Auto-tangled all files.

Author: lcolladotor

_post_template.R

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+#| label: flametree
+#| echo: false
+#| fig-cap-location: "top"
+

index.R

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+

lectures.R

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+

posts/01-welcome/index.R

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+#| eval: false
+## install.packages("tidyverse")
+
+
+
+options(width = 120)
+sessioninfo::session_info()
+

posts/02-introduction-to-r-and-rstudio/index.R

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+#| label: packageinstall
+#| eval: false
+#| echo: true
+## install.packages("ggplot2")
+## 
+## ## Below is an example for installing more than one package at a time:
+## 
+## ## Install R packages for project 0
+## install.packages(
+##     c("postcards", "usethis", "gitcreds")
+## )
+
+
+#| eval: false
+#| echo: true
+## tools::package_dependencies("ggplot2")
+
+
+#| eval: false
+#| echo: true
+## remotes::install_github()
+
+
+#| eval: false
+#| echo: true
+## library("ggplot2")
+
+
+
+options(width = 120)
+sessioninfo::session_info()
+

posts/03-introduction-to-gitgithub/index.R

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+#| label: versioncontrol
+#| echo: false
+#| fig-cap: 'How not to use GitHub [image from PhD Comics]'
+#| out-width: '80%'
+knitr::include_graphics("../../images/phdversioncontrol.gif")
+
+
+#| label: happygitwithr
+#| echo: false
+#| fig-cap: 'A screenshot of the Happy Git with R online book from Jenny Bryan'
+#| out-width: '80%'
+knitr::include_graphics("../../images/happygitwithr.png")
+
+
+#| eval: false
+## install.packages("reprex")
+
+
+
+options(width = 120)
+sessioninfo::session_info()
+

posts/04-reproducible-research/index.R

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+#| label: setup
+#| include: false
+library(here)
+
+
+#| eval: false
+## install.packages(c("here", "sessioninfo"))
+
+
+
+## This is my relative directory
+here::here()
+
+## I can now easily share code to access files from this project
+## such as access to the flight.csv file saved under the data
+## directory.
+here::here("data", "flights.csv")
+
+## This would not be easily shareable as you don't have
+## "/Users/leocollado/Dropbox/Code" on your computer
+full_path <- "/Users/leocollado/Dropbox/Code/jhustatcomputing2023/data/flights.csv"
+
+
+#| eval: false
+## ## Reproducibility information
+## print("Reproducibility information:")
+## Sys.time()
+## proc.time()
+## options(width = 120)
+## sessioninfo::session_info()
+
+
+
+## Reproducibility information
+print("Reproducibility information:")
+Sys.time()
+proc.time()
+options(width = 120)
+sessioninfo::session_info()
+
+
+
+library("colorout") ## Load a package I installed from GitHub
+sessioninfo::session_info()
+
+
+
+options(width = 120)
+sessioninfo::session_info()
+

posts/05-literate-programming/index.R

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+
+data(airquality)
+plot(airquality$Ozone ~ airquality$Wind)
+
+
+
+knitr::include_graphics("https://d33wubrfki0l68.cloudfront.net/61d189fd9cdf955058415d3e1b28dd60e1bd7c9b/9791d/images/rmarkdownflow.png")
+
+
+#| label: missionaccomplished
+#| echo: false
+#| out-width: '60%'
+#| fig-cap: "Mission accomplished!"
+knitr::include_graphics("https://media.giphy.com/media/L4ZZNbDpOCfiX8uYSd/giphy.gif")
+
+
+#| label: hex-blogdown
+#| echo: false
+#| out-width: '30%'
+#| fig-cap: "blogdown logo"
+knitr::include_graphics("https://bookdown.org/yihui/blogdown/images/logo.png")
+
+
+#| label: hex-bookdown
+#| echo: false
+#| out-width: '30%'
+#| fig-cap: "book logo"
+knitr::include_graphics("https://bookdown.org/yihui/bookdown/images/logo.png")
+
+
+
+## library(package)
+
+
+
+## matrix(data, nrow = rows, ncol = cols)
+
+
+
+## if (condition) {
+##     ## Case 1
+## } else if (condition) {
+##     ## Case 2
+## } else if (condition) {
+##     ## Case 3
+## }
+
+
+
+## name <- function(variables) {
+## 
+## }
+
+
+
+## for (variable in vector) {
+## 
+## }
+
+
+
+## # Tue Jan 21 20:20:14 2020 ------------------------------
+
+
+#| eval: false
+## ## Install styler for automatically styling scripts
+## install.packages("styler")
+## 
+## ## Install biocthis
+## if (!require("BiocManager", quietly = TRUE))
+##     install.packages("BiocManager")
+## 
+## BiocManager::install("biocthis")
+
+
+
+## Example code for styling all files that end with .qmd
+cat(readLines(here::here("scripts", "auto_style.R")))
+
+
+#| eval: false
+## ## For the styler addin
+## # Affects the output of: styler:::get_addins_style_transformer_name()
+## # https://github.com/r-lib/styler/blob/acfb42acc2e558e7b57ef133f1470df78b5093fd/R/addins.R#L183
+## options("styler.addins_style_transformer" = "biocthis::bioc_style()")
+
+
+
+options(width = 120)
+sessioninfo::session_info()
+

posts/06-reference-management/index.R

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+
+citation("rmarkdown")
+
+
+
+knitr::write_bib("rmarkdown", file = "my-refs.bib")
+
+
+
+list.files()
+
+
+#| eval: false
+## install.packages(c("bibtex", "RefManageR"))
+
+
+
+options(width = 120)
+sessioninfo::session_info()
+