addInformation.Rmd

---
title: "Extended Information"
output: html_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

## ASR

Method requires a phylogeny and trait information coded as values (no character names).  Method will automatically check if the trait data are discrete or independently and drop tips from the phylogeny which are not part of the trait dataset. Be cautious, missing species in your reconstruction has an influence on your ancestral reconstruction (CITATION).

## Conditions to run ASR

Trait should evolve independently from other non-tested traits.

## Recommended steps before running ASR

Ask Luke Harmon.

## Recommended steps after running ASR

Ask Brian O'Meara or test phylogenetic signal.

## Programs out of ARBOR which do similar analysis

1. Mesquite
2. ace function in the ape package in R
3. RevBayes

## Relevant literature

1. Ref 1
2. Ref 2