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data <- c(120, 130, 110, 105, 121)
n.iter <- 10000
mu.prior <- function(x) dnorm(x, mean=0, sd=10)
sd.prior <- function(x) dnorm(x, mean=0, sd=10)
posterior <- function(x, mu, sigma) sum(c(
                                         dnorm(x, mu, abs(sigma), log=TRUE),
                                         mu.prior(x), sd.prior(x)
                                     ))
proposal <- function(x) x + rnorm(1, 0, sd=.25)
mu <- 90

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# Rough-and-ready body-mass/species-number estimation in mammals and birds
# Will Pearse - 2021-09-19

##########################
# Load data ##############
##########################
library(caper)
library(ape)
library(Pareto)

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#' @export
.reed.2017a <- function(...) {
    data <-read.csv("http://pasta.lternet.edu/package/data/eml/knb-lter-sbc/17/30/a7899f2e57ea29a240be2c00cce7a0d4", as.is=TRUE)
    names(data) <- tolower(names(data))
    data$count[data$count < 0] <- 0
    data$taxon_species[data$taxon_species == -99999] <- NA
    data$taxon_genus[data$taxon_genus == -99999] <- NA

    data$species <- with(data, paste(taxon_genus, taxon_species, sep="_"))

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# Packages
library(geiger)
library(caper)
library(phytools)

# Simulate phylogeny and some traits
tree <- sim.bdtree(n=100)
traits <- sim.char(tree, .01, nsim=7)[,1,]

# Fuss around to make a discrete character

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#!/usr/bin/ruby
require 'optparse'
require 'csv'

options = {}
OptionParser.new do |opts|
  #Defaults
  options[:output] = nil
  options[:input] = nil
  options[:lat] = "lat"

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# PICS and PGLS - oh my!
# Will Pearse - 2018-04-03

# Headers
library(ape)
library(caper)
library(geiger)
library(phytools)
library(mvMORPH)

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# Headers
library(pez)
data(laja)

#############################
# SETUP #####################
#############################
    
# Make a comparative community object from a phylogeny and some
# site-species community data - some invertebrates found in some

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# Functions
library(caper)
find.clade <- function(tree, tips){
    clade.mat <- clade.matrix(tree)$clade.matrix
    sums <- rowSums(clade.mat)
    ancestors <- apply(clade.mat, 1, function(x) all(x[tips]==1))
    sums[!ancestors] <- length(tree$tip.label)
    return(unname(which.min(sums)))
}
bind.replace <- function(backbone, donor, replacing.tip.label){

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#Loading a package
library(pez)

#Building a tree
tree <- read.tree("Vascular_Plants_rooted.dated.tre") #file from http://datadryad.org/resource/doi:10.5061/dryad.63q27
species <- c("Quercus_notreal","Pinus_notreal","Blasia_notreal","Riccia_notreal")
tree <- congeneric.merge(tree, species)
tree <- drop.tip(tree, setdiff(tree$tip.label, species))

#Calculating PD

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#!/usr/bin/ruby
require 'optparse'
require 'json'
require 'open-uri'
require 'nokogiri'

############################
# ARGUMENT PARSING #########
############################
options = {}