tree_physig: Phylogenetic uncertainty - Phylogenetic signal
In sensiPhy: Sensitivity Analysis for Comparative Methods

Description Usage Arguments Details Value Note Author(s) References See Also Examples

Performs phylogenetic signal estimates evaluating uncertainty in trees topology.

tree_physig(
  trait.col,
  data,
  phy,
  n.tree = "all",
  method = "K",
  track = TRUE,
  ...
)

`trait.col`	The name of a column in the provided data frame with trait to be analyzed (e.g. "Body_mass").
`data`	Data frame containing species traits with row names matching tips in `phy`.
`phy`	A phylogeny (class 'phylo') matching `data`.
`n.tree`	Number of times to repeat the analysis with n different trees picked randomly in the multiPhylo file. (If `n.tree` = "all", phylogenetic signal will be estimated among the all set of trees provided in `phy`)
`method`	Method to compute signal: can be "K" or "lambda".
`track`	Print a report tracking function progress (default = TRUE)
`...`	Further arguments to be passed to `phylosig`

This function estimates phylogenetic signal using phylosig to n trees, randomly picked in a multiPhylo file.

Output can be visualised using sensi_plot.

The function tree_physig returns a list with the following components:

Trait: Column name of the trait analysed

data: Original full dataset

tree.physig.estimates: Three number, phylogenetic signal estimate (lambda or K) and the p-value for each run with a different phylogenetic tree.

N.obs: Size of the dataset after matching it with tree tips and removing NA's.

stats: Main statistics for phylogenetic estimates.CI_low and CI_high are the lower and upper limits of the 95

The argument "se" from phylosig is not available in this function. Use the argument "V" instead with intra_physig to indicate the name of the column containing the standard deviation or the standard error of the trait variable instead.

Caterina Penone & Gustavo Paterno

Paterno, G. B., Penone, C. Werner, G. D. A. sensiPhy: An r-package for sensitivity analysis in phylogenetic comparative methods. Methods in Ecology and Evolution 2018, 9(6):1461-1467

Donoghue, M.J. & Ackerly, D.D. (1996). Phylogenetic Uncertainties and Sensitivity Analyses in Comparative Biology. Philosophical Transactions: Biological Sciences, pp. 1241-1249.

Blomberg, S. P., T. Garland Jr., A. R. Ives (2003) Testing for phylogenetic signal in comparative data: Behavioral traits are more labile. Evolution, 57, 717-745.

Pagel, M. (1999) Inferring the historical patterns of biological evolution. Nature, 401, 877-884.

Kamilar, J. M., & Cooper, N. (2013). Phylogenetic signal in primate behaviour, ecology and life history. Philosophical Transactions of the Royal Society B: Biological Sciences, 368: 20120341.

phylosig, tree_phylm,sensi_plot

# Load data:
data(alien)
alien.data<-alien$data
alien.phy<-alien$phy
# Logtransform data
alien.data$logMass <- log(alien.data$adultMass) 
# Run sensitivity analysis:
tree <- tree_physig(trait.col = "logMass", data = alien.data, 
phy = alien.phy, n.tree = 10)
summary(tree)
sensi_plot(tree)
sensi_plot(tree, graphs = 1)
sensi_plot(tree, graphs = 2)