Phylogenetic uncertainty - Phylogenetic signal

Performs phylogenetic signal estimates evaluating uncertainty in trees topology.

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

Arguments

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`

Value

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

Details

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

Output can be visualised using sensi_plot.

Note

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.

References

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.

Examples

# 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)
#> Warning: NA's in response or predictor, rows with NA's were removed
#> Warning: Some phylo tips do not match species in data (this can be due to NA removal) species were dropped from phylogeny or data
#> Used dataset has  92  species that match data and phylogeny
#> 
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summary(tree)
#> $Call
#> tree_physig(trait.col = "logMass", data = alien.data, phy = alien.phy, 
#>     n.tree = 10)
#> 
#> $Summary
#>             mean  CI_low CI_high     min     max
#> estimate 0.76469 0.55378 0.97560 0.14775 0.94925
#> pval     0.00120 0.00075 0.00165 0.00100 0.00300
#> 
sensi_plot(tree)
sensi_plot(tree, graphs = 1)
#> `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
sensi_plot(tree, graphs = 2)
#> `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.