PNC (version 0.1.0)

pnc: Analyze Phylogenetic Niche Conservatism in Ecological Communities

Description

This function performs in-depth phylogenetic niche conservatism analysis for communities by quantifying phylogenetic signal in trait data using multiple statistical methods. The function integrates trait data preprocessing, phylogenetic tree manipulation, optional principal component analysis, and robust statistical testing to provide detailed insights into evolutionary constraints on trait evolution.

Usage

pnc(
  trait_data,
  phylo_tree,
  methods = "lambda",
  pca_axes = c("PC1", "PC2"),
  sig_levels = c(0.001, 0.01, 0.05),
  nsim = 1000,
  verbose = TRUE
)

Value

A data frame containing phylogenetic signal results

Arguments

trait_data

A data frame or matrix containing trait data with species as rows

phylo_tree

A phylogenetic tree object of class "phylo"

methods

Character vector specifying methods to use. Options: "lambda", "K"

pca_axes

Character vector specifying which PCA axes to include (e.g., c("PC1", "PC2"))

sig_levels

Numeric vector of significance levels for marking results

nsim

Number of permutations for significance testing

verbose

Logical indicating whether to show progress and warnings

References

Münkemüller, T., Lavergne, S., Bzeznik, B., Dray, S., Jombart, T., Schiffers, K. and Thuiller, W. (2012). How to measure and test phylogenetic signal. Methods in Ecology and Evolution, 3(4), 743-756. tools:::Rd_expr_doi("10.1111/j.2041-210X.2012.00196.x")

Examples

# \donttest{
#' # Load example data
data(BCI)
data(TRY)

# Extract trait data
sp <- colnames(BCI$com)
subtraits <- extract_traits(sp, TRY, rank = "species",
                            traits = c("LA", "LMA", "LeafN", "PlantHeight", "SeedMass", "SSD"))

# Calculate phylogenetic signal using Lambda method
pnc(subtraits, BCI$phy_species, methods = "lambda")

# Calculate without PCA analysis
pnc(subtraits, BCI$phy_species, methods = "lambda", pca_axes = NULL)
# }