dfalster

library(xlsx)
library(smatr)

# get data, from publication Wright et al 2004. DOI: [10.1038/nature02403](http://doi.org/10.1038/nature02403)
download.file("http://www.nature.com/nature/journal/v428/n6985/extref/nature02403-s2.xls", "wright-2004.xls")
dat.Wright  <- read.xlsx2("wright-2004.xls", sheetIndex=1, startRow=11, stringsAsFactors=FALSE, check.names=TRUE)

## Clean data
dat.Wright <- dat.Wright[names(dat.Wright) != " "] # Drop blank columns
for(v in c("log.LMA","log.LL"))

sckott

Example parallel workflow

In this example, we use the rgbif package to search for occurrence (lat/long) data for 1000 species

Install and load rgbif

install.packages("rgbif")
library("rgbif")

lfender6445

Pry Cheat Sheet

• Youtube Tutorial 2013

Command Line

• pry -r ./config/app_init_file.rb - load your app into a pry session (look at the file loaded by config.ru)
• pry -r ./config/environment.rb - load your rails into a pry session

Debugger

kevinushey

// run me by installing Rcpp and calling sourceCpp on this file

#include <Rcpp.h>
using namespace Rcpp;

// some initial stuff borrowed from R sources

#ifdef WORDS_BIGENDIAN
static const int hw = 0;
static const int lw = 1;

hubgit

Search PubMed for articles in the PMC Open Access Subset for which free full text (i.e. XML) is available:
http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&retmode=xml&term=pubmed+pmc+open+access%5Bfilter%5D+AND+free+full+text%5Bfilter%5D

Find the PMCID for an article by PMID:
http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&db=pmc&retmode=xml&linkname=pubmed_pmc&id=24191168

Fetch full text article XML from PMC by PMCID:
http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pmc&id=3804407

A PMC article for which the full text XML is not available:

chengyin

// 1. Go to page https://www.linkedin.com/settings/email-frequency
// 2. You may need to login 
// 3. Open JS console
//    ([How to?](http://webmasters.stackexchange.com/questions/8525/how-to-open-the-javascript-console-in-different-browsers))
// 4. Copy the following code in and execute
// 5. No more emails
//
// Bookmarklet version: 
// http://chengyin.github.io/linkedin-unsubscribed/

aschweer

document.write('<script type="text/javascript" src="http://api.elsevier.com/javascript/scopussearch.jsp"> </' + 'script>');

callbackCitedbycount = function(){
  if (sciverse.areSearchResultsValid()) {
    var resultObj = sciverse.getSearchResults();
	  if (resultObj.returnedResults >0) {
	    citedbycount = resultObj.results[0].citedbycount;
	    eid = resultObj.results[0].eid;
	    if (citedbycount > 0) {
	      citeHtml = '<span class="bold">Scopus times cited</span>:</span> ';

ramnathv

This is a proof-of-concept of a parser to convert a markdown file to a ctv file, that is required for task views. The basic idea is to use a combination of YAML and markdown sections in the md file, parse it and convert it into a payload, and render it using a template as specified by the ctv package.

Structure of Markdown File

---
name: Working with data on the web
maintainer: Scott Chamberlain, Karthik Ram, Christopher Gandrud
email: scott at ropensci.org
version: 2013-09-17

andrewburgess

/* ============================================
 * bootstrap-infiniteScroll.js
 * ============================================ */

!function ($) {
    'use strict';
    var InfiniteScroll = function (el, options) {
        this.$element = $(el);
        this.$data = $(el).data();
        this.$options = options;

hadley

# We first start by creating a way of escaping the characters that have special
# meaning for html, while making sure we don't end up double-escaping at any
# point. The easiest way to do this is to create an S3 class that allows us to
# distinguish between regular text (that needs escaping) and html (that
# doesn't).
#
# We then write an escape method that leaves html unchanged and escapes the
# special characters (&, <, >) in ordinary text. We also add a method for lists
# for convenience