Package 'phylosignalDB'

Title: Explore Phylogenetic Signals Using Distance-Based Methods
Description: A unified method, called M statistic, is provided for detecting phylogenetic signals in continuous traits, discrete traits, and multi-trait combinations. Blomberg and Garland (2002) <doi:10.1046/j.1420-9101.2002.00472.x> provided a widely accepted statistical definition of the phylogenetic signal, which is the "tendency for related species to resemble each other more than they resemble species drawn at random from the tree". The M statistic strictly adheres to the definition of phylogenetic signal, formulating an index and developing a method of testing in strict accordance with the definition, instead of relying on correlation analysis or evolutionary models. The novel method equivalently expressed the textual definition of the phylogenetic signal as an inequality equation of the phylogenetic and trait distances and constructed the M statistic. Also, there are more distance-based methods under development.
Authors: Liang Yao [aut, cre], Ye Yuan [aut]
Maintainer: Liang Yao <dylanyao@126.com>
License: GPL (>= 3)
Version: 0.2.2
Built: 2025-02-17 06:01:40 UTC
Source: https://github.com/anonymous-eco/phylosignaldb

Help Index

Calculate Gower distance

Description

gower_dist() calculates Gower distance among observations or species.

Usage

gower_dist(x, type = list(), dist_format = c("matrix", "dist"))

Arguments

x

A data frame. The columns usually represent trait data, and the row names are species names.
type

A list for specifying the variable types of the columns in x. Default is numeric type. More details in cluster::daisy().
dist_format

The class of the return value. Default is "matrix".

Value

A matrix or dist object containing the Gower distance among the rows of x.

References

Gower, J.C. (1971) A general coefficient of similarity and some of its properties. Biometrics: 857-871.

Kaufman, L. & Rousseeuw, P.J. (1990) Finding Groups in Data: An Introduction to Cluster Analysis. Wiley, New York.

See Also

cluster::daisy() which this function wraps.

Examples

data("turtles")
# Continuous trait
trait_df <- data.frame(M1 = turtles$traits$M1, row.names = turtles$traits$specie)
trait_dist <- gower_dist(x = trait_df)

# Nominal discrete trait
trait_df <- data.frame(B1 = turtles$traits$B1, row.names = turtles$traits$specie)
trait_dist <- gower_dist(x = trait_df, type = list(factor = 1))

# Ordinal discrete trait
trait_df <- data.frame(CS1 = turtles$traits$CS1, row.names = turtles$traits$specie)
trait_dist <- gower_dist(x = trait_df, type = list(ordered = 1))

# Multi-trait Combinations
trait_df <- data.frame(turtles$traits[, c("M1", "M2", "M3", "M4", "M5")],
                       row.names = turtles$traits$specie)
trait_dist <- gower_dist(x = trait_df, type = list(factor = c("M4", "M5")))

Calculate M statistics after random permutations

Description

M_rand_perm calculates M statistic for trait(s) after randomly permuting the species names or tip labels in phylogeny. The M statistic is a unified method for detecting phylogenetic signals in continuous traits, discrete traits, and multi-trait combinations. Blomberg and Garland (2002) provided a widely accepted statistical definition of the phylogenetic signal, which is the "tendency for related species to resemble each other more than they resemble species drawn at random from the tree". The M statistic strictly adheres to the definition of phylogenetic signal, formulating an index and developing a method of testing in strict accordance with the definition, instead of relying on correlation analysis or evolutionary models. The novel method equivalently expressed the textual definition of the phylogenetic signal as an inequality equation of the phylogenetic and trait distances and constructed the M statistic.

Usage

M_rand_perm(
  trait_dist = NULL,
  phy = NULL,
  reps = 999,
  auto_multi2di = TRUE,
  cores = 1
)

Arguments

trait_dist

A distance object of class matrix or dist. Its row and column names should match the tip labels of the phylogenetic tree (phy). The functions gower_dist() and cluster::daisy() can be used to calculate distances using trait data.
phy

A phylogenetic tree of class phylo.
reps

An integer. The number of random permutations.
auto_multi2di

A logical switch, TRUE or FALSE. Default is TRUE, then function multi2di() in ape package will be called to make the phylogeney (tree) be dichotomous if the tree (phy) contains some polytomies.
cores

Number of cores to be used in parallel processing. Default is 1, indicating no parallel computation is performed. If set to 0, parallel computation is executed using parallel::detectCores() - 1 number of cores.

Value

A list object containing two components. Component ⁠$permuted⁠ is the vector of M values obtained after random permutation for reps times; component ⁠$observed⁠ is the value of M statistic obtained from the original input data.

