josephwb

library(ape);

# like keep.tip, but you can keep internal nodes toooooo
keep.nodes <- function (phy, nds) {
  # stats
  Ntip <- length(phy$tip.label);
  NEWROOT <- Ntip + 1;
  Nnode <- phy$Nnode;
  hasNL <- !is.null(phy$node.label);
  

josephwb

require(phangorn);

# check the monophyletic status of every genus in the tree `phy`
check_genus_monophyly <- function (phy) {
    # get genera. assumes form: Genus_species_whatever
    gens <- sort(unique(sub("_.*", "", phy$tip.label)));
    n <- length(gens);
    cat("Checking ", n, " genera for monophyly status.\n", sep="");
    # the number of descendant tips of the MRCA. preallocate for monotypic genera
    ndec <- rep(1, n);

josephwb

#!/bin/bash

# report files greater than some size (default 100 MB)
# does so recursively starting at some dir (default pwd)

# to make executable, do:
# chmod +x find_large_files.sh

print_help () {
    echo "Recursively find all files larger than some size"

josephwb

# extract subtree induced from a set of tips
subtree.induced <- function (phy, tip) {
    if (!inherits(phy, "phylo")) {
        stop("object \"phy\" is not of class \"phylo\"");
    }
    Ntip <- length(phy$tip.label);
    
    # convert to indices if strings passed in
    if (is.character(tip)) {
        idx <- match(tip, phy$tip.label);

josephwb

# run from BEASTv1.8.*/native
# will compile and install into ../lib/

CC=gcc
CFLAGS=-O2 -funroll-loops
INCLUDES=-I${JAVA_HOME}/include/ -I${JAVA_HOME}/include/linux

all: libNucleotideLikelihoodCore.so libAminoAcidLikelihoodCore.so

.c.o:

josephwb

## written by:
# Joseph W. Brown (josephwb, @j0sephwb)
# Klaus Schliep (KlausVigo, @Klaus_Schlp)
get_mrca_fast <- function(phy, tip) {
    if (!inherits(phy, "phylo")) {
        stop('object "phy" is not of class "phylo"');
    }
    if (length(tip) < 2) {
        return(NULL);
    }

josephwb

#NEXUS

[ *** NOTE (JWB) *** 1st character (all 0, except Dimorphodon_macronyx who was missing the char) in original matrix (Supp. Info. pdf) was a dummy character because TNT is zero-indexed?]
[ It has been deleted here so char indices of 'ordered' list line up. So this martix has 457 chars, while the (incorrect) published matrix has 458.]

Begin data;
Dimensions ntax=75 nchar=457;
[Format Datatype=Standard Missing=? Gap=-;] [MRBAYES]
Format Datatype=Standard SYMBOLS="0 1 2 3 4" Missing=? Gap=-; [PAUP]
MATRIX

josephwb

## Simple makefile to compile BayesTraitsv3 ##
#
# Program info:
# BayesTraits V3.0 (Mar 14 2017)
# Mark Pagel and Andrew Meade
# www.evolution.reading.ac.uk
#
# source: http://www.evolution.rdg.ac.uk/BayesTraitsV3/BayesTraitsV3.html
#
# By default, compiles serial version. To compile threaded version, do:

josephwb

# gist copied from: https://gist.github.com/emhart/89fd49401bc9795d790ef47ca638726f

# for Ubuntu 18, had to do:
# sudo apt-get install portaudio19-dev
# before installing audio package

# might have to install these packages first

library("dplyr");
library("audio");

josephwb

/* Compile with:
 *    g++ -Wall -std=c++11 dummy.cpp -o dummy -O
 * Run as:
 *    ./dummy -s *.txt
 */

#include <iostream>
#include <string>
#include <fstream>
#include <vector>