sckott / rfna_demo.r

Created January 27, 2012 19:02

Demo of using rnfa R package to scrape trait data - in this example for receptacle traits.

	# A web page with taxa names you want to get trait data from
	pg1 <- 'http://www.efloras.org/browse.aspx?flora_id=1&start_taxon_id=10074&page=1'


	# Get the daughter URLs from the taxa on the page, using doMC to speed things up
	urls <- getdaughterURLs(pg1, cores=TRUE, no_cores=2)
	\|======================================================================================================\| 100%


	# Get the receptacle trait state for the taxa

sckott / mvabund.r

Created March 19, 2012 13:29

playing with mvabund

	#### mvabund play
	# install mvabund from CRAN pkg repository
	install.packages("mvabund")
	require(mvabund)

	# plot abundance by copepod species
	data(Tasmania)
	attach(Tasmania)
	tasmvabund <- mvabund(Tasmania$copepods)
	plot(tasmvabund ~ treatment, col = as.numeric(block))

sckott / ggplot2SEM.R

Created May 1, 2012 05:23 — forked from emhart/ggplot2SEM.R

ggplot2 SEM model example

	require(ggplot2); require(gridExtra)

	###Generate box coords
	###A function to generat a blank box for use with geom_path()
	box_coords <- function(x,y,size){
	b.x <- c(rep(x,2) - (size[1] / 2),rep(x,2) + (size[1] / 2))
	b.x[5] <- b.x[1]
	b.y <- c(y-(size[2] / 2),rep(y,2)+(size[2] / 2),y-(size[2] / 2))
	b.y[5] <- b.y[1]
	rmat <- data.frame(cbind(b.x,b.y))

sckott / getgithubstats.r

Created May 5, 2012 13:29

Get github stats (forks and watchers) on user or organization account.

	# Store a function with man lines
	# Go Here: http://beta.opencpu.org/apps/opencpu.demo/storefunction/
	# number: x3e50ee0780
	# link: http://beta.opencpu.org/R/call/store:tmp/x3e50ee0780/png?id='ropensci'&type='org'
	the <- function (id = 'hadley', type = 'user')
	{
	require(RCurl); require(RJSONIO); require(ggplot2); require(reshape2); require(plyr)
	if(type == 'user'){ url = "https://api.github.com/users/" } else
	if(type == 'org'){ url = "https://api.github.com/orgs/" } else
	stop("parameter 'type' has to be either 'user' or 'org' ")

sckott / firstgitdeskpresentation

Created July 5, 2012 19:42

my first gistdeck presentation

	# my first gistdeck presentation



	## This is fun

	* [this is a link to my home page](http://schamberlain.github.com/scott)
	* [and my blog](http://schamberlain.github.com/blog.html)
	* yeah links

sckott / Markdown.md

Created July 5, 2012 19:43

my first gistdeck presentation

This is fun

sckott / Markdown.md

Created July 5, 2012 19:44

my first gistdeck presentation

sckott / getURL_v_GET.r

Created July 5, 2012 23:01

getURL vs. GET

	library(httr); library(plyr); require(RCurl)
	stackexchange_GET <- function(ids, url = "https://api.stackexchange.com/2.0/users/")
	{
	res <- GET(paste0(url, ids), query = list(site = "stackoverflow"))
	json <- parsed_content(res)
	json
	}

	stackexchange_getURL <- function(ids, url = "https://api.stackexchange.com/2.0/users/")
	{

sckott / apistatus.r

Created August 23, 2012 17:09

Check status of APIs used in rOpenSci libraries.

	apistatus <- function() {
	require(RCurl); require(RJSONIO); require(ggplot2); require(XML)

	# PLoS search API
	if(identical(
	RJSONIO::fromJSON(RCurl::getURL(
	"http://api.plos.org/search?q=id:10.1371/journal.pbio.0000012&wt=json"))$response$docs[[1]]$eissn,
	"1545-7885") == TRUE){plos_search_api <- 1} else
	{plos_search_api <- 0}

sckott / matricesfromabddist.r

Created August 28, 2012 00:27

Make network matrices from abundance distributions and calculate network structures

	#######################################################
	###########Community-Network Structure Simulation######
	#######################################################
	library(bipartite)

	# Set of mean and sd combinations of log-normal distribution
	mu<-c(0.5,2.9,5.3)
	sig<-c(0.75,1.6,2.45)

	make.matrices<-function(a,b,nmats){

Scott Chamberlain sckott