sckott’s gists

sckott / phylometa_rand_fxn_one.R

Created April 18, 2011 13:33

Conduct tip shuffle randomization of phylogenetic meta-analysis

	#####################################################################
	# Created by Scott Chamberlain
	# Ecology and Evolutionary Biology Dept., Rice University
	# Houston, TX 77005, USA
	# [email protected]
	# http://schamber.wordpress.com/
	#####################################################################

	##### Directions
	#Put your phylogeny, in format required by phylometa (see Phylometa manual), in your working directory

sckott / CalcDists.R

Created April 20, 2011 14:18

get a matrix of pairwise geographic distances between locations

	# Convert degrees to radians
	deg2rad <- function(deg) return(deg*pi/180)

	# Calculates the geodesic distance between two points specified by
	# radian latitude/longitude using the Haversine formula
	# Ouputs distance between sites 1 and 2 as meters
	gcd.hf <- function(long1, lat1, long2, lat2) {
	R <- 6371 # Earth mean radius [km]
	delta.long <- (long2 - long1)
	delta.lat <- (lat2 - lat1)

sckott / bladjing_twomethods.R

Created April 23, 2011 04:57

Conduct and compare two methods for transforming branch lengths using node ages.

	# Run these functions first (scalePhylo, assign.ages, and assign.brlen)
	# scalePhylo, assign.ages, and assign.brlen written by Gene Hunt (http://paleobiology.si.edu/staff/individuals/hunt.cfm)
	# AdjBrLens written by Scott Chamberlain ([email protected])

	scalePhylo<- function(tr, tip.ages, node.mins=NULL, min.diff=0.1)
	## tr is a 'phylo' object
	## tip.ages is a vector of the ages of terminal taxa (best if this vector has names that match the taxa labels)
	## tip.ages MUST BE A NAMED VECTOR, that is, e.g., names(tipages) <- tree$tip.label [where tipages is a numeric vector of ## the tip ages]
	## node.mins is a vector of optional constraints on nodes
	## min.diff is the minimum branch length that will be imposed

sckott / phylometa_fxn.R

Created April 24, 2011 23:19

Conduct phylogenetic meta-analysis from R calling Phylometa - These are functions needed in the code in file phylometa_inR_run.R.

	#####################################################################
	# Created by Scott Chamberlain
	# Ecology and Evolutionary Biology Dept., Rice University
	# Houston, TX 77005, USA
	# [email protected]
	#####################################################################

	# Function to split confidence intervals, this function is required in the below functions
	CI_split <- function(a){
	dd<-c(gsub("\$","",unlist(strsplit(a[5],","))[1]),gsub("\$","",unlist(strsplit(a[5],","))[2]))

sckott / phylometa_inR_run.R

Created April 24, 2011 23:20

Conduct phylogenetic meta-analysis from R calling Phylometa.

	#####################################################################
	# Created by Scott Chamberlain
	# Ecology and Evolutionary Biology Dept., Rice University
	# Houston, TX 77005, USA
	# [email protected]
	# http://schamber.wordpress.com/
	#####################################################################

	########Directions
	#Put your phylogeny, in format required by phylometa (see Phylometa manual), in your working directory

sckott / phylip_fromR.R

Created April 26, 2011 12:32

Run the Phylip application 'contrast' from R, and get formatted output.

	##############################################
	# Created by Scott Chamberlain
	# Ecology and Evolutionary Biology Dept., Rice University
	# Houston, TX 77005, USA
	# [email protected]
	##############################################
	#### Load packages
	require(stringr); require(ape); require(plyr); require(reshape2)

	#### Set directory

sckott / GetCorrs.R

Created May 12, 2011 12:26

Function for calculating pairwise correlations between b*c columns of data in a data frame

	# a = data frame
	# b = list of variables in x
	# c = list of variables in y
	# method_ = one of pearson, spearman, kendall (or their abbreviations)
	# output is a data frame with as many columns as b * c

	GetCorrs <- function(a, b, c, method_) {
	dfout_ <- list()
	names <- list()
	names_ <- list()

sckott / idata_frame.R

Created May 13, 2011 19:46

Comparison of operations on normal and immutable (see package plyr) data frames

	# load packages
	require(plyr); require(reshape2)

	# Make immutable data frame
	baseball_i <- idata.frame(baseball)

	# Example 1 - idata.frame more than twice as fast
	system.time( replicate(50, ddply( baseball, "year", summarise, mean(rbi))) )
	system.time( replicate(50, ddply( baseball_i, "year", summarise, mean(rbi))) )

sckott / ggtree_v1.R

Created May 17, 2011 19:34

Simple function for plotting phylogenies in ggplot2

	###### Simple function for plotting phylogenies in ggplot2
	# x = a phylo object
	# form = one of: star or ladder
	# dependencies: ape, ggplot2, adephylo (loaded within function)
	ggtree <- function(x, form) {
	# Load packages
	require(ape); require(ggplot2); require(adephylo)

	# Define plotting format
	phytheme_ <- function()

sckott / phylogeneticsignal_sim.R

Created May 18, 2011 04:37

Compare measures of phylogenetic signal on simulated trees

	#### Simulations
	install.packages(c("ape","reshape2","ggplot2"))
	require(ape); require(reshape2); require(ggplot2)
	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")

	# Simulation function physig_sim
	# input: x = number of species in tree
	# output: a vector length two with (K, lamba)
	physig_sim <- function(x) {

Scott Chamberlain sckott