References

Blomberg, S.P. & Garland, T., Jr (2002) Tempo and mode in evolution: phylogenetic inertia, adaptation and comparative methods. Journal of Evolutionary Biology, 15(6): 899-910.

See Also

M_stat() phylosignal_M()

Examples

data("turtles")
# Continuous trait
trait_df <- data.frame(M1 = turtles$traits$M1, row.names = turtles$traits$specie)
trait_dist <- gower_dist(x = trait_df)
M_rand_perm(trait_dist, turtles$phylo, reps = 99) # reps=999 better

# Nominal discrete trait
trait_df <- data.frame(B1 = turtles$traits$B1, row.names = turtles$traits$specie)
trait_dist <- gower_dist(x = trait_df, type = list(factor = 1))
M_rand_perm(trait_dist, turtles$phylo, reps = 99) # reps=999 better

# Ordinal discrete trait
trait_df <- data.frame(CS1 = turtles$traits$CS1, row.names = turtles$traits$specie)
trait_dist <- gower_dist(x = trait_df, type = list(ordered = 1))
M_rand_perm(trait_dist, turtles$phylo, reps = 99) # reps=999 better

# Multi-trait Combinations
trait_df <- data.frame(turtles$traits[, c("M1", "M2", "M3", "M4", "M5")],
                       row.names = turtles$traits$specie)
trait_dist <- gower_dist(x = trait_df, type = list(factor = c("M4", "M5")))
M_rand_perm(trait_dist, turtles$phylo, reps = 99) # reps=999 better

Calculate M statistic

Description

M_stat calculates the value of M statistic as a measurement of the strength of the phylogenetic signal for the trait(s). The trait(s) could be continuous, discrete, or multi-variable. Blomberg and Garland (2002) provided a widely accepted statistical definition of the phylogenetic signal, which is the "tendency for related species to resemble each other more than they resemble species drawn at random from the tree". The M statistic strictly adheres to the definition of phylogenetic signal, formulating an index and developing a method of testing in strict accordance with the definition, instead of relying on correlation analysis or evolutionary models. The novel method equivalently expressed the textual definition of the phylogenetic signal as an inequality equation of the phylogenetic and trait distances and constructed the M statistic.

Usage

M_stat(trait_dist = NULL, phy = NULL, auto_multi2di = TRUE)

Arguments

trait_dist

A distance object of class matrix or dist. Its row and column names should match the tip labels of the phylogenetic tree (phy). The functions gower_dist() and cluster::daisy() can be used to calculate distances using trait data.
phy

A phylogenetic tree of class phylo.
auto_multi2di

A logical switch, TRUE or FALSE. Default is TRUE, then function multi2di() in ape package will be called to make the phylogeney (tree) be dichotomous if the tree (phy) contains some polytomies.

Value

A value that lies between 0 and 1, inclusive.

References

Blomberg, S.P. & Garland, T., Jr (2002) Tempo and mode in evolution: phylogenetic inertia, adaptation and comparative methods. Journal of Evolutionary Biology, 15(6): 899-910.

See Also

M_rand_perm() phylosignal_M()

Examples

data("turtles")
# Continuous trait
trait_df <- data.frame(M1 = turtles$traits$M1, row.names = turtles$traits$specie)
trait_dist <- gower_dist(x = trait_df)
M_stat(trait_dist, turtles$phylo)

# Nominal discrete trait
trait_df <- data.frame(B1 = turtles$traits$B1, row.names = turtles$traits$specie)
trait_dist <- gower_dist(x = trait_df, type = list(factor = 1))
M_stat(trait_dist, turtles$phylo)

# Ordinal discrete trait
trait_df <- data.frame(CS1 = turtles$traits$CS1, row.names = turtles$traits$specie)
trait_dist <- gower_dist(x = trait_df, type = list(ordered = 1))
M_stat(trait_dist, turtles$phylo)

# Multi-trait Combinations
trait_df <- data.frame(turtles$traits[, c("M1", "M2", "M3", "M4", "M5")],
                       row.names = turtles$traits$specie)
trait_dist <- gower_dist(x = trait_df, type = list(factor = c("M4", "M5")))
M_stat(trait_dist, turtles$phylo)

Measure and test phylogenetic signal with M statistic

Description

phylosignal_M computes the M statistic for trait(s) and evaluates its statistical significance through a random permutation test. The M statistic is a unified method for detecting phylogenetic signals in continuous traits, discrete traits, and multi-trait combinations. Blomberg and Garland (2002) provided a widely accepted statistical definition of the phylogenetic signal, which is the "tendency for related species to resemble each other more than they resemble species drawn at random from the tree". The M statistic strictly adheres to the definition of phylogenetic signal, formulating an index and developing a method of testing in strict accordance with the definition, instead of relying on correlation analysis or evolutionary models. The novel method equivalently expressed the textual definition of the phylogenetic signal as an inequality equation of the phylogenetic and trait distances and constructed the M statistic.

