cboettig

# image trees are named something like paup1.tre to paup100.tre
require(ape)
# could use a for loop, but sapply is faster and will parallelize
sapply(1:100, function(i){
  tree <- read.tree(paste("paup", i, ".tre", sep=""))
  pdf(file=paste("paup", i, ".pdf", sep="")) 
  plot(tree) # add fancy plotting options etc,
  dev.off()
})

cboettig

## this function f  will remember whatever options it is passed
f <- function(y, ...){
  out <- y + dnorm(...)
  list(out, opts=list(...))
}
## This is the way to call the function using its exact arguments
a <- f(1, x=4, sd=2, mean=4) 
b <- do.call(f, c(list(y=1), a$opt)) 
identical(a,b) # TRUE

cboettig

#####  socialR header info ##### 
require(socialR)
script <- "example.R" # Must specify the script name! 
gitcommit(script)     # Must commmit at start!

##### Optional but a good idea ##### 
#almost requisite, if not me running "repo"/"dir"
gitopts = list(user = "cboettig", dir = "demo", repo = "socialR") 
on.exit(system("git push")) #  For git links.  May prompt for pw,
tags <- "test"  ## multiple possible: space, delim, multiple items, etc.  

cboettig

data(faithful)
attach(faithful)

 ## EM Algorithm

W = waiting
s = c(0.5, 40, 90, 16, 16)

em = function(W,s) {
  Ep = s[1]*dnorm(W, s[2], sqrt(s[4]))/(s[1]*dnorm(W, s[2], sqrt(s[4])) +

cboettig

data(faithful)
attach(faithful) 
#Assumes two gaussian populations of eruptions
W = waiting
# Guess of the parameters: 
s = c(p=0.5, mu1=50, mu2=90, sigma1=30, sigma2=30) 
 
 
# EXPECTATION STEP
expectation_step <- function(observed, parameters){

cboettig

#segue_test.R
on.exit(stopCluster(myCluster))

library(segue)
setCredentials(getOption("amazon_key"), getOption("amazon_secret"))


# Jeffery Breen's example, adapted with "custom function" works fine
my_fun <- mean # a custom definition
myList <- NULL

cboettig

@ARTICLE{,
 author = {L.H. Yang and V. H. Rudolf},
 title = {Phenology, ontogeny and the effects of climate change on the timing
       of species interactions},
 journal = {Ecology Letters},
 year = {2010},
 volume = {13},
 pages = {1-10},
 doi = {10.1111/j.1461-0248.2009.01402.x},

cboettig

library(segue)
setCredentials(getOption("amazon_key"), getOption("amazon_secret"))
require(mcmcTools)
X <- rnorm(20, 2, 5)
loglik <- function(pars){
    sum( dnorm(X, mean=pars[1], sd=pars[2], log=TRUE) )
  }
prior <- function(pars){
       1/pars[2]^2
}

cboettig

mat <-  rbind(c(1),c(2),c(3))  # three rows, 1 column
layout(mat, height = c(1, .5, .5)) # height of each row
par(mar=c(4,6,4,2)) # can be changed for each subsequent plot

cboettig

## THANKS to David Scott for this one: 
## http://r.789695.n4.nabble.com/Greek-letters-on-a-multi-line-plot-title-td1018642.html


### Change spacing to allow for multiline title 
par(oma=c(2, 0, 4, 0)) 
### Some greek letters 
mu <- 0 
alpha <- 1 
beta <- 2