miss.phylo.d: Phylogenetic signal in missing data

In sensiPhy: Sensitivity Analysis for Comparative Methods

Description

Calculates D statistic (Fritz & Purvis 2010), a measure of phylogenetic signal, for missing data. Missingness is recoded into a binary variable (1=missing, 0=non missing). This function is an adaptation of phylo.d for missing data.

Usage

miss.phylo.d(data, phy, ...)

Arguments

data	Data frame containing species traits with species as row names.
phy	A phylogeny (class 'phylo', see ?ape).
...	Further arguments to be passed to phylo.d.

Details

This function builds on phylo.d to calculate a phylogenetic signal in missing data. The variable of interest, usually a trait, is recoded into a binary variable (1=missing data, 0=non missing data). Then the phylo.d function tests the estimated D value for significant departure from both random association and the clumping expected under a Brownian evolution threshold model (Fritz & Purvis, 2010).

Output can be visualised using print() and plot()

Value

The function miss.phylo.d returns an object of class "phylo.d" with the following components, for complete list of arguments see phylo.d :

DEstimate: The estimated D value

Pval1: A p value, giving the result of testing whether D is significantly different from one

Pval0: A p value, giving the result of testing whether D is significantly different from zero The function also prints the percentage of missing data per variable in the dataset.

Author(s)

Caterina Penone & Gustavo Paterno

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

Fritz, S. A. and Purvis, A. (2010). Selectivity in mammalian extinction risk and threat types: a new measure of phylogenetic signal strength in binary traits. Conservation Biology, 24(4):1042-1051.

David Orme, Rob Freckleton, Gavin Thomas, Thomas Petzoldt, Susanne Fritz, Nick Isaac and Will Pearse (2013). caper: Comparative Analyses of Phylogenetics and Evolution in R. R package version 0.5.2. https://CRAN.R-project.org/package=caper

Examples

# Load caper:
library(caper)
# Load data
data(primates)
data<-alien$data
phy=alien$phy[[1]]

# Test phylogenetic signal for missing data:
sexNAsig <- miss.phylo.d(data,phy,binvar=homeRange)
print(sexNAsig)
plot(sexNAsig)

massNAsig <- miss.phylo.d(data,phy,binvar=adultMass)
print(massNAsig)
plot(massNAsig)

Example output

Loading required package: ape
Loading required package: phylolm
Loading required package: ggplot2
sh: 1: cannot create /dev/null: Permission denied
sh: 1: cannot create /dev/null: Permission denied
Loading required package: MASS
Loading required package: mvtnorm
[1] "Percentage of missing data in traits:"
   family adultMass  gestaLen homeRange   SD_mass  SD_gesta  SD_range 
     0.00      2.13      9.57     44.68      2.13      9.57     44.68 

Calculation of D statistic for the phylogenetic structure of a binary variable

  Data :  data
  Binary variable :  homeRange
  Counts of states:  0 = 52
                     1 = 42
  Phylogeny :  phy
  Number of permutations :  1000

Estimated D :  0.9424949
Probability of E(D) resulting from no (random) phylogenetic structure :  0.307
Probability of E(D) resulting from Brownian phylogenetic structure    :  0

[1] "Percentage of missing data in traits:"
   family adultMass  gestaLen homeRange   SD_mass  SD_gesta  SD_range 
     0.00      2.13      9.57     44.68      2.13      9.57     44.68 

Calculation of D statistic for the phylogenetic structure of a binary variable

  Data :  data
  Binary variable :  adultMass
  Counts of states:  0 = 92
                     1 = 2
  Phylogeny :  phy
  Number of permutations :  1000

Estimated D :  0.9256113
Probability of E(D) resulting from no (random) phylogenetic structure :  0.404
Probability of E(D) resulting from Brownian phylogenetic structure    :  0.248

sensiPhy documentation built on April 14, 2020, 7:15 p.m.