PTMN Module (Plant Trait Multilayer Networks):
Introduced a comprehensive new module for constructing, analyzing, and
visualizing plant trait multilayer networks. This module systematically
integrates multilayer network theory with plant functional trait
analysis and includes three core functions:
PTMN(): Constructs phylogenetic trait multilayer
networks where nodes represent traits organized into layers (e.g.,
organs or functional systems) and edges represent significant
correlations. It supports correlation thresholding, p-value filtering,
FDR correction, and optional phylogenetic correction using independent
contrasts.
PTMN_metrics(): Calculates node-level and global
network metrics for PTMNs, identifying hub traits and cross-layer
modules. Included metrics are interlayer degree, closeness, clustering
coefficient, edge density, path length, and modular association.
PTMN_plot(): Visualizes PTMNs with options for
standard and circular layouts, customizable node and edge aesthetics,
and layer/module highlighting. It clearly differentiates intralayer
edges (black) from interlayer edges (red).
Bug fixes
LHS_strategy_scheme(): Corrected an error in the
strategy description mapping. The trait sequence was previously
misinterpreted as a Leaf-Seed-Height order. The text descriptions in the
strategy column have now been fixed to accurately reflect the standard
Leaf-Height-Seed (L-H-S) framework.
MultiTraits 0.6.0
(2025-10-01)
New Features and Major
Improvements
PTN Module (Plant Trait Network): Functions in
the trait network module have been renamed from the TN_
prefix to PTN_ for consistency (e.g., PTN(),
PTN_metrics()). Functionality for phylogenetic correction
has been added, allowing PTN() and PTN_corr()
to account for species’ evolutionary relatedness during
analysis.
CSR Module: The module has been expanded with
the CSR_hodgson() function, implementing an alternative CSR
classification method based on Hodgson et al. (1999).
NPT Module: A discrete classification scheme has
been added to the Niche Periodic Table module.
Data: A new phylogenetic tree for the PFF
dataset (PFF_tree) has been included to support the new
phylogenetic correction capabilities.
Other minor improvements and documentation enhancements have been
made across the package.
Bug fixes
CSR_plot(): Removed the dependency on
the ggtern package (no longer maintained) and implemented
plotting using ggplot2 to ensure continued compatibility and improve
stability.
MultiTraits 0.5.0 (2025-4-20)
Bug fixes and minor
improvements
Modify the community detection algorithm of the TN_metrics function
to cluster_edge_betweenness
Modified TN function to support unweighted networks
MultiTraits 0.4.0 (2025-4-16)
Bug fixes and minor
improvements
Modified TN_metrics function to support unweighted networks
MultiTraits 0.3.0 (2025-2-21)
Infrastructure
Added unit testing infrastructure using testthat package
Added test coverage for core functions
Bug fixes and minor
improvements
Removed deprecated vegan::summary() call in NPT function in favor of
direct scores() method
MultiTraits 0.2.0
(2024-12-21)
Bug fixes and minor
improvements
Fixed bug where discrete scales could not map aesthetics only
consisting of NAs
Fixed spurious warnings from sec_axis() with
breaks = NULL.
Patterns and gradients are now also enabled in
geom_sf().
The default behaviour of resolution() has been reverted
to pre-3.5.0 behaviour. Whether mapped discrete vectors should be
treated as having resolution of 1 is controlled by the new
discrete argument.
Fixed bug in guide_bins() and
guide_coloursteps() where discrete breaks, such as the
levels produced by cut(), were ordered incorrectly.
Fixed calculation issues in CSR module
Resolved NaN errors in TN module
Optimized visualization effects across all modules (CSR, LHS, NPT,
TN)