phylo.d.subset: Calculates the phylogenetic D statistic across clades within...

In caper: Comparative Analyses of Phylogenetics and Evolution in R

Description

Calculates the D value, a measure of phylogenetic signal in a binary trait, and tests the estimated D value for significant departure from both random association and the clumping expected under a Brownian evolution threshold model. Does this across clades within a phylogeny.

Usage

phylo.d.subset(data, phy, names.col, binvar, permut = 1000, rnd.bias=NULL, 
	           min.tips=1, max.tips=length(data$phy$tip.label), min.nodes=1, 
			   max.nodes=data$phy$Nnode, verbose=FALSE)
## S3 method for class 'phylo.d.subset'
print(x, ...)
## S3 method for class 'phylo.d.subset'
summary(object, ...)

Arguments

data	A 'comparative.data' or 'data.frame' object.
phy	An object of class 'phylo', required when data is not a 'comparative.data' object.
names.col	A name specifying the column in 'data' that matches rows to tips in 'phy', required when data is not a 'comparative.data' object.
binvar	The name of the variable in data holding the binary variable of interest.
permut	Number of permutations to be used in the randomisation test.
rnd.bias	An optional name of a variable in data holding probability weights to bias the generation of the random distribution. See 'destails'
verbose	Logical; do you want to know how many clades are being assessed, and see when each is being assessed?
min.tips	The minimum number of tips a clade should have for it to have a D value calculated. Defaults to 1 (i.e. no limit).
max.tips	The maximum number of species a clade should have for it to have a D value calculated. Defaults to the number of species in the whole phylogeny (i.e. no limit).
min.nodes	The minimum number of nodes a clade should have for it to have a D value calculated. Defaults to 1 (i.e. no limit).
max.nodes	The maximum number of nodes a clade should have for it to have a D value calculated. Defaults to the number of nodes in the whole phylogeny (i.e. no limit).
x	An object of class 'phylo.d.subset'
object	An object of class 'phylo.d.subset'
...	Further arguments to print and summary methods

Details

A wrapper function for phylo.d, calculating D values for clades within a given dataset. These clades can be filtered according to the number of species and nodes using the arguments above. See phylo.d for more details on the method itself.

Any clades for which there is no variation in the binary variable have NA values for all of the below slots.

Value

Returns an object of class 'phylo.d.subset', which is a list of the following:

raw	A list of the raw output from phylo.d for each clade
DEstimate	A vector of the estimated D values
Pval1	A vector of p values, giving the result of testing whether D is significantly different from one, for each clade
Pval0	A vector of p values, giving the result of testing whether D is significantly different from zero, for each clade
phy.depth	A numeric vector giving the age of the clade for which each value was calculated

Author(s)

Susanne Fritz ([e-mail]), Will Pearse and David Orme

References

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.

Examples

data(BritishBirds)
BritishBirds <- comparative.data(BritishBirds.tree, BritishBirds.data, binomial)
# Look at big clades only
## Not run: 
bigClades <- phylo.d.subset(BritishBirds, binvar=Red_list, verbose=TRUE, min.tips=10, min.nodes=5)
print(bigClades)

## End(Not run)

Example output

Loading required package: ape
Loading required package: MASS
Loading required package: mvtnorm

Calculating D values for  39  out of a possible  180 clades.......................................
Calculation of D statistic for the phylogenetic structure of a binary variable
...across multiple clades within a phylogeny

  Data :  BritishBirds.data
  Binary variable :  Red_list
  Phylogeny :  BritishBirds.tree
  Number of permutations :  1000

Estimated D values: 
 0.55595658  0.42911328 12.91723795 21.14955150  0.49496832  0.43260175  0.47042299  0.20089509  0.09091792  0.08912526  0.07356435 -0.10724895 -0.25914953 -0.17044891 -0.11097997 -0.08369418  0.44280862  1.38246215  1.46962888 -5.00282229 -0.59531720 -0.73430327 -0.49375444 -7.71674614  0.32500242  0.16387209  1.96999367  1.94025319  2.00827287  1.89703771  1.86410167  8.66339906  6.29379861  4.06390766  0.35995789  2.66958444 11.36074243 37.99137077  0.96840369
Probabilities of E(D) resulting from no (random) phylogenetic structure : 
0.021 0.388 0.069 0.107 0.046 0.078 0.078 0.357 0.432 0.429 0.459 0.593 0.687 0.619 0.585 0.569 0.339 0.136 0.205 0.925 0.664 0.700 0.566 0.410 0.414 0.446 0.000 0.001 0.036 0.052 0.075 0.037 0.052 0.069 0.443 0.045 0.000 0.000 0.366
Probabilities of E(D) resulting from Brownian phylogenetic structure    : 
0.002 0.191 0.778 0.731 0.003 0.001 0.001 0.005 0.002 0.000 0.000 0.001 0.000 0.021 0.019 0.039 0.177 0.628 0.567 0.000 0.126 0.079 0.288 0.527 0.237 0.224 0.962 0.949 0.801 0.801 0.778 0.779 0.742 0.658 0.478 0.880 0.876 0.881 0.438
Ages of clades                                                        : 
48.87067 31.48075 15.90036 10.73354 43.50966 38.40429 37.58275 34.31127 32.76279 26.05635 23.71699 23.14565 21.23208 17.42345 15.37542 14.92240 13.22074 11.35633  8.81296 20.40032 22.79944 21.03801 19.75306 19.24483 22.73886 19.90633 34.72796 34.34850 34.25345 27.22832 21.50751 14.93878 14.35418 11.65114 16.97445 32.97093 31.85343 31.62970 32.87979

caper documentation built on May 2, 2019, 4:49 p.m.