| You can insert a code chunk within a code chunk in Rmarkdown as shown here. This code chunk was used in my bookdown book "Package as Analysis" to show a SublimeText3 snippet that itself inserts a code chunk | |
| ````html | |
| <snippet> | |
| <content><![CDATA[ | |
| `r ''````{r ${1:chunk_name}} | |
| $0 | |
| ``` | |
| ]]></content> |
| # load libraries individually | |
| library(purrr) | |
| library(magrittr) | |
| library(tidyr) | |
| library(dplyr) | |
| # or just load | |
| library(tidyverse) | |
| # some random data to make my own data frame with |
A repository can use git large file storage ("git-lfs") to manage large data files.
The instructions on installing git-lfs for Mac, Windows, and some linux distros are available on the git-lfs GitHub repo Wiki. Since I did this work remotely on the HMS Research Computing Cluster, I do not have root access and had to install from source.
Commands to get permission to push to GitHub on O2.
eval "$(ssh-agent -s)"
ssh-add ~/.ssh/id_rsa_github
| for (letter in letters) { | |
| cat(letter) | |
| # do some work | |
| Sys.sleep(0.1) | |
| cat("\33[2K\r") | |
| } | |
| cat("done\n") |
| <a href="https://github.com/jhrcook" class="github-corner" aria-label="View source on GitHub"><svg width="80" height="80" viewBox="0 0 250 250" style="fill:#1E80F0; color:#fff; position: absolute; top: 0; border: 0; right: 0;" aria-hidden="true"><path d="M0,0 L115,115 L130,115 L142,142 L250,250 L250,0 Z"></path><path d="M128.3,109.0 C113.8,99.7 119.0,89.6 119.0,89.6 C122.0,82.7 120.5,78.6 120.5,78.6 C119.2,72.0 123.4,76.3 123.4,76.3 C127.3,80.9 125.5,87.3 125.5,87.3 C122.9,97.6 130.6,101.9 134.4,103.2" fill="currentColor" style="transform-origin: 130px 106px;" class="octo-arm"></path><path d="M115.0,115.0 C114.9,115.1 118.7,116.5 119.8,115.4 L133.7,101.6 C136.9,99.2 139.9,98.4 142.2,98.6 C133.8,88.0 127.5,74.4 143.8,58.0 C148.5,53.4 154.0,51.2 159.7,51.0 C160.3,49.4 163.2,43.6 171.4,40.1 C171.4,40.1 176.1,42.5 178.8,56.2 C183.1,58.6 187.2,61.8 190.9,65.4 C194.5,69.0 197.7,73.2 200.1,77.6 C213.8,80.2 216.3,84.9 216.3,84.9 C212.7,93.1 206.9,96.0 205.4,96.6 C205.1,102.4 203.0,107.8 198.3,112.5 C181.9,128.9 168.3 |
Here is how you can link to [a post]({{< ref "/post/some_post.md" >}}) in Academic Kickstarter for Hugo.
| library(tidyverse) | |
| #### MAKING MOCK DATA #### | |
| # Some parameters for amount of data. | |
| n_metabs <- 5 | |
| n_tissues <- 10 | |
| tissues <- purrr::map_chr(1:n_tissues, ~ paste0(sample(letters, 3), collapse="")) | |
| # Make a wide table of data, adding on columns per metabolite |
| # Parse a string given in "# #/# oz" into a decimal value. | |
| parse_ounces <- function(val) { | |
| if (val == "For glass") { return(1) } | |
| if (str_detect(val, "or")) { | |
| val <- str_remove(val, "or.+$") | |
| } | |
| val_pieces <- str_remove_all(val, "oz|slices|tsp|dash") %>% | |
| str_trim() %>% |