Usage

phylosignal_M(
  trait_dist = NULL,
  phy = NULL,
  reps = 999,
  auto_multi2di = TRUE,
  output_M_permuted = FALSE,
  cores = 1
)

Arguments

trait_dist

A distance object of class matrix or dist. Its row and column names should match the tip labels of the phylogenetic tree (phy). The functions gower_dist() and cluster::daisy() can be used to calculate distances using trait data.
phy

A phylogenetic tree of class phylo.
reps

An integer. The number of random permutations.
auto_multi2di

A logical switch, TRUE or FALSE. Default is TRUE, then function multi2di() in ape package will be called to make the phylogeney (tree) be dichotomous if the tree (phy) contains some polytomies.
output_M_permuted

A logical switch, TRUE or FALSE. Default is FALSE. If this logical switch is set to TRUE, the returned list will include the vector of M values obtained after random permutations.
cores

Number of cores to be used in parallel processing. Default is 1, indicating no parallel computation is performed. If set to 0, parallel computation is executed using parallel::detectCores() - 1 number of cores.

Value

A list object containing two components. Component ⁠$permuted⁠ is the vector of M values obtained after random permutation for reps times; component ⁠$observed⁠ is the value of M statistic obtained from the original input data.

References

Blomberg, S.P. & Garland, T., Jr (2002) Tempo and mode in evolution: phylogenetic inertia, adaptation and comparative methods. Journal of Evolutionary Biology, 15(6): 899-910.

See Also

M_stat() M_rand_perm()

Examples

data("turtles")
# Continuous trait
trait_df <- data.frame(M1 = turtles$traits$M1, row.names = turtles$traits$specie)
trait_dist <- gower_dist(x = trait_df)
phylosignal_M(trait_dist, turtles$phylo, reps = 99) # reps=999 better

# Nominal discrete trait
trait_df <- data.frame(B1 = turtles$traits$B1, row.names = turtles$traits$specie)
trait_dist <- gower_dist(x = trait_df, type = list(factor = 1))
phylosignal_M(trait_dist, turtles$phylo, reps = 99) # reps=999 better

# Ordinal discrete trait
trait_df <- data.frame(CS1 = turtles$traits$CS1, row.names = turtles$traits$specie)
trait_dist <- gower_dist(x = trait_df, type = list(ordered = 1))
phylosignal_M(trait_dist, turtles$phylo, reps = 99) # reps=999 better

# Multi-trait Combinations
trait_df <- data.frame(turtles$traits[, c("M1", "M2", "M3", "M4", "M5")],
                       row.names = turtles$traits$specie)
trait_dist <- gower_dist(x = trait_df, type = list(factor = c("M4", "M5")))
phylosignal_M(trait_dist, turtles$phylo, reps = 99) # reps=999 better

Ecological Traits and Phylogeny of Turtles

Description

An ecological trait dataset for turtles. The dataset was derived from the recently published ReptTraits dataset (Oskyrko et al., 2024), extracting species classified under the major group Testudines (comprising 361 species). Only ecological traits with more than 50% of the species having trait records were retained. The phylogeny of turtles was derived by pruning from the maximum clade credibility tree with 288 tips provided in Thomson et al. (2021). Only those species that are present in both the ReptTraits dataset and the turtle phylogenetic tree were selected. Ultimately, the dataset comprised 240 species, encompassing 5 morphology traits, 2 behaviour traits, 2 life history traits, 5 habitat variables, and 2 variables concerning species conservation status.

Usage

turtles
data("turtles")

Format

turtles is a list object with 3 components:

traits

The ecological traits of turtles as an object of class data.frame/tibble.

phylo

The phylogeny of turtles as an object of class phylo.

traits_info

The full names and id of ecological traits.

More details in Oskyrko et al. (2024) and Thomson et al. (2021).

References

Oskyrko, O., Mi, C., Meiri, S. & Du, W. (2024) ReptTraits: a comprehensive dataset of ecological traits in reptiles. Scientific Data, 11(1): 243.

Thomson, R.C., Spinks, P.Q. & Shaffer, H.B. (2021) A global phylogeny of turtles reveals a burst of climate-associated diversification on continental margins. Proceedings of the National Academy of Sciences, 118(7): e2012215118.