PTMN: Plant Trait Multilayer Network Analysis

In MultiTraits: Analyzing and Visualizing Multidimensional Plant Traits

Plant Trait Multilayer Network Analysis

Description

Constructs a phylogenetic trait multilayer network by calculating correlations between traits while accounting for phylogenetic relationships. The function creates a network where nodes represent traits organized into different layers, and edges represent significant correlations between traits.

Usage

PTMN(
  traits_matrix,
  layers_list,
  rThres = 0.2,
  pThres = 0.05,
  method = "pearson",
  phylo_correction = FALSE,
  phylo_tree = NULL
)

Arguments

traits_matrix	A data frame or matrix containing trait values where rows represent species and columns represent traits. Row names should match the tip labels in the phylogenetic tree when phylogenetic correction is used.
layers_list	A named list where each element contains the names of traits belonging to that layer. Names of the list elements represent layer names.
rThres	Numeric. Correlation threshold for filtering weak correlations. Correlations with absolute values below this threshold are set to zero. Default is 0.2.
pThres	Numeric. P-value threshold for statistical significance after FDR correction. Correlations with p-values above this threshold are excluded. Default is 0.05.
method	Character. Correlation method to use. Either "pearson" or "spearman". Default is "pearson".
phylo_correction	Logical. Whether to apply phylogenetic correction using phylogenetic independent contrasts. Default is FALSE.
phylo_tree	A phylo object from the ape package. Required when phylo_correction = TRUE. Should contain all species present in traits_matrix.

Details

The function performs the following steps:

1. Validates input parameters and data consistency

2. Calculates correlation matrix using standard methods or phylogenetic independent contrasts

3. Filters correlations based on correlation and p-value thresholds

4. Applies FDR correction to p-values

5. Constructs an igraph network object

6. Maps traits to their respective layers

7. Returns edge list with layer information

When phylogenetic correction is enabled, the function uses phylogenetic independent contrasts to account for the non-independence of species data due to shared evolutionary history.

Value

A data frame containing the network edges with the following columns:

• node.from: Name of the source trait

• layer.from: Layer name of the source trait

• node.to: Name of the target trait

• layer.to: Layer name of the target trait

• correlation: Correlation coefficient between the traits

Returns an empty data frame with the same structure if no significant correlations are found.

Examples

## Not run: 
# Load example data
data(forest_invader_tree)
data(forest_invader_traits)
traits <- forest_invader_traits[, 6:73]

# Define trait layers
layers <- list(
  shoot_dynamics = c("LeafDuration", "LeafFall50", "LeafRate_max",
                     "Chl_shade50", "LAgain", "FallDuration",
                     "LeafOut", "Chl_sun50", "EmergeDuration",
                     "LeafTurnover"),
  leaf_structure = c("PA_leaf", "Mass_leaf", "Lifespan_leaf",
                     "Thick_leaf", "SLA", "Lobe", "LDMC",
                     "Stomate_size", "Stomate_index"),
  leaf_metabolism = c("J_max", "Vc_max", "Asat_area", "CC_mass",
                      "LSP", "AQY", "CC_area", "Rd_area",
                      "Asat_mass", "WUE", "Rd_mass", "PNUE"),
  leaf_chemistry = c("N_area", "Chl_area", "DNA", "Phenolics",
                     "Cellulose", "N_mass", "N_litter", "Chl_ab",
                     "Chl_mass", "N_res", "C_litter", "C_area",
                     "C_mass", "Ash", "Lignin", "Solubles",
                     "Decomp_leaf", "Hemi"),
  root = c("NPP_root", "SS_root", "SRL", "RTD", "RDMC",
           "NSC_root", "Decomp_root", "Starch_root",
           "C_root", "N_root", "Lignin_root"),
  stem = c("Latewood_diam", "Metaxylem_diam", "Earlywood_diam",
           "NSC_stem", "Vessel_freq", "SS_stem", "Cond_stem",
           "Starch_stem")
)
# Run PTMN analysis without phylogenetic correction
PTMN(traits, layers_list = layers, method = "pearson")

# Run PTMN analysis with phylogenetic correction
PTMN(traits, layers_list = layers, method = "pearson",
     phylo_correction = TRUE, phylo_tree = forest_invader_tree)

## End(Not run)

MultiTraits documentation built on March 22, 2026, 9:06 a.m.