Package: sparseSEM 4.0
Anhui Huang
sparseSEM: Elastic Net Penalized Maximum Likelihood for Structural Equation Models with Network GPT Framework
Provides elastic net penalized maximum likelihood estimator for structural equation models (SEM). The package implements `lasso` and `elastic net` (l1/l2) penalized SEM and estimates the model parameters with an efficient block coordinate ascent algorithm that maximizes the penalized likelihood of the SEM. Hyperparameters are inferred from cross-validation (CV). A Stability Selection (STS) function is also available to provide accurate causal effect selection. The software achieves high accuracy performance through a `Network Generative Pre-trained Transformer` (Network GPT) Framework with two steps: 1) pre-trains the model to generate a complete (fully connected) graph; and 2) uses the complete graph as the initial state to fit the `elastic net` penalized SEM.
Authors:
sparseSEM_4.0.tar.gz
sparseSEM_4.0.tar.gz(r-4.5-noble)sparseSEM_4.0.tar.gz(r-4.4-noble)
sparseSEM_4.0.tgz(r-4.4-emscripten)sparseSEM_4.0.tgz(r-4.3-emscripten)
sparseSEM.pdf |sparseSEM.html✨
sparseSEM/json (API)
| # Install 'sparseSEM' in R: |
| install.packages('sparseSEM', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 1 years agofrom:e5005a0470. Checks:OK: 1 WARNING: 1. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Aug 26 2024 |
| R-4.5-linux-x86_64 | WARNING | Aug 26 2024 |
Exports:elasticNetSEMelasticNetSEMcvelasticNetSEMpointenSEM_stability_selectionenSEM_stability_selection_parallelenSEM_STSlassoSEM
Dependencies:
Elastic Net Enabled Sparse-Aware Maximum Likelihood for Structural Equation Models in Inferring Gene Regulatory Networks
Rendered fromsparseSEM.Rmdusingknitr::rmarkdownon Aug 26 2024.Last update: 2023-08-09
Started: 2023-04-21
Elastic Net Penalized Structural Equation Models
Rendered fromNetwork-Inference-via-sparseSEM.Rmdusingknitr::rmarkdownon Aug 26 2024.Last update: 2023-08-09
Started: 2023-06-11
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| sparseSEM: Elastic Net Penalized Maximum Likelihood for Structural Equation Models with Network GPT Framework | sparseSEM-package sparseSEM |
| True network edges | B |
| The Elastic Net penalized SEM with Network GPT Framework | elasticNetSEM |
| The Elastic Net penalty for SEM with user supplied (alphas, lambdas) for grid search | elasticNetSEMcv |
| The Elastic Net penalty for SEM | elasticNetSEMpoint |
| Stability Selection for the Elastic Net penalized SEM | enSEM_stability_selection |
| Parallel Stability Selection for the Elastic Net penalized SEM | enSEM_stability_selection_parallel |
| The Lasso penalty for SEM | lassoSEM |
| Missing Network Node dependent variable data | Missing |
| Genotype matrix | X |
| Gene expression matrix | Y |
| Yeast cis-QTL Gene Regulatory Network Dataset | yeast cisQTL GRN |