zkamvar

library("gh")
library("base64enc")

# get a file from a repository
get_repo_file <- function(org = "carpentries", lesson = "sandpaper-docs", file = "CONTRIBUTING.md", ...) {
  gh("GET /repos/{org}/{lesson}/contents/{file}", 
    .params = list(
      org = org,
      lesson = lesson,
      file = file

zkamvar

#' List maintainers who still need to respond to the Workbench transition issue
#' 
#' @param org the name of the github organisation
#' @param repo name of the repository
#' @return a character vector of github user names for maintainers who still need to confirm
#'   transition to The Workbench
#'
#' @details The Workbench transition requires maintainers to confirm that they have re-cloned
#'   their local repositories to avoid a situation where they overwrite commits with the old
#'   version of the repository 

zkamvar

library("jsonlite")
library("polite")
library("rvest")
library("purrr")
library("dplyr")


workbench_slugs <- c(
  "r-ecology-lesson",
  "r-socialsci",

zkamvar

{
  "R": {
    "Version": "4.1.0",
    "Repositories": [
      {
        "Name": "carpentries",
        "URL": "https://carpentries.r-universe.dev"
      },
      {
        "Name": "carpentries_archive",

zkamvar

Keybase proof

I hereby claim:

• I am zkamvar on github.
• I am zkamvar (https://keybase.io/zkamvar) on keybase.
• I have a public key ASDqVco4Xm3D5M11ckLrYgE9XyqlHFxA7MwqWszJxWvmSAo

To claim this, I am signing this object:

zkamvar

This compares the differences between pandoc's markdown and markdown_github engines when parsing <div> tags within sections.

Problem

In essence, if a <div> tag contains a header out of order with the main document, its contents will be appended to the div in the html document with markdown_github. If the following div appears after a level 3 header:

<div class='boo'>

## level 2

zkamvar

# test file 
sample_chunk <- " 
```{r hello, testing=as.logical(1), another=1 + 1} 
x <- 1 + 1 # this evaluates to two 
``` 
the value of x is `r x`" 
file = "sample.Rmd" 
writeLines(sample_chunk, con = file) 
# delete temp Rmd file 
on.exit(unlink(file)) 

zkamvar

#!/usr/bin/env Rscript
args <- commandArgs(trailingOnly = TRUE)
if (length(args) != 2) {
	msg <- "
	usage:
	  render-demo.R <demo> <package>
  
	This utility will render the code and figures from a given package as a PDF
	and place them into a directory called `<demo>-generated_files`. This requires
	knitr, rmarkdown and LaTeX to be installed on your system.

zkamvar

title	author	date
Generating a bootstrap dendrogram with hierfstat's genet.dist	Zhian N. Kamvar	2018-08-21

This short tutorial is an answer to the question posed on the poppr forum: https://groups.google.com/forum/?utm_medium=email&utm_source=footer#!msg/poppr/vEQ8vb2oObQ/RjTsndaCEQAJ

My ultimate goal when asking the previous question was to employ aboot in order to create a bootstraped dendrogram based on distances offered by the genet.dist function in hierfstat. That's why I was trying to create a tree based on Nei's distance this way - to verify that it worked! Unfortunately even after reading the aboot documentation, I still fail to understand how to do this. I would be grateful if someone could provide an example of using aboot in combination with genet.dist.

zkamvar

#' Get the size of a single panel
#'
#' @param n the number of panels
#' @param len the overall length of the side
#' @param margin the outer margin width (will be multiplied by 2)
#' @param gutter the space between panels
#'
#' @return a numeric value specifying the panel width/length
#'
#' @examples