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lglasso

https://github.com/jiezhou-2/lglasso

Science Score: 39.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 1 DOI reference(s) in README
  • ○
    Academic publication links
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (14.4%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Basic Info
  • Host: GitHub
  • Owner: jiezhou-2
  • Language: R
  • Default Branch: main
  • Size: 2.92 MB
Statistics
  • Stars: 1
  • Watchers: 0
  • Forks: 0
  • Open Issues: 1
  • Releases: 0
Created over 4 years ago · Last pushed 11 months ago
Metadata Files
Readme

README.Rmd 

---
output: github_document
---



```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

# lglasso



[![CRAN status](https://www.r-pkg.org/badges/version/lglasso)](https://CRAN.R-project.org/package=lglasso)



 

The previous version implementes the algorithms proposed in *Zhou et al. (2024)*,  which aims to estimate the high-dimensional networks  from longitudinal data using Gassian grapical models. Though the overarching goal of the package is the same, i.e., explore the possible associations between high-dimensional data to  improve the estimations of networks. this updated version add three important  functionalities, which are

(1) Estimation of heterogeneous networks for longitudinal data. The models in previous version (i.e., in the 2024 paper) assumed a stationary process for the longitudinal data. This might not be the case in many situations, e.g, the antibody network before and after vaccination,  metabolite network before and after the initialization of the treatment for cancer patients.  In this version of *lglasso*, the function *lglasso* are extended to accommodate such important scenarios.   

(2) Extension to general clustered data. This extension is motivated by our study of metabolome data in different tissues of mice. We have 
the metabolome data in colon, ileum,  portal blood peripheral blood from same mouse. It has been observed that these data are closely correlated which is not a surprise since they are from same mouse.  When it comes to interaction networks, this package extends the algorithms for longitudinal data to such general clustered data and can estimate both general and tissue-wise networks.   


(3) This version provide function  *CVlglasso* to facilitate the selection of tuning parameter. 




## Installation

You can install the development version of lglasso from [GitHub](https://github.com/) with:

First, install the package remotes:

```
install.packages("remotes")
```

Then install lglasso :

```
remotes::install_github("jiezhou-2/lglasso", ref ="main") 
```



## How to use

 Please see [package website](https://jiezhou-2.github.io/lglasso/). 
 
 
**Reference** 

[1] Zhou J, Gui J, Viles WD, Chen H, Li S, Madan JC, Coker MO, Hoen AG. Identifying stationary microbial interaction networks based on irregularly spaced longitudinal 16S rRNA gene sequencing data. Front Microbiomes. 2024;3:1366948. doi: 10.3389/frmbi.2024.1366948. Epub 2024 Jun 2. PMID: 40687607; PMCID: PMC12276884.

[2] Friedman J., Hastie T., Tibshirani R. (2019)  Graphical Lasso: Estimation of Gaussian Graphical Models, Version: 1.11.


[3] Matt Galloway (2025),  CVglasso: Lasso Penalized Precision Matrix Estimation, version 1.0

Owner

  • Name: Jie Zhou
  • Login: jiezhou-2
  • Kind: user
  • Location: Lebanon, New Hampshire
  • Company: Dartmouth College

Biostatistician in Dartmouth College

GitHub Events

Total
  • Watch event: 1
  • Push event: 30
  • Gollum event: 1
  • Create event: 1
Last Year
  • Watch event: 1
  • Push event: 30
  • Gollum event: 1
  • Create event: 1

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 12
  • Total Committers: 1
  • Avg Commits per committer: 12.0
  • Development Distribution Score (DDS): 0.0
Past Year
  • Commits: 2
  • Committers: 1
  • Avg Commits per committer: 2.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
jiezhou-2 c****t@g****m 12

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 1
  • Total pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Total issue authors: 1
  • Total pull request authors: 0
  • Average comments per issue: 0.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • jiezhou-2 (1)
Pull Request Authors
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 203 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 1
  • Total maintainers: 1
cran.r-project.org: lglasso

Longitudinal Graphical Lasso

  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 203 Last month
Rankings
Forks count: 28.8%
Dependent packages count: 29.8%
Stargazers count: 35.2%
Dependent repos count: 35.5%
Average: 42.3%
Downloads: 82.1%
Maintainers (1)
chowstat@gmail.com
Last synced: 11 months ago

Dependencies

DESCRIPTION cran
  • R >= 2.10 depends
  • Rcpp >= 1.0.7 imports
  • glasso * imports
  • stats * imports
  • knitr * suggests
  • rmarkdown * suggests