642; 105 | } 106 | -------------------------------------------------------------------------------- /intro_presentation/assets/libraries/highlighters/highlight.js/css/pojoaque.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/grunwaldlab/Reproducible-science-in-R/0bb8e62689e0fb7c813051551342c046144f389b/intro_presentation/assets/libraries/highlighters/highlight.js/css/pojoaque.jpg -------------------------------------------------------------------------------- /intro_presentation/assets/libraries/highlighters/highlight.js/css/school_book.css: -------------------------------------------------------------------------------- 1 | /* 2 | 3 | School Book style from goldblog.com.ua (c) Zaripov Yura 4 | 5 | */ 6 | 7 | pre code { 8 | display: block; padding: 15px 0.5em 0.5em 30px; 9 | font-size: 11px !important; 10 | line-height:16px !important; 11 | } 12 | 13 | pre{ 14 | background:#f6f6ae url(./school_book.png); 15 | border-top: solid 2px #d2e8b9; 16 | border-bottom: solid 1px #d2e8b9; 17 | } 18 | 19 | pre .keyword, 20 | pre .literal, 21 | pre .change, 22 | pre .winutils, 23 | pre .flow, 24 | pre .lisp .title, 25 | pre .tex .special { 26 | color:#005599; 27 | font-weight:bold; 28 | } 29 | 30 | pre code, 31 | pre .ruby .subst, 32 | pre .tag .keyword { 33 | color: #3E5915; 34 | } 35 | 36 | pre .string, 37 | pre .title, 38 | pre .haskell .type, 39 | pre .tag .value, 40 | pre .css .rules .value, 41 | pre .preprocessor, 42 | pre .ruby .symbol, 43 | pre .ruby .symbol .string, 44 | pre .ruby .symbol .keyword, 45 | pre .ruby .symbol .keymethods, 46 | pre .ruby .instancevar, 47 | pre .ruby .class .parent, 48 | pre .built_in, 49 | pre .sql .aggregate, 50 | pre .django .template_tag, 51 | pre .django .variable, 52 | pre .smalltalk .class, 53 | pre .javadoc, 54 | pre .ruby .string, 55 | pre .django .filter .argument, 56 | pre .smalltalk .localvars, 57 | pre .smalltalk .array, 58 | pre .attr_selector, 59 | pre .pseudo, 60 | pre .addition, 61 | pre .stream, 62 | pre .envvar, 63 | pre .apache .tag, 64 | pre .apache .cbracket, 65 | pre .nginx .built_in, 66 | pre .tex .command { 67 | color: #2C009F; 68 | } 69 | 70 | pre .comment, 71 | pre .java .annotation, 72 | pre .python .decorator, 73 | pre .template_comment, 74 | pre .pi, 75 | pre .doctype, 76 | pre .deletion, 77 | pre .shebang, 78 | pre .apache .sqbracket { 79 | color: #E60415; 80 | } 81 | 82 | pre .keyword, 83 | pre .literal, 84 | pre .css .id, 85 | pre .phpdoc, 86 | pre .title, 87 | pre .haskell .type, 88 | pre .vbscript .built_in, 89 | pre .sql .aggregate, 90 | pre .rsl .built_in, 91 | pre .smalltalk .class, 92 | pre .xml .tag .title, 93 | pre .diff .header, 94 | pre .chunk, 95 | pre .winutils, 96 | pre .bash .variable, 97 | pre .apache .tag, 98 | pre .tex .command, 99 | pre .request, 100 | pre .status { 101 | font-weight: bold; 102 | } 103 | 104 | pre .coffeescript .javascript, 105 | pre .xml .css, 106 | pre .xml .javascript, 107 | pre .xml .vbscript, 108 | pre .tex .formula { 109 | opacity: 0.5; 110 | } 111 | -------------------------------------------------------------------------------- /intro_presentation/assets/libraries/highlighters/highlight.js/css/school_book.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/grunwaldlab/Reproducible-science-in-R/0bb8e62689e0fb7c813051551342c046144f389b/intro_presentation/assets/libraries/highlighters/highlight.js/css/school_book.png -------------------------------------------------------------------------------- /intro_presentation/assets/libraries/highlighters/highlight.js/css/solarized_dark.css: -------------------------------------------------------------------------------- 1 | /* 2 | 3 | Orginal Style from ethanschoonover.com/solarized (c) Jeremy Hull 4 | 5 | */ 6 | 7 | pre code { 8 | display: block; padding: 0.5em; 9 | background: #002b36; color: #839496; 10 | } 11 | 12 | pre .comment, 13 | pre .template_comment, 14 | pre .diff .header, 15 | pre .doctype, 16 | pre .pi, 17 | pre .lisp .string, 18 | pre .javadoc { 19 | color: #586e75; 20 | font-style: italic; 21 | } 22 | 23 | pre .keyword, 24 | pre .winutils, 25 | pre .method, 26 | pre .addition, 27 | pre .css .tag, 28 | pre .request, 29 | pre .status { 30 | color: #859900; 31 | } 32 | 33 | pre .number, 34 | pre .command, 35 | pre .string, 36 | pre .tag .value, 37 | pre .phpdoc, 38 | pre .tex .formula, 39 | pre .regexp, 40 | pre .hexcolor { 41 | color: #2aa198; 42 | } 43 | 44 | pre .title, 45 | pre .localvars, 46 | pre .chunk, 47 | pre .decorator, 48 | pre .builtin, 49 | pre .built_in, 50 | pre .identifier, 51 | pre .title .keymethods, 52 | pre .vhdl .literal, 53 | pre .id { 54 | color: #268bd2; 55 | } 56 | 57 | pre .attribute, 58 | pre .variable, 59 | pre .instancevar, 60 | pre .lisp .body, 61 | pre .smalltalk .number, 62 | pre .constant, 63 | pre .class .title, 64 | pre .parent, 65 | pre .haskell .type { 66 | color: #b58900; 67 | } 68 | 69 | pre .preprocessor, 70 | pre .preprocessor .keyword, 71 | pre .shebang, 72 | pre .symbol, 73 | pre .diff .change, 74 | pre .special, 75 | pre .keymethods, 76 | pre .attr_selector, 77 | pre .important, 78 | pre .subst, 79 | pre .cdata { 80 | color: #cb4b16; 81 | } 82 | 83 | pre .deletion { 84 | color: #dc322f; 85 | } 86 | 87 | pre .tex .formula { 88 | background: #073642; 89 | } 90 | -------------------------------------------------------------------------------- /intro_presentation/assets/libraries/highlighters/highlight.js/css/solarized_light.css: -------------------------------------------------------------------------------- 1 | /* 2 | 3 | Orginal Style from ethanschoonover.com/solarized (c) Jeremy Hull 4 | 5 | */ 6 | 7 | pre code { 8 | display: block; padding: 0.5em; 9 | background: #fdf6e3; color: #657b83; 10 | } 11 | 12 | pre .comment, 13 | pre .template_comment, 14 | pre .diff .header, 15 | pre .doctype, 16 | pre .pi, 17 | pre .lisp .string, 18 | pre .javadoc { 19 | color: #93a1a1; 20 | font-style: italic; 21 | } 22 | 23 | pre .keyword, 24 | pre .winutils, 25 | pre .method, 26 | pre .addition, 27 | pre .css .tag, 28 | pre .request, 29 | pre .status { 30 | color: #859900; 31 | } 32 | 33 | pre .number, 34 | pre .command, 35 | pre .string, 36 | pre .tag .value, 37 | pre .phpdoc, 38 | pre .tex .formula, 39 | pre .regexp, 40 | pre .hexcolor { 41 | color: #2aa198; 42 | } 43 | 44 | pre .title, 45 | pre .localvars, 46 | pre .chunk, 47 | pre .decorator, 48 | pre .builtin, 49 | pre .built_in, 50 | pre .identifier, 51 | pre .title .keymethods, 52 | pre .vhdl .literal, 53 | pre .id { 54 | color: #268bd2; 55 | } 56 | 57 | pre .attribute, 58 | pre .variable, 59 | pre .instancevar, 60 | pre .lisp .body, 61 | pre .smalltalk .number, 62 | pre .constant, 63 | pre .class .title, 64 | pre .parent, 65 | pre .haskell .type { 66 | color: #b58900; 67 | } 68 | 69 | pre .preprocessor, 70 | pre .preprocessor .keyword, 71 | pre .shebang, 72 | pre .symbol, 73 | pre .diff .change, 74 | pre .special, 75 | pre .keymethods, 76 | pre .attr_selector, 77 | pre .important, 78 | pre .subst, 79 | pre .cdata { 80 | color: #cb4b16; 81 | } 82 | 83 | pre .deletion { 84 | color: #dc322f; 85 | } 86 | 87 | pre .tex .formula { 88 | background: #eee8d5; 89 | } 90 | -------------------------------------------------------------------------------- /intro_presentation/assets/libraries/highlighters/highlight.js/css/sunburst.css: -------------------------------------------------------------------------------- 1 | /* 2 | 3 | Sunburst-like style (c) Vasily Polovnyov 4 | 5 | */ 6 | 7 | pre code { 8 | display: block; padding: 0.5em; 9 | background: #000; color: #f8f8f8; 10 | } 11 | 12 | pre .comment, 13 | pre .template_comment, 14 | pre .javadoc { 15 | color: #aeaeae; 16 | font-style: italic; 17 | } 18 | 19 | pre .keyword, 20 | pre .ruby .function .keyword, 21 | pre .request, 22 | pre .status { 23 | color: #E28964; 24 | } 25 | 26 | pre .function .keyword, 27 | pre .sub .keyword, 28 | pre .method, 29 | pre .list .title { 30 | color: #99CF50; 31 | } 32 | 33 | pre .string, 34 | pre .tag .value, 35 | pre .cdata, 36 | pre .filter .argument, 37 | pre .attr_selector, 38 | pre .apache .cbracket, 39 | pre .date, 40 | pre .tex .command { 41 | color: #65B042; 42 | } 43 | 44 | pre .subst { 45 | color: #DAEFA3; 46 | } 47 | 48 | pre .regexp { 49 | color: #E9C062; 50 | } 51 | 52 | pre .title, 53 | pre .sub .identifier, 54 | pre .pi, 55 | pre .tag, 56 | pre .tag .keyword, 57 | pre .decorator, 58 | pre .shebang, 59 | pre .input_number { 60 | color: #89BDFF; 61 | } 62 | 63 | pre .class .title, 64 | pre .haskell .type, 65 | pre .smalltalk .class, 66 | pre .javadoctag, 67 | pre .yardoctag, 68 | pre .phpdoc { 69 | text-decoration: underline; 70 | } 71 | 72 | pre .symbol, 73 | pre .ruby .symbol .string, 74 | pre .ruby .symbol .keyword, 75 | pre .ruby .symbol .keymethods, 76 | pre .number { 77 | color: #3387CC; 78 | } 79 | 80 | pre .params, 81 | pre .variable { 82 | color: #3E87E3; 83 | } 84 | 85 | pre .css .tag, 86 | pre .rules .property, 87 | pre .pseudo, 88 | pre .tex .special { 89 | color: #CDA869; 90 | } 91 | 92 | pre .css .class { 93 | color: #9B703F; 94 | } 95 | 96 | pre .rules .keyword { 97 | color: #C5AF75; 98 | } 99 | 100 | pre .rules .value { 101 | color: #CF6A4C; 102 | } 103 | 104 | pre .css .id { 105 | color: #8B98AB; 106 | } 107 | 108 | pre .annotation, 109 | pre .apache .sqbracket, 110 | pre .nginx .built_in { 111 | color: #9B859D; 112 | } 113 | 114 | pre .preprocessor { 115 | color: #8996A8; 116 | } 117 | 118 | pre .hexcolor, 119 | pre .css .value .number { 120 | color: #DD7B3B; 121 | } 122 | 123 | pre .css .function { 124 | color: #DAD085; 125 | } 126 | 127 | pre .diff .header, 128 | pre .chunk, 129 | pre .tex .formula { 130 | background-color: #0E2231; 131 | color: #F8F8F8; 132 | font-style: italic; 133 | } 134 | 135 | pre .diff .change { 136 | background-color: #4A410D; 137 | color: #F8F8F8; 138 | } 139 | 140 | pre .addition { 141 | background-color: #253B22; 142 | color: #F8F8F8; 143 | } 144 | 145 | pre .deletion { 146 | background-color: #420E09; 147 | color: #F8F8F8; 148 | } 149 | -------------------------------------------------------------------------------- /intro_presentation/assets/libraries/highlighters/highlight.js/css/tomorrow.css: -------------------------------------------------------------------------------- 1 | /* Tomorrow Theme */ 2 | /* http://jmblog.github.com/color-themes-for-google-code-highlightjs */ 3 | /* Original theme - https://github.com/chriskempson/tomorrow-theme */ 4 | /* http://jmblog.github.com/color-themes-for-google-code-highlightjs */ 5 | .tomorrow-comment, pre .comment, pre .title { 6 | color: #8e908c; 7 | } 8 | 9 | .tomorrow-red, pre .variable, pre .attribute, pre .tag, pre .regexp, pre .ruby .constant, pre .xml .tag .title, pre .xml .pi, pre .xml .doctype, pre .html .doctype, pre .css .id, pre .css .class, pre .css .pseudo { 10 | color: #c82829; 11 | } 12 | 13 | .tomorrow-orange, pre .number, pre .preprocessor, pre .built_in, pre .literal, pre .params, pre .constant { 14 | color: #f5871f; 15 | } 16 | 17 | .tomorrow-yellow, pre .class, pre .ruby .class .title, pre .css .rules .attribute { 18 | color: #eab700; 19 | } 20 | 21 | .tomorrow-green, pre .string, pre .value, pre .inheritance, pre .header, pre .ruby .symbol, pre .xml .cdata { 22 | color: #718c00; 23 | } 24 | 25 | .tomorrow-aqua, pre .css .hexcolor { 26 | color: #3e999f; 27 | } 28 | 29 | .tomorrow-blue, pre .function, pre .python .decorator, pre .python .title, pre .ruby .function .title, pre .ruby .title .keyword, pre .perl .sub, pre .javascript .title, pre .coffeescript .title { 30 | color: #4271ae; 31 | } 32 | 33 | .tomorrow-purple, pre .keyword, pre .javascript .function { 34 | color: #8959a8; 35 | } 36 | 37 | pre code { 38 | display: block; 39 | background: white; 40 | color: #4d4d4c; 41 | font-family: Menlo, Monaco, Consolas, monospace; 42 | line-height: 1.5; 43 | border: 1px solid #ccc; 44 | padding: 10px; 45 | } -------------------------------------------------------------------------------- /intro_presentation/assets/libraries/highlighters/highlight.js/css/tomorrow_night.css: -------------------------------------------------------------------------------- 1 | /* Tomorrow Night Theme */ 2 | /* http://jmblog.github.com/color-themes-for-google-code-highlightjs */ 3 | /* Original theme - https://github.com/chriskempson/tomorrow-theme */ 4 | /* http://jmblog.github.com/color-themes-for-google-code-highlightjs */ 5 | .tomorrow-comment, pre .comment, pre .title { 6 | color: #969896; 7 | } 8 | 9 | .tomorrow-red, pre .variable, pre .attribute, pre .tag, pre .regexp, pre .ruby .constant, pre .xml .tag .title, pre .xml .pi, pre .xml .doctype, pre .html .doctype, pre .css .id, pre .css .class, pre .css .pseudo { 10 | color: #cc6666; 11 | } 12 | 13 | .tomorrow-orange, pre .number, pre .preprocessor, pre .built_in, pre .literal, pre .params, pre .constant { 14 | color: #de935f; 15 | } 16 | 17 | .tomorrow-yellow, pre .class, pre .ruby .class .title, pre .css .rules .attribute { 18 | color: #f0c674; 19 | } 20 | 21 | .tomorrow-green, pre .string, pre .value, pre .inheritance, pre .header, pre .ruby .symbol, pre .xml .cdata { 22 | color: #b5bd68; 23 | } 24 | 25 | .tomorrow-aqua, pre .css .hexcolor { 26 | color: #8abeb7; 27 | } 28 | 29 | .tomorrow-blue, pre .function, pre .python .decorator, pre .python .title, pre .ruby .function .title, pre .ruby .title .keyword, pre .perl .sub, pre .javascript .title, pre .coffeescript .title { 30 | color: #81a2be; 31 | } 32 | 33 | .tomorrow-purple, pre .keyword, pre .javascript .function { 34 | color: #b294bb; 35 | } 36 | 37 | pre code { 38 | display: block; 39 | background: #1d1f21; 40 | color: #c5c8c6; 41 | font-family: Menlo, Monaco, Consolas, monospace; 42 | line-height: 1.5; 43 | border: 1px solid #ccc; 44 | padding: 10px; 45 | } -------------------------------------------------------------------------------- /intro_presentation/assets/libraries/highlighters/highlight.js/css/vs.css: -------------------------------------------------------------------------------- 1 | /* 2 | 3 | Visual Studio-like style based on original C# coloring by Jason Diamond 4 | 5 | */ 6 | pre code { 7 | display: block; padding: 0.5em; 8 | } 9 | 10 | pre .comment, 11 | pre .annotation, 12 | pre .template_comment, 13 | pre .diff .header, 14 | pre .chunk, 15 | pre .apache .cbracket { 16 | color: rgb(0, 128, 0); 17 | } 18 | 19 | pre .keyword, 20 | pre .id, 21 | pre .built_in, 22 | pre .smalltalk .class, 23 | pre .winutils, 24 | pre .bash .variable, 25 | pre .tex .command, 26 | pre .request, 27 | pre .status { 28 | color: rgb(0, 0, 255); 29 | } 30 | 31 | pre .string, 32 | pre .title, 33 | pre .parent, 34 | pre .tag .value, 35 | pre .rules .value, 36 | pre .rules .value .number, 37 | pre .ruby .symbol, 38 | pre .ruby .symbol 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rgb(163, 21, 21); } 84 | pre .vhdl .attribute { color: #00B0E8; } 85 | -------------------------------------------------------------------------------- /intro_presentation/assets/libraries/highlighters/highlight.js/css/xcode.css: -------------------------------------------------------------------------------- 1 | /* 2 | 3 | XCode style (c) Angel Garcia 4 | 5 | */ 6 | 7 | pre code { 8 | display: block; padding: 0.5em; 9 | background: #fff; color: black; 10 | } 11 | 12 | pre .comment, 13 | pre .template_comment, 14 | pre .javadoc, 15 | pre .comment * { 16 | color: rgb(0,106,0); 17 | } 18 | 19 | pre .keyword, 20 | pre .literal { 21 | color: rgb(170,13,145); 22 | } 23 | pre .method, 24 | pre .list .title, 25 | pre .tag .title, 26 | pre .setting .value, 27 | pre .winutils, 28 | pre .tex .command, 29 | pre .http .title, 30 | pre .request, 31 | pre .status { 32 | color: #008; 33 | } 34 | 35 | pre .envvar, 36 | pre .tex .special { 37 | color: #660; 38 | } 39 | 40 | pre .string { 41 | color: rgb(196,26,22); 42 | } 43 | pre .tag .value, 44 | pre .cdata, 45 | pre .filter .argument, 46 | pre .attr_selector, 47 | pre .apache .cbracket, 48 | pre .date, 49 | pre .regexp { 50 | color: #080; 51 | } 52 | 53 | pre .sub .identifier, 54 | pre .pi, 55 | pre .tag, 56 | pre .tag .keyword, 57 | pre .decorator, 58 | pre .ini .title, 59 | pre .shebang, 60 | pre .input_number, 61 | pre .hexcolor, 62 | pre .rules .value, 63 | pre .css .value .number, 64 | pre .symbol, 65 | pre .ruby .symbol .string, 66 | pre .ruby .symbol .keyword, 67 | pre .ruby .symbol .keymethods, 68 | pre .number, 69 | pre .css .function { 70 | color: rgb(28,0,207); 71 | } 72 | 73 | pre .class .title, 74 | pre .haskell .type, 75 | pre .smalltalk .class, 76 | pre .javadoctag, 77 | pre .yardoctag, 78 | pre .phpdoc, 79 | pre .typename, 80 | pre .tag .attribute, 81 | pre .doctype, 82 | pre .class .id, 83 | pre .built_in, 84 | pre .setting, 85 | pre .params { 86 | color: rgb(92,38,153); 87 | } 88 | 89 | pre .variable { 90 | color: rgb(63,110,116); 91 | } 92 | pre .css .tag, 93 | pre .rules .property, 94 | pre .pseudo, 95 | pre .subst { 96 | color: #000; 97 | } 98 | 99 | pre .css .class, pre .css .id { 100 | color: #9B703F; 101 | } 102 | 103 | pre .value .important { 104 | color: #ff7700; 105 | font-weight: bold; 106 | } 107 | 108 | pre .rules .keyword { 109 | color: #C5AF75; 110 | } 111 | 112 | pre .annotation, 113 | pre .apache .sqbracket, 114 | pre .nginx .built_in { 115 | color: #9B859D; 116 | } 117 | 118 | pre .preprocessor, 119 | pre .preprocessor * { 120 | color: rgb(100,56,32); 121 | } 122 | 123 | pre .tex .formula { 124 | background-color: #EEE; 125 | font-style: italic; 126 | } 127 | 128 | pre .diff .header, 129 | pre .chunk { 130 | color: #808080; 131 | font-weight: bold; 132 | } 133 | 134 | pre .diff .change { 135 | background-color: #BCCFF9; 136 | } 137 | 138 | pre .addition { 139 | background-color: #BAEEBA; 140 | } 141 | 142 | pre .deletion { 143 | background-color: #FFC8BD; 144 | } 145 | 146 | pre .comment .yardoctag { 147 | font-weight: bold; 148 | } 149 | 150 | pre .method .id { 151 | color: #000; 152 | } 153 | -------------------------------------------------------------------------------- /intro_presentation/assets/libraries/highlighters/highlight.js/css/zenburn.css: -------------------------------------------------------------------------------- 1 | /* 2 | 3 | Zenburn style from voldmar.ru (c) Vladimir Epifanov 4 | based on dark.css by Ivan Sagalaev 5 | 6 | */ 7 | 8 | pre code { 9 | display: block; padding: 0.5em; 10 | background: #3F3F3F; 11 | color: #DCDCDC; 12 | } 13 | 14 | pre .keyword, 15 | pre .tag, 16 | pre .css .class, 17 | pre .css .id, 18 | pre .lisp .title, 19 | pre .request, 20 | pre .status { 21 | color: #E3CEAB; 22 | } 23 | 24 | pre .django .template_tag, 25 | pre .django .variable, 26 | pre .django .filter .argument { 27 | color: #DCDCDC; 28 | } 29 | 30 | pre .number, 31 | pre .date { 32 | color: #8CD0D3; 33 | } 34 | 35 | pre .dos .envvar, 36 | pre .dos .stream, 37 | pre .variable, 38 | pre .apache .sqbracket { 39 | color: #EFDCBC; 40 | } 41 | 42 | pre .dos .flow, 43 | pre .diff .change, 44 | pre .python .exception, 45 | pre .python .built_in, 46 | pre .literal, 47 | pre .tex .special { 48 | color: #EFEFAF; 49 | } 50 | 51 | pre .diff .chunk, 52 | pre .ruby .subst { 53 | color: #8F8F8F; 54 | } 55 | 56 | pre .dos .keyword, 57 | pre .python .decorator, 58 | pre .title, 59 | pre .haskell .type, 60 | pre .diff .header, 61 | pre .ruby .class .parent, 62 | pre .apache .tag, 63 | pre .nginx .built_in, 64 | pre .tex .command, 65 | pre .input_number { 66 | color: #efef8f; 67 | } 68 | 69 | pre .dos .winutils, 70 | pre .ruby .symbol, 71 | pre .ruby .symbol .string, 72 | pre .ruby .symbol .keyword, 73 | pre .ruby .symbol .keymethods, 74 | pre .ruby .string, 75 | pre .ruby .instancevar { 76 | color: #DCA3A3; 77 | } 78 | 79 | pre .diff .deletion, 80 | pre .string, 81 | pre .tag .value, 82 | pre .preprocessor, 83 | pre .built_in, 84 | pre .sql 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| Luke Mahé 6 | 7 | Modified By: 8 | Ramnath Vaidyanathan 9 | 10 | URL: https://code.google.com/p/io-2012-slides 11 | 12 | LICENSE: Apache 2.0 13 | -------------------------------------------------------------------------------- /intro_presentation/libraries/frameworks/io2012/config.yml: -------------------------------------------------------------------------------- 1 | io2012: 2 | theme: NULL 3 | layout: default 4 | -------------------------------------------------------------------------------- /intro_presentation/libraries/frameworks/io2012/css/fonts.css: -------------------------------------------------------------------------------- 1 | @font-face { 2 | font-family: 'Open Sans'; 3 | font-style: normal; 4 | font-weight: 400; 5 | src: local('Open Sans'), local('OpenSans'), url(../fonts/OpenSans.woff) format('woff'); 6 | } 7 | @font-face { 8 | font-family: 'Open Sans'; 9 | font-style: normal; 10 | font-weight: 700; 11 | src: local('Open Sans Bold'), local('OpenSans-Bold'), url(../fonts/OpenSans-Bold.woff) format('woff'); 12 | } 13 | @font-face { 14 | font-family: 'Open Sans'; 15 | font-style: italic; 16 | font-weight: 700; 17 | src: local('Open Sans Bold Italic'), local('OpenSans-BoldItalic'), url(../fonts/OpenSans-BoldItalic.woff) format('woff'); 18 | } 19 | @font-face { 20 | font-family: 'Open Sans'; 21 | font-style: italic; 22 | font-weight: 400; 23 | src: local('Open Sans Italic'), local('OpenSans-Italic'), url(../fonts/OpenSans-Italic.woff) format('woff'); 24 | } 25 | -------------------------------------------------------------------------------- /intro_presentation/libraries/frameworks/io2012/css/phone.css: -------------------------------------------------------------------------------- 1 | /*Smartphones (portrait and landscape) ----------- */ 2 | /*@media only screen 3 | and (min-width : 320px) 4 | and (max-width : 480px) { 5 | 6 | }*/ 7 | /* Smartphones (portrait) ----------- */ 8 | /* Styles */ 9 | /* line 17, ../scss/phone.scss */ 10 | slides 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(function(window) { 2 | 3 | var ORIGIN_ = location.protocol + '//' + location.host; 4 | 5 | function SlideController() { 6 | this.popup = null; 7 | this.isPopup = window.opener; 8 | 9 | if (this.setupDone()) { 10 | window.addEventListener('message', this.onMessage_.bind(this), false); 11 | 12 | // Close popups if we reload the main window. 13 | window.addEventListener('beforeunload', function(e) { 14 | if (this.popup) { 15 | this.popup.close(); 16 | } 17 | }.bind(this), false); 18 | } 19 | } 20 | 21 | SlideController.PRESENTER_MODE_PARAM = 'presentme'; 22 | 23 | SlideController.prototype.setupDone = function() { 24 | var params = location.search.substring(1).split('&').map(function(el) { 25 | return el.split('='); 26 | }); 27 | 28 | var presentMe = null; 29 | for (var i = 0, param; param = params[i]; ++i) { 30 | if (param[0].toLowerCase() == SlideController.PRESENTER_MODE_PARAM) { 31 | presentMe = param[1] == 'true'; 32 | break; 33 | } 34 | } 35 | 36 | if (presentMe !