nmatzke

import Pkg
using Pkg  # for Pkg.add, Pkg.PackageSpec

using DifferentialEquations
using Plots
using BenchmarkTools 	# for @benchmark
using LSODA          	# for lsoda()
#Pkg.resolve()

using Sundials # for CVODE_BDF() e.g.

nmatzke

########################################################
# Revising Chris Rackauckas's "exp_euler_test.jl" from
# Julia 0.6 so it works in Julia 1.1
########################################################
# 
# Original 0.6 code from:
# 
# ChrisRackauckas/exp_euler_test.jl
# https://gist.github.com/ChrisRackauckas/cf91f4575b0587a45c72620384612b82

nmatzke

require("ape")

# print tree in hierarchical format
#######################################################
# prt
#######################################################
#' Print tree in table format
#' 
#' Learning and using APE's tree structure can be difficult and confusing because much of the information is
#' implicit.  This function prints the entire

nmatzke

# Laying out the likelihood equation in ape::birthdeath
# Calculating LnL of a tree under a birth-death process

#######################################################
# Located in:
# /drives/GDrive/z_help/ClaSSE_LnLs/grok_classe_setup/
#######################################################

nmatzke

install.packages("devtools")
library(devtools)
install_github("nmatzke/rexpokit")

install.packages("phytools")
library(phytools)
install.packages("geomorph")
install.packages("BioGeoBEARS")

install.packages("plot3D")

nmatzke

# Simple setup of a human/chimp/etc. phylogeny
# by Nick Matzke

#######################################################
# Phylogeny versus cladogram
#######################################################

# Tree specification
newick_string = "((((human:6,chimp:6):1,gorilla:7):6,orang:13):5,gibbon:18);"
tr = read.tree(file="",text=string)

nmatzke

#######################################################
# Figuring out the Beast2 GeneralSubstitutionModel
#######################################################


# The Beast2 documentation says:
# 
# file:///Applications/BEAST_2.4.3/Beast2_XML_as_HTML_help/beast.evolution.substitutionmodel.GeneralSubstitutionModel.html

nmatzke

#######################################################
# These functions are some utilitys for dealing with
# annoying features of R's use of data.frames, e.g.
# the tendency for some functions to have something that 
# looks like a data.frame, but is actually a series of lists.
#
# Also, dfnums_to_numeric semi-intelligently converts
# columns with numeric data to numeric (rather than 
# factor or character).
#######################################################

nmatzke

# Example converting between 
# birth rate, death rate (speciation and extinction) 
# and 
# r (diversification rate) and epsilon (relative death rate)

library(ape)
library(BioGeoBEARS)

# Load the Psychotria tree
trfn = np(paste(addslash(extdata_dir), "Psychotria_5.2.newick", sep=""))

nmatzke

# Install optimx
install.packages("optimx", dependencies=TRUE, repos="http://cran.rstudio.com")

# Install BioGeoBEARS from CRAN 0-cloud:
#install.packages("BioGeoBEARS", dependencies=TRUE, repos="http://cran.rstudio.com")

# If default install for BioGeoBEARS doesn't work, install dependencies in this order, 
# then install BioGeoBEARS from source:
install.packages("Rcpp", dependencies=TRUE)
install.packages("RcppArmadillo", dependencies=TRUE)