View prt_alone_v1.R
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
View birthdeath_treemodel.R
# 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/
#######################################################
View R package installs
install.packages("devtools")
library(devtools)
install_github("nmatzke/rexpokit")
install.packages("phytools")
library(phytools)
install.packages("geomorph")
install.packages("BioGeoBEARS")
install.packages("plot3D")
View phylo_vs_cladogram.R
# 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)
View Beast2_GeneralSubstitutionModel_v1.R
#######################################################
# 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
View data_frame_utilities_v1.R
#######################################################
# 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).
#######################################################
View birthdeath_example
# 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=""))
View Nicks_packages
# 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)
View num_unobservable_patterns_v2.R
#######################################################
# Calculating the number of unobservable site patterns
# for the Mk-parsimony-informative ascertainment bias
# correction
#
# by Nick Matzke, 2015-2016
#
# Free to re-use; we are preparing an ms on this issue,
# please email nick.matzke@anu.edu.au if interested.
#
View _genericR_v1.R
# =============================================
# genericR_v1.R: many useful utility functions
# for R
#
# by Nick Matzke
# Copyright 2011-infinity
# matzkeATberkeley.edu
# January 2011
#
# Please link/cite if you use this, email me if you have