== null) { 37 | localStorage.ENABLE_PRESENTOR_MODE = presentMe; 38 | // TODO: use window.history.pushState to update URL instead of the redirect. 39 | if (window.history.replaceState) { 40 | window.history.replaceState({}, '', location.pathname); 41 | } else { 42 | location.replace(location.pathname); 43 | return false; 44 | } 45 | } 46 | 47 | var enablePresenterMode = localStorage.getItem('ENABLE_PRESENTOR_MODE'); 48 | if (enablePresenterMode && JSON.parse(enablePresenterMode)) { 49 | // Only open popup from main deck. Don't want recursive popup opening! 50 | if (!this.isPopup) { 51 | var opts = 'menubar=no,location=yes,resizable=yes,scrollbars=no,status=no'; 52 | this.popup = window.open(location.href, 'mywindow', opts); 53 | 54 | // Loading in the popup? Trigger the hotkey for turning presenter mode on. 55 | this.popup.addEventListener('load', function(e) { 56 | var evt = this.popup.document.createEvent('Event'); 57 | evt.initEvent('keydown', true, true); 58 | evt.keyCode = 'P'.charCodeAt(0); 59 | this.popup.document.dispatchEvent(evt); 60 | // this.popup.document.body.classList.add('with-notes'); 61 | // document.body.classList.add('popup'); 62 | }.bind(this), false); 63 | } 64 | } 65 | 66 | return true; 67 | } 68 | 69 | SlideController.prototype.onMessage_ = function(e) { 70 | var data = e.data; 71 | 72 | // Restrict messages to being from this origin. Allow local developmet 73 | // from file:// though. 74 | // TODO: It would be dope if FF implemented location.origin! 75 | if (e.origin != ORIGIN_ && ORIGIN_.indexOf('file://') != 0) { 76 | alert('Someone tried to postMessage from an unknown origin'); 77 | return; 78 | } 79 | 80 | // if (e.source.location.hostname != 'localhost') { 81 | // alert('Someone tried to postMessage from an unknown origin'); 82 | // return; 83 | // } 84 | 85 | if ('keyCode' in data) { 86 | var evt = document.createEvent('Event'); 87 | evt.initEvent('keydown', true, true); 88 | evt.keyCode = data.keyCode; 89 | document.dispatchEvent(evt); 90 | } 91 | }; 92 | 93 | SlideController.prototype.sendMsg = function(msg) { 94 | // // Send message to popup window. 95 | // if (this.popup) { 96 | // this.popup.postMessage(msg, ORIGIN_); 97 | // } 98 | 99 | // Send message to main window. 100 | if (this.isPopup) { 101 | // TODO: It would be dope if FF implemented location.origin. 102 | window.opener.postMessage(msg, '*'); 103 | } 104 | }; 105 | 106 | window.SlideController = SlideController; 107 | 108 | })(window); 109 | 110 | -------------------------------------------------------------------------------- /intro_presentation/libraries/frameworks/io2012/js/slide_config.js: -------------------------------------------------------------------------------- 1 | var SLIDE_CONFIG = { 2 | // Slide settings 3 | settings: { 4 | useBuilds: true, // Default: true. False will turn off slide animation builds. 5 | usePrettify: false, // Default: true 6 | enableSlideAreas: false, // Default: true. False turns off the click areas on either slide of the slides. 7 | enableTouch: true, // Default: true. If touch support should enabled. Note: the device must support touch. 8 | //analytics: 'UA-XXXXXXXX-1', // TODO: Using this breaks GA for some reason (probably requirejs). Update your tracking code in template.html instead. 9 | favIcon: false, 10 | fonts: [ 11 | 'Open Sans:regular,semibold,italic,italicsemibold', 12 | 'Inconsolata' 13 | ], 14 | //theme: ['mytheme'], // Add your own custom themes or styles in /theme/css. Leave off the .css extension. 15 | }, 16 | }; -------------------------------------------------------------------------------- /intro_presentation/libraries/frameworks/io2012/js/slides.js: -------------------------------------------------------------------------------- 1 | require(['order!slide_config','order!modernizr.custom.45394', 'order!hammer', 2 | 'order!slide-controller', 'order!slide-deck'], function(someModule) { 3 | }); 4 | -------------------------------------------------------------------------------- /intro_presentation/libraries/highlighters/highlight.js/css/arta.css: -------------------------------------------------------------------------------- 1 | /* 2 | Date: 17.V.2011 3 | Author: pumbur 4 | */ 5 | 6 | pre code 7 | { 8 | display: block; padding: 0.5em; 9 | background: #222; 10 | } 11 | 12 | pre .profile .header *, 13 | pre .ini .title 14 | { 15 | color: #fff; 16 | } 17 | 18 | pre .comment, 19 | pre .javadoc, 20 | pre .preprocessor, 21 | pre .preprocessor .title, 22 | pre .shebang, 23 | pre .profile .summary, 24 | pre .diff, 25 | pre .pi, 26 | pre .doctype, 27 | pre .tag, 28 | pre .template_comment, 29 | pre .css .rules, 30 | pre .tex .special 31 | { 32 | color: #444; 33 | } 34 | 35 | pre .string, 36 | pre .symbol, 37 | pre .diff .change, 38 | pre .regexp, 39 | pre .xml .attribute, 40 | pre .smalltalk .char, 41 | pre .xml .value, 42 | pre .ini .value 43 | { 44 | color: #ffcc33; 45 | } 46 | 47 | pre .number, 48 | pre .addition 49 | { 50 | color: #00cc66; 51 | } 52 | 53 | pre .built_in, 54 | pre .literal, 55 | pre .vhdl .typename, 56 | pre .go .constant, 57 | pre .go .typename, 58 | pre .ini .keyword, 59 | pre .lua .title, 60 | pre .perl .variable, 61 | pre .php .variable, 62 | pre .mel .variable, 63 | pre .django .variable, 64 | pre .css .funtion, 65 | pre .smalltalk .method, 66 | pre .hexcolor, 67 | pre .important, 68 | pre .flow, 69 | pre .inheritance, 70 | pre .parser3 .variable 71 | { 72 | color: #32AAEE; 73 | } 74 | 75 | pre .keyword, 76 | pre .tag .title, 77 | pre .css .tag, 78 | pre .css .class, 79 | pre .css .id, 80 | pre .css .pseudo, 81 | pre .css .attr_selector, 82 | pre .lisp .title, 83 | pre .winutils, 84 | pre .tex .command, 85 | pre .request, 86 | pre .status 87 | { 88 | color: #6644aa; 89 | } 90 | 91 | pre .title, 92 | pre .ruby .constant, 93 | pre .vala .constant, 94 | pre .parent, 95 | pre .deletion, 96 | pre .template_tag, 97 | pre .css .keyword, 98 | pre .objectivec .class .id, 99 | pre .smalltalk .class, 100 | pre .lisp .keyword, 101 | pre .apache .tag, 102 | pre .nginx .variable, 103 | pre .envvar, 104 | pre .bash .variable, 105 | pre .go .built_in, 106 | pre .vbscript .built_in, 107 | pre .lua .built_in, 108 | pre .rsl .built_in, 109 | pre .tail, 110 | pre .avrasm .label, 111 | pre .tex .formula, 112 | pre .tex .formula * 113 | { 114 | color: #bb1166; 115 | } 116 | 117 | pre .yardoctag, 118 | pre .phpdoc, 119 | pre .profile .header, 120 | pre .ini .title, 121 | pre .apache .tag, 122 | pre .parser3 .title 123 | { 124 | font-weight: bold; 125 | } 126 | 127 | pre .coffeescript .javascript, 128 | pre .xml .javascript, 129 | pre .xml .css, 130 | pre .xml .cdata 131 | { 132 | opacity: 0.6; 133 | } 134 | 135 | pre code, 136 | pre .javascript, 137 | pre .css, 138 | pre .xml, 139 | pre .subst, 140 | pre .diff .chunk, 141 | pre .css .value, 142 | pre .css .attribute, 143 | pre .lisp .string, 144 | pre .lisp .number, 145 | pre .tail .params, 146 | pre .container, 147 | pre .haskell *, 148 | pre .erlang *, 149 | pre .erlang_repl * 150 | { 151 | color: #aaa; 152 | } 153 | -------------------------------------------------------------------------------- /intro_presentation/libraries/highlighters/highlight.js/css/ascetic.css: -------------------------------------------------------------------------------- 1 | /* 2 | 3 | Original style from softwaremaniacs.org (c) Ivan Sagalaev 4 | 5 | */ 6 | 7 | pre code { 8 | display: block; padding: 0.5em; 9 | background: white; color: black; 10 | } 11 | 12 | pre .string, 13 | pre .tag .value, 14 | pre .filter .argument, 15 | pre .addition, 16 | pre .change, 17 | pre .apache .tag, 18 | pre .apache .cbracket, 19 | pre .nginx .built_in, 20 | pre .tex .formula { 21 | color: #888; 22 | } 23 | 24 | pre .comment, 25 | pre .template_comment, 26 | pre .shebang, 27 | pre .doctype, 28 | pre .pi, 29 | pre .javadoc, 30 | pre .deletion, 31 | pre .apache .sqbracket { 32 | color: #CCC; 33 | } 34 | 35 | pre .keyword, 36 | pre .tag .title, 37 | pre .css .tag, 38 | pre .ini .title, 39 | pre .winutils, 40 | pre .flow, 41 | pre .lisp .title, 42 | pre .apache .tag, 43 | pre .tex .command, 44 | pre .http .title, 45 | pre .request, 46 | pre .status { 47 | font-weight: bold; 48 | } 49 | -------------------------------------------------------------------------------- /intro_presentation/libraries/highlighters/highlight.js/css/brown_paper.css: -------------------------------------------------------------------------------- 1 | /* 2 | 3 | Brown Paper style from goldblog.com.ua (c) Zaripov Yura 4 | 5 | */ 6 | 7 | pre code { 8 | display: block; padding: 0.5em; 9 | background:#b7a68e url(./brown_papersq.png); 10 | } 11 | 12 | pre .keyword, 13 | pre .literal, 14 | pre .change, 15 | pre .winutils, 16 | pre .flow, 17 | pre .lisp .title, 18 | pre .tex .special, 19 | pre .request, 20 | pre .status { 21 | color:#005599; 22 | font-weight:bold; 23 | } 24 | 25 | pre code, 26 | pre .ruby .subst, 27 | pre .tag .keyword { 28 | color: #363C69; 29 | } 30 | 31 | pre .string, 32 | pre .title, 33 | pre .haskell .type, 34 | pre .tag .value, 35 | pre .css .rules .value, 36 | pre .preprocessor, 37 | pre .ruby .symbol, 38 | pre .ruby .symbol .string, 39 | pre .ruby .symbol .keyword, 40 | pre .ruby .symbol .keymethods, 41 | pre .ruby .instancevar, 42 | pre .ruby .class .parent, 43 | pre .built_in, 44 | pre .sql .aggregate, 45 | pre .django .template_tag, 46 | pre .django .variable, 47 | pre .smalltalk .class, 48 | pre .javadoc, 49 | pre .ruby .string, 50 | pre .django .filter .argument, 51 | pre .smalltalk .localvars, 52 | pre .smalltalk .array, 53 | pre .attr_selector, 54 | pre .pseudo, 55 | pre .addition, 56 | pre .stream, 57 | pre .envvar, 58 | pre .apache .tag, 59 | pre .apache .cbracket, 60 | pre .tex .number { 61 | color: #2C009F; 62 | } 63 | 64 | pre .comment, 65 | pre .java .annotation, 66 | pre .python .decorator, 67 | pre .template_comment, 68 | pre .pi, 69 | pre .doctype, 70 | pre .deletion, 71 | pre .shebang, 72 | pre .apache .sqbracket, 73 | pre .nginx .built_in, 74 | pre .tex .formula { 75 | color: #802022; 76 | } 77 | 78 | pre .keyword, 79 | pre .literal, 80 | pre .css .id, 81 | pre .phpdoc, 82 | pre .title, 83 | pre .haskell .type, 84 | pre .vbscript .built_in, 85 | pre .sql .aggregate, 86 | pre .rsl .built_in, 87 | pre .smalltalk .class, 88 | pre .diff .header, 89 | pre .chunk, 90 | pre .winutils, 91 | pre .bash .variable, 92 | pre .apache .tag, 93 | pre .tex .command { 94 | font-weight: bold; 95 | } 96 | 97 | pre .coffeescript .javascript, 98 | pre .xml .css, 99 | pre .xml .javascript, 100 | pre .xml .vbscript, 101 | pre .tex .formula { 102 | opacity: 0.8; 103 | } 104 | -------------------------------------------------------------------------------- /intro_presentation/libraries/highlighters/highlight.js/css/brown_papersq.