sckott’s gists

sckott / randmat.r

Created August 28, 2012 19:09

speed of random matrix algorithms

	mm <- matrix(0, 10, 5)
	m <- 10
	n <- 5

	> system.time( replicate(1000, apply(mm, c(1,2), function(x) sample(c(0,1),1)) ) ) # @recology_
	user system elapsed
	0.414 0.015 0.429
	> system.time( replicate(1000, matrix(rbinom(10*5,1,.5),ncol=5,nrow=10) ) ) # @distribecology
	user system elapsed
	0.012 0.000 0.012

sckott / comparfxn.r

Created September 2, 2012 15:35

Comparison of functions for comparative phylogenetics

	> # Load
	require(motmot); require(geiger); require(picante)
	source("http://anolis.oeb.harvard.edu/~liam/R-phylogenetics/phylosig/v0.3/phylosig.R")
	source("http://anolis.oeb.harvard.edu/~liam/R-phylogenetics/fastBM/v0.4/fastBM.R")

	# Make tree
	tree <- rcoal(10)

	# Transform branch lengths
	> system.time( replicate(1000, transformPhylo(tree, model = "lambda", lambda = 0.5)) ) # motmot

sckott / gggraph.r

Created September 2, 2012 16:42

basic ggplot food web graphs

	# ggplot network graphics functions
	# g = an igraph graph object, any igraph graph object
	# vplace = type of vertex placement assignment, one of rnorm, runif, etc.

	gggraph <- function(g, vplace = rnorm) {

	require(ggplot2)

	g_ <- get.edgelist(g)
	g_df <- as.data.frame(g_)

sckott / binmat_comparison.r

Created September 5, 2012 16:44

Comparison of binary matrix algorithms (minus the Rcpparmadillo versions).

	library(inline); library(compiler); library(rbenchmark)

	n <- 500
	k <- 100

	scott <- function(N, K) {
	mm <- matrix(0, N, K)
	apply(mm, c(1, 2), function(x) sample(c(0, 1), 1))
	}
	scottComp <- cmpfun(scott)

sckott / newphylomaticfxn.r

Created September 7, 2012 00:53

example of new phylomatic function - getting trees from R.

	# Example of new phylomatic
	install_github('taxize_', 'ropensci', branch="phylomatic_fix")
	library(taxize)

	dat_ <- c("Amylotheca_subumbellata","Impatiens_davidi","Gonocarpus_leptothecus","Calochortus_argillosus","Gagea_sarmentosa","Lilium_lankongense","Cephalanthera_rubra","Bicuiba_oleifera","Guatteria_dolichopoda","Iteadaphne_caudata")

	tree <- get_phylomatic_tree(taxa = dat_)
	> tree

	Phylogenetic tree with 10 tips and 9 internal nodes.

sckott / suppressnamespacewarning.r

Created September 12, 2012 17:45

gotta suppress the damn namespace warning in XML

	library(httr); library(XML)
	url <- "http://data.gbif.org/ws/rest/occurrence/list?scientificname=Accipiter%20erythronemius&coordinatestatus=TRUE&maxresults=100"
	tt <- content(GET(url), as="text")
	out <- xmlTreeParse(tt)$doc$children$gbifResponse

	d> getNodeSet(out, "//to:TaxonOccurrence") # throws errors even though the output is what I want
	Namespace prefix to on TaxonOccurrence is not defined
	Namespace prefix to on catalogNumber is not defined
	Namespace prefix to on country is not defined

sckott / rgbif_occurrencelist_providerkey.r

Created September 25, 2012 19:52

Example of getting a provider key and running occurrence list with the key.

	install_github('rgbif', 'schamberlain') # my branch is the newest
	library(rgbif)
	providers(name="UK National Biodiversity Network") # get numeric key for the NBN

	> occurrencelist(sciname="Ursus", dataproviderkey=172, latlongdf=T) # should give you a data.frame like below
	taxonName country decimalLatitude decimalLongitude catalogNumber earliestDateCollected latestDateCollected
	1 Abietinaria abietina GB 59.01977 -2.9031110 13389886 1995-06-20 1995-06-20
	2 Abietinaria abietina GB 60.84050 -0.9006389 13389540 1988-06-02 1988-06-02
	3 Abietinaria abietina GB 56.55398 -5.4213445 13389523 1989-06-18 1989-06-18
	4 Abra alba GB 49.91424 -6.3364116 13392162 1988-09-19 1988-09-19

sckott / write_fasta.r

Created October 12, 2012 22:55

Write fasta file, which is ready to run in ClustalW for multiple sequence alignment.

	# Clustal doesn't like when there are spaces in species names, so `write_fasta` fixes that in case you forget.
	write_fasta <- function (sequences, file.out) {
	outfile <- file(description = file.out, open = "w")
	write.oneseq <- function(sequence, name) {
	if(grepl("\\s", name)){name<-gsub("\\s", "_", name)} else{name<-name}
	writeLines(paste(">", name, sep = ""), outfile)
	writeLines(sequence[[1]], outfile)
	}
	sapply(seq_len(length(sequences)), function(x) write.oneseq(
	sequence=as.character(sequences[[x]]), name=names(sequences[x])))

sckott / downstream2.r

Created October 16, 2012 17:41

Retrieve all taxa names or TSNs (taxonomic serial numbers) downstream in hierarchy from given TSN.

	install.packages("devtools") # need devtools to use install_github()
	require(devtools)

	install_github("ritis", "ropensci") # need for the function searchbyscientificname below
	require(ritis)

	install_github("taxize_", "ropensci", ref="downstream_fix") # Installs packages in development directly from Github
	library(taxize)

	tsn1 <- searchbyscientificname("Osteichthyes") # get TSN for Osteichthyes (bony fish)

sckott / Rpumpkin.r

Created October 31, 2012 22:55

Run the code, then click three times to cut a piece out of your pumpkin

Scott Chamberlain sckott