muschellij2

# rm(list=ls())

convert_index <- function(infile="index_original.html", outfile = "index.html"){
	trim <- function (x) gsub("^\\s+|\\s+$", "", x)
	
	ff <- file(infile)
	
	dat <- readLines(ff)
	close(ff)
	where.scene <- which(dat == "        r0 = new X.renderer('r0');")

muschellij2

#!/bin/bash

echo "I ran a script" > blah.txt

sudo apt-get update
sudo apt-get install -y --no-install-recommends \
    file \
    git \
    libapparmor1 \
    libgc1c2 \

muschellij2

better_fetch_pubmed_data = function (pubmed_id_list, retstart = 0, retmax = 500, format = "xml", 
                                     encoding = "UTF8") 
{
  myIDlist <- pubmed_id_list
  if ((!is.list(myIDlist)) | is.na(myIDlist$WebEnv) | is.na(myIDlist$QueryKey) | 
      is.na(myIDlist$Count) | !is.integer(as.integer(retstart)) | 
      !is.integer(as.integer(retmax))) {
    message("There is an issue with the PubMed ID list you supplied. Please, call the function again and supply the result of a <get_pubmed_ids()> call as argument. Thank you.")
    return(NULL)
  }

muschellij2

old_package_version = function(repos = getOption("repos")) {
  all_info = vector(mode = "list", length = length(repos))
  names(all_info) = repos
  for (repo in repos) {
    # taken from remotes:::package_find_archives
    archive <- tryCatch({
      tf <- tempfile(fileext = ".gz")
      on.exit(unlink(tf), add = TRUE)
      remotes:::download(tf, sprintf("%s/src/contrib/Meta/archive.rds",
                                     repo))

muschellij2

library(rvest)
library(xml2)
library(sf)
library(geojsonio)
url = "http://www.landxml.org/webapps/landxmlsamples.aspx"

url_file = paste0("http://landxml.org/schema/LandXML-2.0/",
                  "samples/Carlson%20Software/nunosurf.xml")
xml_file = file.path("~/Downloads", basename(url_file))
if (!file.exists(xml_file)) {

muschellij2

# remotes::install_github('muschellij2/knitr')
library(knitr)

rmd_to_df = function(file) {
  x = xfun::read_utf8(file)
  on.exit(knitr::knit_code$restore(), add = TRUE)
  res = knitr:::split_file(x, patterns = knitr::all_patterns$md)
  classes = sapply(res, attr, "class")
  blocks = res[classes %in% "block"]
  params = lapply(blocks, function(el) {

muschellij2

read_mat = function(mat) {
  L = try({
    R.matlab::readMat(mat)
  })
  if (!inherits(L, "try-error")) {
    return(L)
  }
  
  names = rhdf5::h5ls(mat)$name
  convert_mat_string = function(x) {

muschellij2

walk_source <- function(
  file = NULL, 
  delay = 1.5, 
  clear_each_cmd = TRUE,
  wait_for_press = TRUE,
  style = styler::tidyverse_style,
  record_screen = TRUE,
  ...
) {
  if (record_screen) {

muschellij2

file_exists = function(...) {
  x = list(...)
  x = unlist(...)
  x = unname(x)
  df = data.frame(x = x, 
                  bn = basename(x),
                  dn = dirname(x),
                  index = 1:length(x),
                  stringsAsFactors = FALSE)
  dn = unique(df$dn)

muschellij2

/*  BET - Brain Extraction Tool

    BETv1 Steve Smith
    BETv2 Mickael Pechaud, Mark Jenkinson, Steve Smith
    FMRIB Image Analysis Group

    Copyright (C) 1999-2006 University of Oxford  */

/*  Part of FSL - FMRIB's Software Library