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/grunwaldlab/Reproducible-science-in-R/0bb8e62689e0fb7c813051551342c046144f389b/intro_presentation/libraries/highlighters/highlight.js/css/brown_papersq.png -------------------------------------------------------------------------------- /intro_presentation/libraries/highlighters/highlight.js/css/dark.css: -------------------------------------------------------------------------------- 1 | /* 2 | 3 | Dark style from softwaremaniacs.org (c) Ivan Sagalaev 4 | 5 | */ 6 | 7 | pre code { 8 | display: block; padding: 0.5em; 9 | background: #444; 10 | } 11 | 12 | pre .keyword, 13 | pre .literal, 14 | pre .change, 15 | pre .winutils, 16 | pre .flow, 17 | pre .lisp .title, 18 | pre .tex .special { 19 | color: white; 20 | } 21 | 22 | pre code, 23 | pre .ruby .subst { 24 | color: #DDD; 25 | } 26 | 27 | pre .string, 28 | pre .title, 29 | pre .haskell .type, 30 | pre .ini .title, 31 | pre .tag .value, 32 | pre .css .rules .value, 33 | pre .preprocessor, 34 | pre .ruby .symbol, 35 | pre .ruby .symbol .string, 36 | pre .ruby .symbol .keyword, 37 | pre .ruby .symbol .keymethods, 38 | pre .ruby .instancevar, 39 | pre .ruby .class .parent, 40 | pre .built_in, 41 | pre .sql .aggregate, 42 | pre .django .template_tag, 43 | pre .django .variable, 44 | pre .smalltalk .class, 45 | pre .javadoc, 46 | pre .ruby .string, 47 | pre .django .filter .argument, 48 | pre .smalltalk .localvars, 49 | pre .smalltalk .array, 50 | pre .attr_selector, 51 | pre .pseudo, 52 | pre .addition, 53 | pre .stream, 54 | pre .envvar, 55 | pre .apache .tag, 56 | pre .apache .cbracket, 57 | pre .tex .command, 58 | pre .input_number { 59 | color: #D88; 60 | } 61 | 62 | pre .comment, 63 | pre .java .annotation, 64 | pre .python .decorator, 65 | pre .template_comment, 66 | pre .pi, 67 | pre .doctype, 68 | pre .deletion, 69 | pre .shebang, 70 | pre .apache .sqbracket, 71 | pre .tex .formula { 72 | color: #777; 73 | } 74 | 75 | pre .keyword, 76 | pre .literal, 77 | pre .title, 78 | pre .css .id, 79 | pre .phpdoc, 80 | pre .haskell .type, 81 | pre .vbscript .built_in, 82 | pre .sql .aggregate, 83 | pre .rsl .built_in, 84 | pre .smalltalk .class, 85 | pre .diff .header, 86 | pre .chunk, 87 | pre .winutils, 88 | pre .bash .variable, 89 | pre .apache .tag, 90 | pre .tex .special, 91 | pre .request, 92 | pre .status { 93 | font-weight: bold; 94 | } 95 | 96 | pre .coffeescript .javascript, 97 | pre .xml .css, 98 | pre .xml .javascript, 99 | pre .xml .vbscript, 100 | pre .tex .formula { 101 | opacity: 0.5; 102 | } 103 | -------------------------------------------------------------------------------- /intro_presentation/libraries/highlighters/highlight.js/css/default.css: -------------------------------------------------------------------------------- 1 | /* 2 | 3 | Original style from softwaremaniacs.org (c) Ivan Sagalaev 4 | 5 | */ 6 | 7 | pre code { 8 | display: block; padding: 0.5em; 9 | background: #F0F0F0; 10 | } 11 | 12 | pre code, 13 | pre .ruby .subst, 14 | pre .tag .title, 15 | pre .lisp .title { 16 | color: black; 17 | } 18 | 19 | pre .string, 20 | pre .title, 21 | pre .constant, 22 | pre .parent, 23 | pre .tag .value, 24 | pre .rules .value, 25 | pre .rules .value .number, 26 | pre .preprocessor, 27 | pre .ruby .symbol, 28 | pre .ruby .symbol .string, 29 | pre .ruby .symbol .keyword, 30 | pre .ruby .symbol .keymethods, 31 | pre .instancevar, 32 | pre .aggregate, 33 | pre .template_tag, 34 | pre .django .variable, 35 | pre .smalltalk .class, 36 | pre .addition, 37 | pre .flow, 38 | pre .stream, 39 | pre .bash .variable, 40 | pre .apache .tag, 41 | pre .apache .cbracket, 42 | pre .tex .command, 43 | pre .tex .special, 44 | pre .erlang_repl .function_or_atom, 45 | pre .markdown .header { 46 | color: #800; 47 | } 48 | 49 | pre .comment, 50 | pre .annotation, 51 | pre .template_comment, 52 | pre .diff .header, 53 | pre .chunk, 54 | pre .markdown .blockquote { 55 | color: #888; 56 | } 57 | 58 | pre .number, 59 | pre .date, 60 | pre .regexp, 61 | pre .literal, 62 | pre .smalltalk .symbol, 63 | pre .smalltalk .char, 64 | pre .go .constant, 65 | pre .change, 66 | pre .markdown .bullet, 67 | pre .markdown .link_url { 68 | color: #080; 69 | } 70 | 71 | pre .label, 72 | pre .javadoc, 73 | pre .ruby .string, 74 | pre .decorator, 75 | pre .filter .argument, 76 | pre .localvars, 77 | pre .array, 78 | pre .attr_selector, 79 | pre .important, 80 | pre .pseudo, 81 | pre .pi, 82 | pre .doctype, 83 | pre .deletion, 84 | pre .envvar, 85 | pre .shebang, 86 | pre .apache .sqbracket, 87 | pre .nginx .built_in, 88 | pre .tex .formula, 89 | pre .erlang_repl .reserved, 90 | pre .input_number, 91 | pre .markdown .link_label, 92 | pre .vhdl .attribute { 93 | color: #88F 94 | } 95 | 96 | pre .keyword, 97 | pre .id, 98 | pre .phpdoc, 99 | pre .title, 100 | pre .built_in, 101 | pre .aggregate, 102 | pre .css .tag, 103 | pre .javadoctag, 104 | pre .phpdoc, 105 | pre .yardoctag, 106 | pre .smalltalk .class, 107 | pre .winutils, 108 | pre .bash .variable, 109 | pre .apache .tag, 110 | pre .go .typename, 111 | pre .tex .command, 112 | pre .markdown .strong, 113 | pre .request, 114 | pre .status { 115 | font-weight: bold; 116 | } 117 | 118 | pre .markdown .emphasis { 119 | font-style: italic; 120 | } 121 | 122 | pre .nginx .built_in { 123 | font-weight: normal; 124 | } 125 | 126 | pre .coffeescript .javascript, 127 | pre .xml .css, 128 | pre .xml .javascript, 129 | pre .xml .vbscript, 130 | pre .tex .formula { 131 | opacity: 0.5; 132 | } 133 | -------------------------------------------------------------------------------- /intro_presentation/libraries/highlighters/highlight.js/css/far.css: -------------------------------------------------------------------------------- 1 | /* 2 | 3 | FAR Style (c) MajestiC 4 | 5 | */ 6 | 7 | pre code { 8 | display: block; padding: 0.5em; 9 | background: #000080; 10 | } 11 | 12 | pre code, 13 | .ruby .subst { 14 | color: #0FF; 15 | } 16 | 17 | pre .string, 18 | pre .ruby .string, 19 | pre .haskell .type, 20 | pre .tag .value, 21 | pre .css .rules .value, 22 | pre .css .rules .value .number, 23 | pre .preprocessor, 24 | pre .ruby .symbol, 25 | pre .ruby .symbol .string, 26 | pre .ruby .symbol .keyword, 27 | pre .ruby .symbol .keymethods, 28 | pre .built_in, 29 | pre .sql .aggregate, 30 | pre .django .template_tag, 31 | pre .django .variable, 32 | pre .smalltalk .class, 33 | pre .addition, 34 | pre .apache .tag, 35 | pre .apache .cbracket, 36 | pre .tex .command { 37 | color: #FF0; 38 | } 39 | 40 | pre .keyword, 41 | pre .css .id, 42 | pre .title, 43 | pre .haskell .type, 44 | pre .vbscript .built_in, 45 | pre .sql .aggregate, 46 | pre .rsl .built_in, 47 | pre .smalltalk .class, 48 | pre .xml .tag .title, 49 | pre .winutils, 50 | pre .flow, 51 | pre .change, 52 | pre .envvar, 53 | pre .bash .variable, 54 | pre .tex .special { 55 | color: #FFF; 56 | } 57 | 58 | pre .comment, 59 | pre .phpdoc, 60 | pre .javadoc, 61 | pre .java .annotation, 62 | pre .template_comment, 63 | pre .deletion, 64 | pre .apache .sqbracket, 65 | pre .tex .formula { 66 | color: #888; 67 | } 68 | 69 | pre .number, 70 | pre .date, 71 | pre .regexp, 72 | pre .literal, 73 | pre .smalltalk .symbol, 74 | pre .smalltalk .char { 75 | color: #0F0; 76 | } 77 | 78 | pre .python .decorator, 79 | pre .django .filter .argument, 80 | pre .smalltalk .localvars, 81 | pre .smalltalk .array, 82 | pre .attr_selector, 83 | pre .pseudo, 84 | pre .xml .pi, 85 | pre .diff .header, 86 | pre .chunk, 87 | pre .shebang, 88 | pre .nginx .built_in, 89 | pre .input_number { 90 | color: #008080; 91 | } 92 | 93 | pre .keyword, 94 | pre .css .id, 95 | pre .title, 96 | pre .haskell .type, 97 | pre .vbscript .built_in, 98 | pre .sql .aggregate, 99 | pre .rsl .built_in, 100 | pre .smalltalk .class, 101 | pre .winutils, 102 | pre .flow, 103 | pre .apache .tag, 104 | pre .nginx .built_in, 105 | pre .tex .command, 106 | pre .tex .special, 107 | pre .request, 108 | pre .status { 109 | font-weight: bold; 110 | } 111 | -------------------------------------------------------------------------------- /intro_presentation/libraries/highlighters/highlight.js/css/github.css: -------------------------------------------------------------------------------- 1 | /* 2 | 3 | github.com style (c) Vasily Polovnyov 4 | 5 | */ 6 | 7 | pre code { 8 | display: block; padding: 0.5em; 9 | color: #000; 10 | background: #f8f8ff 11 | } 12 | 13 | pre .comment, 14 | pre .template_comment, 15 | pre .diff .header, 16 | pre .javadoc { 17 | color: #998; 18 | font-style: italic 19 | } 20 | 21 | pre .keyword, 22 | pre .css .rule .keyword, 23 | pre .winutils, 24 | pre .javascript .title, 25 | pre .lisp .title, 26 | pre .subst, 27 | pre .request, 28 | pre .status { 29 | color: #000; 30 | font-weight: bold 31 | } 32 | 33 | pre .number, 34 | pre .hexcolor { 35 | color: #40a070 36 | } 37 | 38 | pre .string, 39 | pre .tag .value, 40 | pre .phpdoc, 41 | pre .tex .formula { 42 | color: #d14 43 | } 44 | 45 | pre .title, 46 | pre .id { 47 | color: #900; 48 | font-weight: bold 49 | } 50 | 51 | pre .javascript .title, 52 | pre .lisp .title, 53 | pre .subst { 54 | font-weight: normal 55 | } 56 | 57 | pre .class .title, 58 | pre .haskell .type, 59 | pre .vhdl .literal, 60 | pre .tex .command { 61 | color: #458; 62 | font-weight: bold 63 | } 64 | 65 | pre .tag, 66 | pre .tag .title, 67 | pre .rules .property, 68 | pre .django .tag .keyword { 69 | color: #000080; 70 | font-weight: normal 71 | } 72 | 73 | pre .attribute, 74 | pre .variable, 75 | pre .instancevar, 76 | pre .lisp .body { 77 | color: #008080 78 | } 79 | 80 | pre .regexp { 81 | color: #009926 82 | } 83 | 84 | pre .class { 85 | color: #458; 86 | font-weight: bold 87 | } 88 | 89 | pre .symbol, 90 | pre .ruby .symbol .string, 91 | pre .ruby .symbol .keyword, 92 | pre .ruby .symbol .keymethods, 93 | pre .lisp .keyword, 94 | pre .tex .special, 95 | pre .input_number { 96 | color: #990073 97 | } 98 | 99 | pre .builtin, 100 | pre .built_in, 101 | pre .lisp .title { 102 | color: #0086b3 103 | } 104 | 105 | pre .preprocessor, 106 | pre .pi, 107 | pre .doctype, 108 | pre .shebang, 109 | pre .cdata { 110 | color: #999; 111 | font-weight: bold 112 | } 113 | 114 | pre .deletion { 115 | background: #fdd 116 | } 117 | 118 | pre .addition { 119 | background: #dfd 120 | } 121 | 122 | pre .diff .change { 123 | background: #0086b3 124 | } 125 | 126 | pre .chunk { 127 | color: #aaa 128 | } 129 | 130 | pre .tex .formula { 131 | opacity: 0.5; 132 | } 133 | -------------------------------------------------------------------------------- /intro_presentation/libraries/highlighters/highlight.js/css/googlecode.css: -------------------------------------------------------------------------------- 1 | /* 2 | 3 | Google Code style (c) Aahan Krish 4 | 5 | */ 6 | 7 | pre code { 8 | display: block; padding: 0.5em; 9 | background: white; color: black; 10 | } 11 | 12 | pre .comment, 13 | pre .template_comment, 14 | pre .javadoc, 15 | pre .comment * { 16 | color: #800; 17 | } 18 | 19 | pre .keyword, 20 | pre .method, 21 | pre .list .title, 22 | pre .tag .title, 23 | pre .setting .value, 24 | pre .winutils, 25 | pre .tex .command, 26 | pre .http .title, 27 | pre .request, 28 | pre .status { 29 | color: #008; 30 | } 31 | 32 | pre .envvar, 33 | pre .tex .special { 34 | color: #660; 35 | } 36 | 37 | pre .string, 38 | pre .tag .value, 39 | pre .cdata, 40 | pre .filter .argument, 41 | pre .attr_selector, 42 | pre .apache .cbracket, 43 | pre .date, 44 | pre .regexp { 45 | color: #080; 46 | } 47 | 48 | pre .sub .identifier, 49 | pre .pi, 50 | pre .tag, 51 | pre .tag .keyword, 52 | pre .decorator, 53 | pre .ini .title, 54 | pre .shebang, 55 | pre .input_number, 56 | pre .hexcolor, 57 | pre .rules .value, 58 | pre .css .value .number, 59 | pre .literal, 60 | pre .symbol, 61 | pre .ruby .symbol .string, 62 | pre .ruby .symbol .keyword, 63 | pre .ruby .symbol .keymethods, 64 | pre .number, 65 | pre .css .function { 66 | color: #066; 67 | } 68 | 69 | pre .class .title, 70 | pre .haskell .type, 71 | pre .smalltalk .class, 72 | pre .javadoctag, 73 | pre .yardoctag, 74 | pre .phpdoc, 75 | pre .typename, 76 | pre .tag .attribute, 77 | pre .doctype, 78 | pre .class .id, 79 | pre .built_in, 80 | pre .setting, 81 | pre .params, 82 | pre .variable { 83 | color: #606; 84 | } 85 | 86 | pre .css .tag, 87 | pre .rules .property, 88 | pre .pseudo, 89 | pre .subst { 90 | color: #000; 91 | } 92 | 93 | pre .css .class, pre .css .id { 94 | color: #9B703F; 95 | } 96 | 97 | pre .value .important { 98 | color: #ff7700; 99 | font-weight: bold; 100 | } 101 | 102 | pre .rules .keyword { 103 | color: #C5AF75; 104 | } 105 | 106 | pre .annotation, 107 | pre .apache .sqbracket, 108 | pre .nginx .built_in { 109 | color: #9B859D; 110 | } 111 | 112 | pre .preprocessor, 113 | pre .preprocessor * { 114 | color: #444; 115 | } 116 | 117 | pre .tex .formula { 118 | background-color: #EEE; 119 | font-style: italic; 120 | } 121 | 122 | pre .diff .header, 123 | pre .chunk { 124 | color: #808080; 125 | font-weight: bold; 126 | } 127 | 128 | pre .diff .change { 129 | background-color: #BCCFF9; 130 | } 131 | 132 | pre .addition { 133 | background-color: #BAEEBA; 134 | } 135 | 136 | pre .deletion { 137 | background-color: #FFC8BD; 138 | } 139 | 140 | pre .comment .yardoctag { 141 | font-weight: bold; 142 | } 143 | -------------------------------------------------------------------------------- /intro_presentation/libraries/highlighters/highlight.js/css/hemisu-light.css: -------------------------------------------------------------------------------- 1 | /* Hemisu Light */ 2 | /* http://jmblog.github.com/color-themes-for-google-code-highlightjs */ 3 | /* Original theme - http://noahfrederick.com/vim-color-scheme-hemisu/ */ 4 | /* http://jmblog.github.com/color-themes-for-google-code-highlightjs */ 5 | .hemisu-comment, pre .comment, pre .xml .doctype, pre .html .doctype { 6 | color: #999999; 7 | } 8 | 9 | .hemisu-accent1, pre .number, pre .ruby .keyword { 10 | color: #538192; 11 | } 12 | 13 | .hemisu-accent2, pre .string, pre .regexp, pre .xml .value, pre .html .value { 14 | color: #739200; 15 | } 16 | 17 | .hemisu-accent3, pre .keyword, pre .title, pre .constant, pre .xml .tag, pre .html .tag, pre .css .rules .attribute { 18 | color: #ff0055; 19 | } 20 | 21 | .hemisu-accent4 { 22 | color: #503d15; 23 | } 24 | 25 | pre code { 26 | display: block; 27 | background: white; 28 | color: #111111; 29 | font-family: Menlo, Monaco, Consolas, monospace; 30 | line-height: 1.5; 31 | border: 1px solid #ccc; 32 | padding: 10px; 33 | } 34 | pre .xml .tag .title { 35 | color: #111111; 36 | } 37 | pre .html .tag .title { 38 | color: #111111; 39 | } -------------------------------------------------------------------------------- /intro_presentation/libraries/highlighters/highlight.js/css/idea.css: -------------------------------------------------------------------------------- 1 | /* 2 | 3 | Intellij Idea-like styling (c) Vasily Polovnyov 4 | 5 | */ 6 | 7 | pre code { 8 | display: block; padding: 0.5em; 9 | color: #000; 10 | background: #fff; 11 | } 12 | 13 | pre .subst, 14 | pre .title { 15 | font-weight: normal; 16 | color: #000; 17 | } 18 | 19 | pre .comment, 20 | pre .template_comment, 21 | pre .javadoc, 22 | pre .diff .header { 23 | color: #808080; 24 | font-style: italic; 25 | } 26 | 27 | pre .annotation, 28 | pre .decorator, 29 | pre .preprocessor, 30 | pre .doctype, 31 | pre .pi, 32 | pre .chunk, 33 | pre .shebang, 34 | pre .apache .cbracket, 35 | pre .input_number, 36 | pre .http .title { 37 | color: #808000; 38 | } 39 | 40 | pre .tag, 41 | pre .pi { 42 | background: #efefef; 43 | } 44 | 45 | pre .tag .title, 46 | pre .id, 47 | pre .attr_selector, 48 | pre .pseudo, 49 | pre .literal, 50 | pre .keyword, 51 | pre .hexcolor, 52 | pre .css .function, 53 | pre .ini .title, 54 | pre .css .class, 55 | pre .list .title, 56 | pre .tex .command, 57 | pre .request, 58 | pre .status { 59 | font-weight: bold; 60 | color: #000080; 61 | } 62 | 63 | pre .attribute, 64 | pre .rules .keyword, 65 | pre .number, 66 | pre .date, 67 | pre .regexp, 68 | pre .tex .special { 69 | font-weight: bold; 70 | color: #0000ff; 71 | } 72 | 73 | pre .number, 74 | pre .regexp { 75 | font-weight: normal; 76 | } 77 | 78 | pre .string, 79 | pre .value, 80 | pre .filter .argument, 81 | pre .css .function .params, 82 | pre .apache .tag { 83 | color: #008000; 84 | font-weight: bold; 85 | } 86 | 87 | pre .symbol, 88 | pre .ruby .symbol .string, 89 | pre .ruby .symbol .keyword, 90 | pre .ruby .symbol .keymethods, 91 | pre .char, 92 | pre .tex .formula { 93 | color: #000; 94 | background: #d0eded; 95 | font-style: italic; 96 | } 97 | 98 | pre .phpdoc, 99 | pre .yardoctag, 100 | pre .javadoctag { 101 | text-decoration: underline; 102 | } 103 | 104 | pre .variable, 105 | pre .envvar, 106 | pre .apache .sqbracket, 107 | pre .nginx .built_in { 108 | color: #660e7a; 109 | } 110 | 111 | pre .addition { 112 | background: #baeeba; 113 | } 114 | 115 | pre .deletion { 116 | background: #ffc8bd; 117 | } 118 | 119 | pre .diff .change { 120 | background: #bccff9; 121 | } 122 | -------------------------------------------------------------------------------- /intro_presentation/libraries/highlighters/highlight.js/css/ir_black.css: -------------------------------------------------------------------------------- 1 | /* 2 | IR_Black style (c) Vasily Mikhailitchenko 3 | */ 4 | 5 | pre code { 6 | display: block; padding: 0.5em; 7 | background: #000; color: #f8f8f8; 8 | } 9 | 10 | pre .shebang, 11 | pre .comment, 12 | pre .template_comment, 13 | pre .javadoc { 14 | color: #7c7c7c; 15 | } 16 | 17 | pre .keyword, 18 | pre .tag, 19 | pre .tex .command, 20 | pre .request, 21 | pre .status { 22 | color: #96CBFE; 23 | } 24 | 25 | pre .sub .keyword, 26 | pre .method, 27 | pre .list .title { 28 | color: #FFFFB6; 29 | } 30 | 31 | pre .string, 32 | pre .tag .value, 33 | pre .cdata, 34 | pre .filter .argument, 35 | pre .attr_selector, 36 | pre .apache .cbracket, 37 | pre .date { 38 | color: #A8FF60; 39 | } 40 | 41 | pre .subst { 42 | color: #DAEFA3; 43 | } 44 | 45 | pre .regexp { 46 | color: #E9C062; 47 | } 48 | 49 | pre .title, 50 | pre .sub .identifier, 51 | pre .pi, 52 | pre .decorator, 53 | pre .tex .special, 54 | pre .haskell .type, 55 | pre .constant, 56 | pre .smalltalk .class, 57 | pre .javadoctag, 58 | pre .yardoctag, 59 | pre .phpdoc, 60 | pre .nginx .built_in { 61 | color: #FFFFB6; 62 | } 63 | 64 | pre .symbol, 65 | pre .ruby .symbol .string, 66 | pre .ruby .symbol .keyword, 67 | pre .ruby .symbol .keymethods, 68 | pre .number, 69 | pre .variable, 70 | pre .vbscript, 71 | pre .literal { 72 | color: #C6C5FE; 73 | } 74 | 75 | pre .css .tag { 76 | color: #96CBFE; 77 | } 78 | 79 | pre .css .rules .property, 80 | pre .css .id { 81 | color: #FFFFB6; 82 | } 83 | 84 | pre .css .class { 85 | color: #FFF; 86 | } 87 | 88 | pre .hexcolor { 89 | color: #C6C5FE; 90 | } 91 | 92 | pre .number { 93 | color:#FF73FD; 94 | } 95 | 96 | pre .tex .formula { 97 | opacity: 0.7; 98 | } 99 | -------------------------------------------------------------------------------- /intro_presentation/libraries/highlighters/highlight.js/css/magula.css: -------------------------------------------------------------------------------- 1 | /* 2 | Description: Magula style for highligh.js 3 | Author: Ruslan Keba 4 | Website: http://rukeba.com/ 5 | Version: 1.0 6 | Date: 2009-01-03 7 | Music: Aphex Twin / Xtal 8 | */ 9 | 10 | pre code { 11 | display: block; padding: 0.5em; 12 | background-color: #f4f4f4; 13 | } 14 | 15 | pre code, 16 | pre .ruby .subst, 17 | pre .lisp .title { 18 | color: black; 19 | } 20 | 21 | pre .string, 22 | pre .title, 23 | pre .parent, 24 | pre .tag .value, 25 | pre .rules .value, 26 | pre .rules .value .number, 27 | pre .preprocessor, 28 | pre .ruby .symbol, 29 | pre .ruby .symbol .string, 30 | pre .ruby .symbol .keyword, 31 | pre .ruby .symbol .keymethods, 32 | pre .instancevar, 33 | pre .aggregate, 34 | pre .template_tag, 35 | pre .django .variable, 36 | pre .smalltalk .class, 37 | pre .addition, 38 | pre .flow, 39 | pre .stream, 40 | pre .bash .variable, 41 | pre .apache .cbracket { 42 | color: #050; 43 | } 44 | 45 | pre .comment, 46 | pre .annotation, 47 | pre .template_comment, 48 | pre .diff .header, 49 | pre .chunk { 50 | color: #777; 51 | } 52 | 53 | pre .number, 54 | pre .date, 55 | pre .regexp, 56 | pre .literal, 57 | pre .smalltalk .symbol, 58 | pre .smalltalk .char, 59 | pre .change, 60 | pre .tex .special { 61 | color: #800; 62 | } 63 | 64 | pre .label, 65 | pre .javadoc, 66 | pre .ruby .string, 67 | pre .decorator, 68 | pre .filter .argument, 69 | pre .localvars, 70 | pre .array, 71 | pre .attr_selector, 72 | pre .pseudo, 73 | pre .pi, 74 | pre .doctype, 75 | pre .deletion, 76 | pre .envvar, 77 | pre .shebang, 78 | pre .apache .sqbracket, 79 | pre .nginx .built_in, 80 | pre .tex .formula, 81 | pre .input_number { 82 | color: #00e; 83 | } 84 | 85 | pre .keyword, 86 | pre .id, 87 | pre .phpdoc, 88 | pre .title, 89 | pre .built_in, 90 | pre .aggregate, 91 | pre .smalltalk .class, 92 | pre .winutils, 93 | pre .bash .variable, 94 | pre .apache .tag, 95 | pre .xml .tag, 96 | pre .tex .command, 97 | pre .request, 98 | pre .status { 99 | font-weight: bold; 100 | color: navy; 101 | } 102 | 103 | pre .nginx .built_in { 104 | font-weight: normal; 105 | } 106 | 107 | pre .coffeescript .javascript, 108 | pre .xml .css, 109 | pre .xml .javascript, 110 | pre .xml .vbscript, 111 | pre .tex .formula { 112 | opacity: 0.5; 113 | } 114 | 115 | /* --- */ 116 | pre .apache .tag { 117 | font-weight: bold; 118 | color: blue; 119 | } 120 | 121 | -------------------------------------------------------------------------------- /intro_presentation/libraries/highlighters/highlight.js/css/monokai.css: -------------------------------------------------------------------------------- 1 | /* 2 | Monokai style - ported by Luigi Maselli - http://grigio.org 3 | */ 4 | 5 | pre code { 6 | display: block; padding: 0.5em; 7 | background: #272822; 8 | } 9 | 10 | pre .params .identifier .keymethods { 11 | color: #FD971F; 12 | } 13 | 14 | pre .tag, 15 | pre .tag .title, 16 | pre .keyword, 17 | pre .literal, 18 | pre .change, 19 | pre .winutils, 20 | pre .flow, 21 | pre .lisp .title, 22 | pre .tex .special { 23 | color: #F92672; 24 | } 25 | 26 | pre code { 27 | color: #DDD; 28 | } 29 | 30 | pre code .constant { 31 | color: #66D9EF; 32 | } 33 | 34 | pre .class .title { 35 | color: white; 36 | } 37 | 38 | pre .attribute, 39 | pre .symbol, 40 | pre .value, 41 | pre .regexp { 42 | color: #BF79DB; 43 | } 44 | 45 | pre .tag .value, 46 | pre .string, 47 | pre .ruby .subst, 48 | pre .title, 49 | pre .haskell .type, 50 | pre .preprocessor, 51 | pre .ruby .instancevar, 52 | pre .ruby .class .parent, 53 | pre .built_in, 54 | pre .sql .aggregate, 55 | pre .django .template_tag, 56 | pre .django .variable, 57 | pre .smalltalk .class, 58 | pre .javadoc, 59 | pre .ruby .string, 60 | pre .django .filter .argument, 61 | pre .smalltalk .localvars, 62 | pre .smalltalk .array, 63 | pre .attr_selector, 64 | pre .pseudo, 65 | pre .addition, 66 | pre .stream, 67 | pre .envvar, 68 | pre .apache .tag, 69 | pre .apache .cbracket, 70 | pre .tex .command, 71 | pre .input_number { 72 | color: #A6E22E; 73 | } 74 | 75 | pre .comment, 76 | pre .java .annotation, 77 | pre .python .decorator, 78 | pre .template_comment, 79 | pre .pi, 80 | pre .doctype, 81 | pre .deletion, 82 | pre .shebang, 83 | pre .apache .sqbracket, 84 | pre .tex .formula { 85 | color: #75715E; 86 | } 87 | 88 | pre .keyword, 89 | pre .literal, 90 | pre .css .id, 91 | pre .phpdoc, 92 | pre .title, 93 | pre .haskell .type, 94 | pre .vbscript .built_in, 95 | pre .sql .aggregate, 96 | pre .rsl .built_in, 97 | pre .smalltalk .class, 98 | pre .diff .header, 99 | pre .chunk, 100 | pre .winutils, 101 | pre .bash .variable, 102 | pre .apache .tag, 103 | pre .tex .special, 104 | pre .request, 105 | pre .status { 106 | font-weight: bold; 107 | } 108 | 109 | pre .coffeescript .javascript, 110 | pre .xml .css, 111 | pre .xml .javascript, 112 | pre .xml .vbscript, 113 | pre .tex .formula { 114 | opacity: 0.5; 115 | } 116 | -------------------------------------------------------------------------------- /intro_presentation/libraries/highlighters/highlight.js/css/pojoaque.css: -------------------------------------------------------------------------------- 1 | /* 2 | 3 | Pojoaque Style by Jason Tate 4 | http://web-cms-designs.com/ftopict-10-pojoaque-style-for-highlight-js-code-highlighter.html 5 | Based on Solarized Style from http://ethanschoonover.com/solarized 6 | 7 | */ 8 | 9 | pre code { 10 | display: block; padding: 0.5em; 11 | color: #DCCF8F; 12 | background: url(./pojoaque.jpg) repeat scroll left top #181914; 13 | } 14 | 15 | pre .comment, 16 | pre .template_comment, 17 | pre .diff .header, 18 | pre .doctype, 19 | pre .lisp .string, 20 | pre .javadoc { 21 | color: #586e75; 22 | font-style: italic; 23 | } 24 | 25 | pre .keyword, 26 | pre .css .rule .keyword, 27 | pre .winutils, 28 | pre .javascript .title, 29 | pre .method, 30 | pre .addition, 31 | pre .css .tag, 32 | pre .lisp .title { 33 | color: #B64926; 34 | } 35 | 36 | pre .number, 37 | pre .command, 38 | pre .string, 39 | pre .tag .value, 40 | pre .phpdoc, 41 | pre .tex .formula, 42 | pre .regexp, 43 | pre .hexcolor { 44 | color: #468966; 45 | } 46 | 47 | pre .title, 48 | pre .localvars, 49 | pre .function .title, 50 | pre .chunk, 51 | pre .decorator, 52 | pre .builtin, 53 | pre .built_in, 54 | pre .lisp .title, 55 | pre .identifier, 56 | pre .title .keymethods, 57 | pre .id { 58 | color: #FFB03B; 59 | } 60 | 61 | pre .attribute, 62 | pre .variable, 63 | pre .instancevar, 64 | pre .lisp .body, 65 | pre .smalltalk .number, 66 | pre .constant, 67 | pre .class .title, 68 | pre .parent, 69 | pre .haskell .type { 70 | color: #b58900; 71 | } 72 | 73 | pre .css .attribute { 74 | color: #b89859; 75 | } 76 | 77 | pre .css .number,pre .css .hexcolor{ 78 | color: #DCCF8F; 79 | } 80 | 81 | pre .css .class { 82 | color: #d3a60c; 83 | } 84 | 85 | pre .preprocessor, 86 | pre .pi, 87 | pre .shebang, 88 | pre .symbol, 89 | pre .diff .change, 90 | pre .special, 91 | pre .keymethods, 92 | pre .attr_selector, 93 | pre .important, 94 | pre .subst, 95 | pre .cdata { 96 | color: #cb4b16; 97 | } 98 | 99 | pre .deletion { 100 | color: #dc322f; 101 | } 102 | 103 | pre .tex .formula { 104 | background: #073642; 105 | } 106 | -------------------------------------------------------------------------------- /intro_presentation/libraries/highlighters/highlight.js/css/pojoaque.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/grunwaldlab/Reproducible-science-in-R/0bb8e62689e0fb7c813051551342c046144f389b/intro_presentation/libraries/highlighters/highlight.js/css/pojoaque.jpg -------------------------------------------------------------------------------- /intro_presentation/libraries/highlighters/highlight.js/css/school_book.css: -------------------------------------------------------------------------------- 1 | /* 2 | 3 | School Book style from goldblog.com.ua (c) Zaripov Yura 4 | 5 | */ 6 | 7 | pre code { 8 | display: block; padding: 15px 0.5em 0.5em 30px; 9 | font-size: 11px !important; 10 | line-height:16px !important; 11 | } 12 | 13 | pre{ 14 | background:#f6f6ae url(./school_book.png); 15 | border-top: solid 2px #d2e8b9; 16 | border-bottom: solid 1px #d2e8b9; 17 | } 18 | 19 | pre .keyword, 20 | pre .literal, 21 | pre .change, 22 | pre .winutils, 23 | pre .flow, 24 | pre .lisp .title, 25 | pre .tex .special { 26 | color:#005599; 27 | font-weight:bold; 28 | } 29 | 30 | pre code, 31 | pre .ruby .subst, 32 | pre .tag .keyword { 33 | color: #3E5915; 34 | } 35 | 36 | pre .string, 37 | pre .title, 38 | pre .haskell .type, 39 | pre .tag .value, 40 | pre .css .rules .value, 41 | pre .preprocessor, 42 | pre .ruby .symbol, 43 | pre .ruby .symbol .string, 44 | pre .ruby .symbol .keyword, 45 | pre .ruby .symbol .keymethods, 46 | pre .ruby .instancevar, 47 | pre .ruby .class .parent, 48 | pre .built_in, 49 | pre .sql .aggregate, 50 | pre .django .template_tag, 51 | pre .django .variable, 52 | pre .smalltalk .class, 53 | pre .javadoc, 54 | pre .ruby .string, 55 | pre .django .filter .argument, 56 | pre .smalltalk .localvars, 57 | pre .smalltalk .array, 58 | pre .attr_selector, 59 | pre .pseudo, 60 | pre .addition, 61 | pre .stream, 62 | pre .envvar, 63 | pre .apache .tag, 64 | pre .apache .cbracket, 65 | pre .nginx .built_in, 66 | pre .tex .command { 67 | color: #2C009F; 68 | } 69 | 70 | pre .comment, 71 | pre .java .annotation, 72 | pre .python .decorator, 73 | pre .template_comment, 74 | pre .pi, 75 | pre .doctype, 76 | pre .deletion, 77 | pre .shebang, 78 | pre .apache .sqbracket { 79 | color: #E60415; 80 | } 81 | 82 | pre .keyword, 83 | pre .literal, 84 | pre .css .id, 85 | pre .phpdoc, 86 | pre .title, 87 | pre .haskell .type, 88 | pre .vbscript .built_in, 89 | pre .sql .aggregate, 90 | pre .rsl .built_in, 91 | pre .smalltalk .class, 92 | pre .xml .tag .title, 93 | pre .diff .header, 94 | pre .chunk, 95 | pre .winutils, 96 | pre .bash .variable, 97 | pre .apache .tag, 98 | pre .tex .command, 99 | pre .request, 100 | pre .status { 101 | font-weight: bold; 102 | } 103 | 104 | pre .coffeescript .javascript, 105 | pre .xml .css, 106 | pre .xml .javascript, 107 | pre .xml .vbscript, 108 | pre .tex .formula { 109 | opacity: 0.5; 110 | } 111 | -------------------------------------------------------------------------------- /intro_presentation/libraries/highlighters/highlight.js/css/school_book.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/grunwaldlab/Reproducible-science-in-R/0bb8e62689e0fb7c813051551342c046144f389b/intro_presentation/libraries/highlighters/highlight.js/css/school_book.png -------------------------------------------------------------------------------- /intro_presentation/libraries/highlighters/highlight.js/css/solarized_dark.css: -------------------------------------------------------------------------------- 1 | /* 2 | 3 | Orginal Style from ethanschoonover.com/solarized (c) Jeremy Hull 4 | 5 | */ 6 | 7 | pre code { 8 | display: block; padding: 0.5em; 9 | background: #002b36; color: #839496; 10 | } 11 | 12 | pre .comment, 13 | pre .template_comment, 14 | pre .diff .header, 15 | pre .doctype, 16 | pre .pi, 17 | pre .lisp .string, 18 | pre .javadoc { 19 | color: #586e75; 20 | font-style: italic; 21 | } 22 | 23 | pre .keyword, 24 | pre .winutils, 25 | pre .method, 26 | pre .addition, 27 | pre .css .tag, 28 | pre .request, 29 | pre .status { 30 | color: #859900; 31 | } 32 | 33 | pre .number, 34 | pre .command, 35 | pre .string, 36 | pre .tag .value, 37 | pre .phpdoc, 38 | pre .tex .formula, 39 | pre .regexp, 40 | pre .hexcolor { 41 | color: #2aa198; 42 | } 43 | 44 | pre .title, 45 | pre .localvars, 46 | pre .chunk, 47 | pre .decorator, 48 | pre .builtin, 49 | pre .built_in, 50 | pre .identifier, 51 | pre .title .keymethods, 52 | pre .vhdl .literal, 53 | pre .id { 54 | color: #268bd2; 55 | } 56 | 57 | pre .attribute, 58 | pre .variable, 59 | pre .instancevar, 60 | pre .lisp .body, 61 | pre .smalltalk .number, 62 | pre .constant, 63 | pre .class .title, 64 | pre .parent, 65 | pre .haskell .type { 66 | color: #b58900; 67 | } 68 | 69 | pre .preprocessor, 70 | pre .preprocessor .keyword, 71 | pre .shebang, 72 | pre .symbol, 73 | pre .diff .change, 74 | pre .special, 75 | pre .keymethods, 76 | pre .attr_selector, 77 | pre .important, 78 | pre .subst, 79 | pre .cdata { 80 | color: #cb4b16; 81 | } 82 | 83 | pre .deletion { 84 | color: #dc322f; 85 | } 86 | 87 | pre .tex .formula { 88 | background: #073642; 89 | } 90 | -------------------------------------------------------------------------------- /intro_presentation/libraries/highlighters/highlight.js/css/solarized_light.css: -------------------------------------------------------------------------------- 1 | /* 2 | 3 | Orginal Style from ethanschoonover.com/solarized (c) Jeremy Hull 4 | 5 | */ 6 | 7 | pre code { 8 | display: block; padding: 0.5em; 9 | background: #fdf6e3; color: #657b83; 10 | } 11 | 12 | pre .comment, 13 | pre .template_comment, 14 | pre .diff .header, 15 | pre .doctype, 16 | pre .pi, 17 | pre .lisp .string, 18 | pre .javadoc { 19 | color: #93a1a1; 20 | font-style: italic; 21 | } 22 | 23 | pre .keyword, 24 | pre .winutils, 25 | pre .method, 26 | pre .addition, 27 | pre .css .tag, 28 | pre .request, 29 | pre .status { 30 | color: #859900; 31 | } 32 | 33 | pre .number, 34 | pre .command, 35 | pre .string, 36 | pre .tag .value, 37 | pre .phpdoc, 38 | pre .tex .formula, 39 | pre .regexp, 40 | pre .hexcolor { 41 | color: #2aa198; 42 | } 43 | 44 | pre .title, 45 | pre .localvars, 46 | pre .chunk, 47 | pre .decorator, 48 | pre .builtin, 49 | pre .built_in, 50 | pre .identifier, 51 | pre .title .keymethods, 52 | pre .vhdl .literal, 53 | pre .id { 54 | color: #268bd2; 55 | } 56 | 57 | pre .attribute, 58 | pre .variable, 59 | pre .instancevar, 60 | pre .lisp .body, 61 | pre .smalltalk .number, 62 | pre .constant, 63 | pre .class .title, 64 | pre .parent, 65 | pre .haskell .type { 66 | color: #b58900; 67 | } 68 | 69 | pre .preprocessor, 70 | pre .preprocessor .keyword, 71 | pre .shebang, 72 | pre .symbol, 73 | pre .diff .change, 74 | pre .special, 75 | pre .keymethods, 76 | pre .attr_selector, 77 | pre .important, 78 | pre .subst, 79 | pre .cdata { 80 | color: #cb4b16; 81 | } 82 | 83 | pre .deletion { 84 | color: #dc322f; 85 | } 86 | 87 | pre .tex .formula { 88 | background: #eee8d5; 89 | } 90 | -------------------------------------------------------------------------------- /intro_presentation/libraries/highlighters/highlight.js/css/sunburst.css: -------------------------------------------------------------------------------- 1 | /* 2 | 3 | Sunburst-like style (c) Vasily Polovnyov 4 | 5 | */ 6 | 7 | pre code { 8 | display: block; padding: 0.5em; 9 | background: #000; color: #f8f8f8; 10 | } 11 | 12 | pre .comment, 13 | pre .template_comment, 14 | pre .javadoc { 15 | color: #aeaeae; 16 | font-style: italic; 17 | } 18 | 19 | pre .keyword, 20 | pre .ruby .function .keyword, 21 | pre .request, 22 | pre .status { 23 | color: #E28964; 24 | } 25 | 26 | pre .function .keyword, 27 | pre .sub .keyword, 28 | pre .method, 29 | pre .list .title { 30 | color: #99CF50; 31 | } 32 | 33 | pre .string, 34 | pre .tag .value, 35 | pre .cdata, 36 | pre .filter .argument, 37 | pre .attr_selector, 38 | pre .apache .cbracket, 39 | pre .date, 40 | pre .tex .command { 41 | color: #65B042; 42 | } 43 | 44 | pre .subst { 45 | color: #DAEFA3; 46 | } 47 | 48 | pre .regexp { 49 | color: #E9C062; 50 | } 51 | 52 | pre .title, 53 | pre .sub .identifier, 54 | pre .pi, 55 | pre .tag, 56 | pre .tag .keyword, 57 | pre .decorator, 58 | pre .shebang, 59 | pre .input_number { 60 | color: #89BDFF; 61 | } 62 | 63 | pre .class .title, 64 | pre .haskell .type, 65 | pre .smalltalk .class, 66 | pre .javadoctag, 67 | pre .yardoctag, 68 | pre .phpdoc { 69 | text-decoration: underline; 70 | } 71 | 72 | pre .symbol, 73 | pre .ruby .symbol .string, 74 | pre .ruby .symbol .keyword, 