Phylogenetic Structural Equation Model

Applies phylogenetic comparative methods (PCM) and phylogenetic trait imputation using structural equation models (SEM), extending methods from Thorson et al. (2023) . This implementation includes a minimal set of features, to allow users to easily read all of the documentation and source code. PCM using SEM includes phylogenetic linear models and structural equation models as nested submodels, but also allows imputation of missing values. Features and comparison with other packages are described in Thorson and van der Bijl (2023) .

Structural Equation Modeling Tables

For confirmatory factor analysis ('CFA') and structural equation models ('SEM') estimated with the 'lavaan' package, this package provides functions to create model summary tables and model comparison tables for hypothesis testing. Tables can be produced in 'LaTeX', 'HTML', or comma separated variables ('CSV').

Network Structural Equation Modeling

The network structural equation modeling conducts a network statistical analysis on a data frame of coincident observations of multiple continuous variables [1]. It builds a pathway model by exploring a pool of domain knowledge guided candidate statistical relationships between each of the variable pairs, selecting the 'best fit' on the basis of a specific criteria such as adjusted r-squared value. This material is based upon work supported by the U.S. National Science Foundation Award EEC-2052776 and EEC-2052662 for the MDS-Rely IUCRC Center, under the NSF Solicitation: NSF 20-570 Industry-University Cooperative Research Centers Program [1] Bruckman, Laura S., Nicholas R. Wheeler, Junheng Ma, Ethan Wang, Carl K. Wang, Ivan Chou, Jiayang Sun, and Roger H. French. (2013) .

Piecewise Structural Equation Modelling

Conduct dsep tests (piecewise SEM) of a directed, or mixed, acyclic graph without latent variables (but possibly with implicitly marginalized or conditioned latent variables that create dependent errors) based on linear, generalized linear, or additive modelswith or without a nesting structure for the data. Also included are functions to do desp tests step-by-step,exploratory path analysis, and Monte Carlo X2 probabilities. This package accompanies Shipley, B, (2026).Cause and Correlation in Biology: A User's Guide to Path Analysis, StructuralEquations and Causal Inference (3rd edition). Cambridge University Press.

Identifiability of Linear Structural Equation Models

Provides routines to check identifiability of linear structural equation models and factor analysis models. The routines are based on the graphical representation of structural equation models.

Building and Estimating Structural Equation Models

A powerful, easy to use syntax for specifying and estimating complex Structural Equation Models. Models can be estimated using Partial Least Squares Path Modeling or Covariance-Based Structural Equation Modeling or covariance based Confirmatory Factor Analysis (Ray, Danks, and Valdez 2021 ).

Case Influence in Structural Equation Models

A set of tools for evaluating several measures of case influence for structural equation models.

Helper Functions for Structural Equation Modeling

An assortment of helper functions for doing structural equation modeling, mainly by 'lavaan' for now. Most of them are time-saving functions for common tasks in doing structural equation modeling and reading the output. This package is not for functions that implement advanced statistical procedures. It is a light-weight package for simple functions that do simple tasks conveniently, with as few dependencies as possible.

Spatially Explicit Structural Equation Modeling

Structural equation modeling is a powerful statistical approach for the testing of networks of direct and indirect theoretical causal relationships in complex data sets with inter-correlated dependent and independent variables. Here we implement a simple method for spatially explicit structural equation modeling based on the analysis of variance co-variance matrices calculated across a range of lag distances. This method provides readily interpreted plots of the change in path coefficients across scale.

Bootstrapping Helpers for Structural Equation Modelling

A collection of helper functions for forming bootstrapping confidence intervals and examining bootstrap estimates in structural equation modelling. Currently supports models fitted by the 'lavaan' package by Rosseel (2012) .