POUMM

An R-package implementing the univariate Phylogenetic Ornstein-Uhlenbeck Mixed Model

https://github.com/venelin/poumm

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An R-package implementing the univariate Phylogenetic Ornstein-Uhlenbeck Mixed Model

README.Rmd

---
output: github_document
---



```{r, echo = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "README-"
)
```

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# The Phylogenetic Ornstein-Uhlenbeck Mixed Model
The Phylogenetic Ornstein-Uhlenbeck Mixed Model (POUMM) allows to estimate the phylogenetic heritability of a continuous trait, to test hypotheses of neutral evolution versus stabilizing selection, to quantify the strength of stabilizing selection, to estimate measurement error and to make predictions about the evolution of a phenotype and phenotypic variation in a population. The POUMM package provides an easy and efficient way to perform this variety of analyses on large macro-evolutionary or epidemic trees. It implements a fast-likelihood calculation algorithm enabling MCMC-sampling with millions of iterations within minutes on contemporary multiple core processors. The package provides functions for configuring the fit of the model and a number of standard generic functions such as logLik, plot, summary, allowing a visual and a statistical assessment of the goodness of fit. This is an important step before using the model fit to answer relevant biological questions.

# Using the R-package
Here is a quick example on how to use the package on a simulated tree and trait data:

```{r, results="hide", eval=FALSE, echo=TRUE}
# number of tips
N <- 500 

# phylogeny
tr <- ape::rtree(N)

# for the example, simulate trait values on the tree according to a POUMM model.
z <- rVNodesGivenTreePOUMM(
  tree = tr,   
  z0 = 0,      # fixed value at the root
  alpha = 2,   # selection strength of the OU process
  theta = 3,   # long term mean of the OU process
  sigma = 1,   # unit-time standard deviation of the OU process
  sigmae = 1   # standard deviation of the non-heritable component
)[1:N]         # only the values at the N tips will be available in reality

# A combined ML and MCMC fit of the model with default parameter settings.
fit <- POUMM(z, tr)

plot(fit)
summary(fit)
AIC(fit)
BIC(fit)
coef(fit)
logLik(fit)
fitted(fit)
plot(resid(fit))
abline(h=0)

# fit PMM to the same data and do a likelihood ratio test
fitPMM <- POUMM(z, tr)
lmtest::lrtest(fitPMM, fit)
```

For an introduction to the model parameters and the package, read the [User guide](https://venelin.github.io/POUMM/articles/UserGuide.html). More advanced topics, such as parametrizations and interpretations of the model fit are covered in the other package [vignettes](https://venelin.github.io/POUMM/articles/index.html) and in the package  help-pages, e.g. `?POUMM`, `?specifyPOUMM`, `?summary.POUMM`, `?plot.POUMM`.

# Installing the R-package
Read the section [Installing the POUMM R-package](https://venelin.github.io/POUMM/articles/UserGuide.html#Installing) in [Get started](https://venelin.github.io/POUMM/articles/UserGuide.html).

# Package source-code
The package source-code is available on [github](https://github.com/venelin/POUMM).

# Licence and copyright

Copyright 2015-2020 Venelin Mitov

Source code to POUMM is made available under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. POUMM is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for details.

# Package web-page
Check-out the package [web-page](https://venelin.github.io/POUMM/index.html) for the latest news and further documentation.

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