75 | pre .ruby .symbol .keymethods, 76 | pre .number { 77 | color: #3387CC; 78 | } 79 | 80 | pre .params, 81 | pre .variable { 82 | color: #3E87E3; 83 | } 84 | 85 | pre .css .tag, 86 | pre .rules .property, 87 | pre .pseudo, 88 | pre .tex .special { 89 | color: #CDA869; 90 | } 91 | 92 | pre .css .class { 93 | color: #9B703F; 94 | } 95 | 96 | pre .rules .keyword { 97 | color: #C5AF75; 98 | } 99 | 100 | pre .rules .value { 101 | color: #CF6A4C; 102 | } 103 | 104 | pre .css .id { 105 | color: #8B98AB; 106 | } 107 | 108 | pre .annotation, 109 | pre .apache .sqbracket, 110 | pre .nginx .built_in { 111 | color: #9B859D; 112 | } 113 | 114 | pre .preprocessor { 115 | color: #8996A8; 116 | } 117 | 118 | pre .hexcolor, 119 | pre .css .value .number { 120 | color: #DD7B3B; 121 | } 122 | 123 | pre .css .function { 124 | color: #DAD085; 125 | } 126 | 127 | pre .diff .header, 128 | pre .chunk, 129 | pre .tex .formula { 130 | background-color: #0E2231; 131 | color: #F8F8F8; 132 | font-style: italic; 133 | } 134 | 135 | pre .diff .change { 136 | background-color: #4A410D; 137 | color: #F8F8F8; 138 | } 139 | 140 | pre .addition { 141 | background-color: #253B22; 142 | color: #F8F8F8; 143 | } 144 | 145 | pre .deletion { 146 | background-color: #420E09; 147 | color: #F8F8F8; 148 | } 149 | -------------------------------------------------------------------------------- /intro_presentation/libraries/highlighters/highlight.js/css/tomorrow.css: -------------------------------------------------------------------------------- 1 | /* Tomorrow Theme */ 2 | /* http://jmblog.github.com/color-themes-for-google-code-highlightjs */ 3 | /* Original theme - https://github.com/chriskempson/tomorrow-theme */ 4 | /* http://jmblog.github.com/color-themes-for-google-code-highlightjs */ 5 | .tomorrow-comment, pre .comment, pre .title { 6 | color: #8e908c; 7 | } 8 | 9 | .tomorrow-red, pre .variable, pre .attribute, pre .tag, pre .regexp, pre .ruby .constant, pre .xml .tag .title, pre .xml .pi, pre .xml .doctype, pre .html .doctype, pre .css .id, pre .css .class, pre .css .pseudo { 10 | color: #c82829; 11 | } 12 | 13 | .tomorrow-orange, pre .number, pre .preprocessor, pre .built_in, pre .literal, pre .params, pre .constant { 14 | color: #f5871f; 15 | } 16 | 17 | .tomorrow-yellow, pre .class, pre .ruby .class .title, pre .css .rules .attribute { 18 | color: #eab700; 19 | } 20 | 21 | .tomorrow-green, pre .string, pre .value, pre .inheritance, pre .header, pre .ruby .symbol, pre .xml .cdata { 22 | color: #718c00; 23 | } 24 | 25 | .tomorrow-aqua, pre .css .hexcolor { 26 | color: #3e999f; 27 | } 28 | 29 | .tomorrow-blue, pre .function, pre .python .decorator, pre .python .title, pre .ruby .function .title, pre .ruby .title .keyword, pre .perl .sub, pre .javascript .title, pre .coffeescript .title { 30 | color: #4271ae; 31 | } 32 | 33 | .tomorrow-purple, pre .keyword, pre .javascript .function { 34 | color: #8959a8; 35 | } 36 | 37 | pre code { 38 | display: block; 39 | background: white; 40 | color: #4d4d4c; 41 | font-family: Menlo, Monaco, Consolas, monospace; 42 | line-height: 1.5; 43 | border: 1px solid #ccc; 44 | padding: 10px; 45 | } -------------------------------------------------------------------------------- /intro_presentation/libraries/highlighters/highlight.js/css/tomorrow_night.css: -------------------------------------------------------------------------------- 1 | /* Tomorrow Night Theme */ 2 | /* http://jmblog.github.com/color-themes-for-google-code-highlightjs */ 3 | /* Original theme - https://github.com/chriskempson/tomorrow-theme */ 4 | /* http://jmblog.github.com/color-themes-for-google-code-highlightjs */ 5 | .tomorrow-comment, pre .comment, pre .title { 6 | color: #969896; 7 | } 8 | 9 | .tomorrow-red, pre .variable, pre .attribute, pre .tag, pre .regexp, pre .ruby .constant, pre .xml .tag .title, pre .xml .pi, pre .xml .doctype, pre .html .doctype, pre .css .id, pre .css .class, pre .css .pseudo { 10 | color: #cc6666; 11 | } 12 | 13 | .tomorrow-orange, pre .number, pre .preprocessor, pre .built_in, pre .literal, pre .params, pre .constant { 14 | color: #de935f; 15 | } 16 | 17 | .tomorrow-yellow, pre .class, pre .ruby .class .title, pre .css .rules .attribute { 18 | color: #f0c674; 19 | } 20 | 21 | .tomorrow-green, pre .string, pre .value, pre .inheritance, pre .header, pre .ruby .symbol, pre .xml .cdata { 22 | color: #b5bd68; 23 | } 24 | 25 | .tomorrow-aqua, pre .css .hexcolor { 26 | color: #8abeb7; 27 | } 28 | 29 | .tomorrow-blue, pre .function, pre .python .decorator, pre .python .title, pre .ruby .function .title, pre .ruby .title .keyword, pre .perl .sub, pre .javascript .title, pre .coffeescript .title { 30 | color: #81a2be; 31 | } 32 | 33 | .tomorrow-purple, pre .keyword, pre .javascript .function { 34 | color: #b294bb; 35 | } 36 | 37 | pre code { 38 | display: block; 39 | background: #1d1f21; 40 | color: #c5c8c6; 41 | font-family: Menlo, Monaco, Consolas, monospace; 42 | line-height: 1.5; 43 | border: 1px solid #ccc; 44 | padding: 10px; 45 | } -------------------------------------------------------------------------------- /intro_presentation/libraries/highlighters/highlight.js/css/vs.css: -------------------------------------------------------------------------------- 1 | /* 2 | 3 | Visual Studio-like style based on original C# coloring by Jason Diamond 4 | 5 | */ 6 | pre code { 7 | display: block; padding: 0.5em; 8 | } 9 | 10 | pre .comment, 11 | pre .annotation, 12 | pre .template_comment, 13 | pre .diff .header, 14 | pre .chunk, 15 | pre .apache .cbracket { 16 | color: rgb(0, 128, 0); 17 | } 18 | 19 | pre .keyword, 20 | pre .id, 21 | pre .built_in, 22 | pre .smalltalk .class, 23 | pre .winutils, 24 | pre .bash .variable, 25 | pre .tex .command, 26 | pre .request, 27 | pre .status { 28 | color: rgb(0, 0, 255); 29 | } 30 | 31 | pre .string, 32 | pre .title, 33 | pre .parent, 34 | pre .tag .value, 35 | pre .rules .value, 36 | pre .rules .value .number, 37 | pre .ruby .symbol, 38 | pre .ruby .symbol .string, 39 | pre .ruby .symbol .keyword, 40 | pre .ruby .symbol .keymethods, 41 | pre .instancevar, 42 | pre .aggregate, 43 | pre .template_tag, 44 | pre .django .variable, 45 | pre .addition, 46 | pre .flow, 47 | pre .stream, 48 | pre .apache .tag, 49 | pre .date, 50 | pre .tex .formula { 51 | color: rgb(163, 21, 21); 52 | } 53 | 54 | pre .ruby .string, 55 | pre .decorator, 56 | pre .filter .argument, 57 | pre .localvars, 58 | pre .array, 59 | pre .attr_selector, 60 | pre .pseudo, 61 | pre .pi, 62 | pre .doctype, 63 | pre .deletion, 64 | pre .envvar, 65 | pre .shebang, 66 | pre .preprocessor, 67 | pre .userType, 68 | pre .apache .sqbracket, 69 | pre .nginx .built_in, 70 | pre .tex .special, 71 | pre .input_number { 72 | color: rgb(43, 145, 175); 73 | } 74 | 75 | pre .phpdoc, 76 | pre .javadoc, 77 | pre .xmlDocTag { 78 | color: rgb(128, 128, 128); 79 | } 80 | 81 | pre .vhdl .typename { font-weight: bold; } 82 | pre .vhdl .string { color: #666666; } 83 | pre .vhdl .literal { color: rgb(163, 21, 21); } 84 | pre .vhdl .attribute { color: #00B0E8; } 85 | -------------------------------------------------------------------------------- /intro_presentation/libraries/highlighters/highlight.js/css/xcode.css: -------------------------------------------------------------------------------- 1 | /* 2 | 3 | XCode style (c) Angel Garcia 4 | 5 | */ 6 | 7 | pre code { 8 | display: block; padding: 0.5em; 9 | background: #fff; color: black; 10 | } 11 | 12 | pre .comment, 13 | pre .template_comment, 14 | pre .javadoc, 15 | pre .comment * { 16 | color: rgb(0,106,0); 17 | } 18 | 19 | pre .keyword, 20 | pre .literal { 21 | color: rgb(170,13,145); 22 | } 23 | pre .method, 24 | pre .list .title, 25 | pre .tag .title, 26 | pre .setting .value, 27 | pre .winutils, 28 | pre .tex .command, 29 | pre .http .title, 30 | pre .request, 31 | pre .status { 32 | color: #008; 33 | } 34 | 35 | pre .envvar, 36 | pre .tex .special { 37 | color: #660; 38 | } 39 | 40 | pre .string { 41 | color: rgb(196,26,22); 42 | } 43 | pre .tag .value, 44 | pre .cdata, 45 | pre .filter .argument, 46 | pre .attr_selector, 47 | pre .apache .cbracket, 48 | pre .date, 49 | pre .regexp { 50 | color: #080; 51 | } 52 | 53 | pre .sub .identifier, 54 | pre .pi, 55 | pre .tag, 56 | pre .tag .keyword, 57 | pre .decorator, 58 | pre .ini .title, 59 | pre .shebang, 60 | pre .input_number, 61 | pre .hexcolor, 62 | pre .rules .value, 63 | pre .css .value .number, 64 | pre .symbol, 65 | pre .ruby .symbol .string, 66 | pre .ruby .symbol .keyword, 67 | pre .ruby .symbol .keymethods, 68 | pre .number, 69 | pre .css .function { 70 | color: rgb(28,0,207); 71 | } 72 | 73 | pre .class .title, 74 | pre .haskell .type, 75 | pre .smalltalk .class, 76 | pre .javadoctag, 77 | pre .yardoctag, 78 | pre .phpdoc, 79 | pre .typename, 80 | pre .tag .attribute, 81 | pre .doctype, 82 | pre .class .id, 83 | pre .built_in, 84 | pre .setting, 85 | pre .params { 86 | color: rgb(92,38,153); 87 | } 88 | 89 | pre .variable { 90 | color: rgb(63,110,116); 91 | } 92 | pre .css .tag, 93 | pre .rules .property, 94 | pre .pseudo, 95 | pre .subst { 96 | color: #000; 97 | } 98 | 99 | pre .css .class, pre .css .id { 100 | color: #9B703F; 101 | } 102 | 103 | pre .value .important { 104 | color: #ff7700; 105 | font-weight: bold; 106 | } 107 | 108 | pre .rules .keyword { 109 | color: #C5AF75; 110 | } 111 | 112 | pre .annotation, 113 | pre .apache .sqbracket, 114 | pre .nginx .built_in { 115 | color: #9B859D; 116 | } 117 | 118 | pre .preprocessor, 119 | pre .preprocessor * { 120 | color: rgb(100,56,32); 121 | } 122 | 123 | pre .tex .formula { 124 | background-color: #EEE; 125 | font-style: italic; 126 | } 127 | 128 | pre .diff .header, 129 | pre .chunk { 130 | color: #808080; 131 | font-weight: bold; 132 | } 133 | 134 | pre .diff .change { 135 | background-color: #BCCFF9; 136 | } 137 | 138 | pre .addition { 139 | background-color: #BAEEBA; 140 | } 141 | 142 | pre .deletion { 143 | background-color: #FFC8BD; 144 | } 145 | 146 | pre .comment .yardoctag { 147 | font-weight: bold; 148 | } 149 | 150 | pre .method .id { 151 | color: #000; 152 | } 153 | -------------------------------------------------------------------------------- /intro_presentation/libraries/highlighters/highlight.js/css/zenburn.css: -------------------------------------------------------------------------------- 1 | /* 2 | 3 | Zenburn style from voldmar.ru (c) Vladimir Epifanov 4 | based on dark.css by Ivan Sagalaev 5 | 6 | */ 7 | 8 | pre code { 9 | display: block; padding: 0.5em; 10 | background: #3F3F3F; 11 | color: #DCDCDC; 12 | } 13 | 14 | pre .keyword, 15 | pre .tag, 16 | pre .css .class, 17 | pre .css .id, 18 | pre .lisp .title, 19 | pre .request, 20 | pre .status { 21 | color: #E3CEAB; 22 | } 23 | 24 | pre .django .template_tag, 25 | pre .django .variable, 26 | pre .django .filter .argument { 27 | color: #DCDCDC; 28 | } 29 | 30 | pre .number, 31 | pre .date { 32 | color: #8CD0D3; 33 | } 34 | 35 | pre .dos .envvar, 36 | pre .dos .stream, 37 | pre .variable, 38 | pre .apache .sqbracket { 39 | color: #EFDCBC; 40 | } 41 | 42 | pre .dos .flow, 43 | pre .diff .change, 44 | pre .python .exception, 45 | pre .python .built_in, 46 | pre .literal, 47 | pre .tex .special { 48 | color: #EFEFAF; 49 | } 50 | 51 | pre .diff .chunk, 52 | pre .ruby .subst { 53 | color: #8F8F8F; 54 | } 55 | 56 | pre .dos .keyword, 57 | pre .python .decorator, 58 | pre .title, 59 | pre .haskell .type, 60 | pre .diff .header, 61 | pre .ruby .class .parent, 62 | pre .apache .tag, 63 | pre .nginx .built_in, 64 | pre .tex .command, 65 | pre .input_number { 66 | color: #efef8f; 67 | } 68 | 69 | pre .dos .winutils, 70 | pre .ruby .symbol, 71 | pre .ruby .symbol .string, 72 | pre .ruby .symbol .keyword, 73 | pre .ruby .symbol .keymethods, 74 | pre .ruby .string, 75 | pre .ruby .instancevar { 76 | color: #DCA3A3; 77 | } 78 | 79 | pre .diff .deletion, 80 | pre .string, 81 | pre .tag .value, 82 | pre .preprocessor, 83 | pre .built_in, 84 | pre .sql .aggregate, 85 | pre .javadoc, 86 | pre .smalltalk .class, 87 | pre .smalltalk .localvars, 88 | pre .smalltalk .array, 89 | pre .css .rules .value, 90 | pre .attr_selector, 91 | pre .pseudo, 92 | pre .apache .cbracket, 93 | pre .tex .formula { 94 | color: #CC9393; 95 | } 96 | 97 | pre .shebang, 98 | pre .diff .addition, 99 | pre .comment, 100 | pre .java .annotation, 101 | pre .template_comment, 102 | pre .pi, 103 | pre .doctype { 104 | color: #7F9F7F; 105 | } 106 | 107 | pre .coffeescript .javascript, 108 | pre .xml .css, 109 | pre .xml .javascript, 110 | pre .xml .vbscript, 111 | pre .tex .formula { 112 | opacity: 0.5; 113 | } 114 | 115 | -------------------------------------------------------------------------------- /make_gh_page.R: -------------------------------------------------------------------------------- 1 | if (!require("git2r")){ 2 | install.packages("git2r", repos = "https://cran.rstudio.org") 3 | library("git2r") 4 | } 5 | library('rmarkdown') 6 | repo <- git2r::repository() 7 | current_branch <- git2r::head(repo)@name 8 | git2r::checkout(repo, "gh-pages") 9 | git2r::merge(repo, current_branch) 10 | rmarkdown::render_site() 11 | git2r::add(repo, "*") 12 | git2r::commit(repo, "update website", session = TRUE) 13 | git2r::checkout(repo, current_branch) -------------------------------------------------------------------------------- /presentation_notes/markdown.Rmd: -------------------------------------------------------------------------------- 1 | ## What we are going to do 2 | 3 | * In this section of the workshop you will be learning how to use Markdown. 4 | * Markdown can be used to create PDF and HTML files, like the website for this workshop. 5 | * At the end of this section you will be replicating introduction of this document, which was written in pure Markdown. [show AUDPC example]. You will try to make the rest of the document in the next section when we talk about R markdown, which as extension of Markdown. 6 | 7 | ## RSudio 8 | 9 | * Markdown can be written with any text editor, but we will be using the text editor embedded in R Studio. 10 | * If you are not familiar with Studio, it is a basically an R session combined with a text editor and a file browser. (smart phone analogy). 11 | * You can do everything with just a text editor and R, but R Studio makes it much easier. 12 | * One useful feature of R Studio is R projects; R projects are basically folders with some extra information about the state of Studio, allowing you to close R Studio and come back to your work later without redoing things. (e.g. "unsaved" changes are preserved) 13 | * They also encourage you to compartmentalized your projects, which leads to better organizations. 14 | 15 | ## Optional examples prep 16 | 17 | * We will be going through a series of examples demonstrating the features of markdown. 18 | * If you want, you can follow along by copying the examples or typing something similar, but there will be an exercises at the end of this section for you to practice as well so you can wait for those if you prefer. 19 | * If you are going to follow along with the examples, open up R Studio and create a new R project by clicking on the drop down menu at the top right and selecting "New Project". Select "New directory" and then "Empty project". Name the project something like "examples" and make it a sub directory of the workshop directory you created earlier. 20 | * Now create a new Rmd file as shown on the website. 21 | * Rmd is the file extension for RMardown, an extended verison of Mardown that we will cover in the next section; the typical file extenison for pure Mardown is ".md". 22 | 23 | ## Introduction 24 | 25 | * Markdown is a simple set of conventions for writing plain text that is readable by both people and computers. 26 | * Plain text refers to text files without any type of formatting such as fonts or text sizes. It is the type of file edited using notepad in Windows and textedit on OSX. 27 | * If you have not used plain text before for things like programming and configuration files this might be confusing at first, but once you get an intuition for how plain text files are used, Markdown should be easy to understand. 28 | * The simplicity of mardown is its greatest asset; it can be learned quickly and is intuitive enough that people unfamiliar with it can still read it. You might have read Markdown in the past an not even realized that it was a specific type of text format. 29 | * Unlike file formats like DOCX, Markdown is not associated with any one program and is typically the input rather than the output of a program. 30 | * Many different programs, including R and R Studio, can read files containing Markdown and convert into more aesthetically pleasing formats such as HTML, PDF, or DOCX. 31 | 32 | 33 | ## Text types 34 | 35 | * Although markdown is written in plain text and you cannot change fonts or text sizes in the Markdown itself, there are patterns you can used to indicate how text should appear once the Markdown is processed. 36 | 37 | 38 | ## Exercise 39 | 40 | * Download the audpc directory and uncompress it in the workshop folder you made earlier. 41 | * Open the project in R Studio by clicking on the .Rproj file or selecting "open project" from R studio. 42 | * Create a file called "README.md" and replicate the background section of the audpc report. 43 | * You might want to use the "Markdown quick reference" in R Studio. 44 | 45 | ## What we did 46 | 47 | ... 48 | -------------------------------------------------------------------------------- /presentation_notes/rmarkdown.Rmd: -------------------------------------------------------------------------------- 1 | ## What we are going to do 2 | 3 | * In this section, we are going to introduce R Markdown and use it to reproduce two example documents. 4 | * We will be recreating the R Markdown used to create the audpc analysis [show] as we introduce the relevant subjects. 5 | * Afterwards, you will write R Markdown to produce something like the phtophthora infestins word document. 6 | * R Markdown is very flexible and complex so don't try to memorize everything now. Just remember what is possible and use cheat sheets and guides to look up how to use the features you need. 7 | * You will get plenty of practice doing the exercises, so don't try to follow along with the example code; periodically we will stop to do part of the exercise after we cover the needed material. 8 | 9 | ## Introduction 10 | 11 | * R markdown is an extension of standard markdown that allows R code to be displayed and run when a Markdown document is rendered. 12 | * Results of the code, such as text output and graphs are added to the output document. 13 | * This makes it very useful for combining notes and analyses in the same file and makes updating or rerunning analyses easy. 14 | 15 | ## Code evaluation 16 | 17 | [go through example code] 18 | 19 | ## Text results 20 | 21 | [go through example code] 22 | 23 | ## First audpc part 24 | 25 | * Create a new file in the audpc r project called "audpc_report.Rmd" and delete any template code. 26 | * Copy the Markdown you created from README.md into this new file 27 | * Create the R Markdown code needed to recreate the "load packages" section. 28 | * Dont worry about the title or the date for now 29 | 30 | 31 | ## Tables 32 | 33 | [go through example code] 34 | 35 | ## Second audpc part 36 | 37 | * Make the R Markdown code for the "Parse input file" and "Tidy up the data" sections 38 | 39 | 40 | ## Figures 41 | 42 | [go through example code] 43 | 44 | ## Third audpc part 45 | 46 | * Make the R Markdown code for rest of the document 47 | 48 | ## YAML 49 | 50 | [go through example code] 51 | 52 | ## Forth audpc part 53 | 54 | * Using a YAML header, add the title and date to the document 55 | 56 | ## P infestins example 57 | 58 | * Download the p infestins example directory and uncompress it in the workshop folder 59 | * Take the code from the R file and the and the text from the word document and use R Markdown to recreate the analysis. 60 | 61 | ## What we did 62 | 63 | ... -------------------------------------------------------------------------------- /quilt_config.yml: -------------------------------------------------------------------------------- 1 | type: "Rmd" 2 | theme: flatly 3 | name_sep: "---" 4 | use_file_names: TRUE 5 | menu_name_parser: !expr function(x) gsub('^[0-9]*--', '', x) 6 | placement: 7 | - index.Rmd: 8 | - "" 9 | -------------------------------------------------------------------------------- /tutorial.css: -------------------------------------------------------------------------------- 1 | .example_frame { 2 | width: 125%; 3 | height: 125%; 4 | -ms-zoom: .8; 5 | -moz-transform-origin: 0 0; 6 | -moz-transform: scale(.8); 7 | -o-transform: scale(.8); 8 | -o-transform-origin: 0 0; 9 | -webkit-transform: scale(.8); 10 | -webkit-transform-origin: 0 0; 11 | } 12 | 13 | 14 | /* 15 | Your basic centered image 16 | */ 17 | .knit_image { 18 | display: block; 19 | margin-left: auto; 20 | margin-right: auto; 21 | } 22 | 23 | /* 24 | This will place a small black border around an image and also add some padding 25 | to the top and bottom of an image. 26 | */ 27 | .knit_border { 28 | display: block; 29 | border: solid black; 30 | border-radius: 5px; 31 | box-shadow: 10px 10px 20px -5px gray; 32 | margin-top: 10px; 33 | margin-bottom: 20px; 34 | } 35 | 36 | 37 | /* 38 | Defining widths for displaying window sizes. The small window looks a bit silly 39 | in the center, so it's placed to the left. These are used with .knit_border and 40 | .knit_image 41 | */ 42 | .big_window { 43 | width: 90%; 44 | } 45 | .med_window { 46 | width: 75%; 47 | } 48 | .small_window { 49 | width: 50%; 50 | margin-left: 0; 51 | } 52 | 53 | 54 | 55 | .rmd_example_outer { 56 | width: 100%; 57 | } 58 | 59 | .rmd_example_inner { 60 | width: 50%; 61 | float: left; 62 | height: 100% 63 | } 64 | 65 | .rmd_example_code { 66 | height: 100% 67 | } 68 | 69 | 70 | .rmd_example_result { 71 | background-color: lightyellow; 72 | border-style: dotted; 73 | border-width: 3px; 74 | border-color: #007fff; 75 | padding: 10px 20px; 76 | margin: 0px 0px 20px 0px; 77 | zoom: 1; 78 | -moz-transform: scale(1); 79 | } 80 | 81 | #exercise { 82 | display: block; 83 | width: 100%; 84 | font-weight: bold; 85 | background: #e6ffff; 86 | margin-left: auto; 87 | margin-right: auto; 88 | padding: 20px 25px; 89 | border-width: 3px; 90 | border-style: solid; 91 | border-color: #1695A3; 92 | border-radius: 20px; 93 | /*box-shadow: 10px 10px 20px -5px gray;*/ 94 | } 95 | 96 | div.r-help-page { 97 | background-color: #f9f9f9; 98 | border-bottom: #ddd 1px solid; 99 | margin-bottom: 10px; 100 | padding: 10px; 101 | } 102 | 103 | div.r-help-page:hover { 104 | background-color: #f4f4f4; 105 | } --------------------------------------------------------------------------------