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micd

Multiple Imputation in Causal Graph Discovery

https://github.com/bips-hb/micd

Science Score: 23.0%

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    Found 4 DOI reference(s) in README
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    Links to: medrxiv.org, wiley.com
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    Low similarity (10.3%) to scientific vocabulary

Keywords

causal-discovery graphical-models multiple-imputation r-package
Last synced: 6 months ago · JSON representation

Repository

Multiple Imputation in Causal Graph Discovery

Basic Info
  • Host: GitHub
  • Owner: bips-hb
  • License: gpl-3.0
  • Language: R
  • Default Branch: master
  • Homepage:
  • Size: 342 KB
Statistics
  • Stars: 5
  • Watchers: 5
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Topics
causal-discovery graphical-models multiple-imputation r-package
Created over 7 years ago · Last pushed about 3 years ago
Metadata Files
Readme

README.md

Multiple Imputation for Causal Graph Discovery (micd)

Add-on to the R package pcalg for handling missing data in contrataint-based causal graph discovery. Supports continuous, discrete and mixed data. Two options are available: 1) gaussCItwd, disCItwd and mixedCItwd perform test-wise deletion, where missing observations are deleted as necessary on a test-by-test basis; 2) gaussMItest, disMItest and mixedMItest perform conditional independence tests on multiply imputed data. Each of these functions can be used as a plug-in to pcalg::skeleton, pcalg::pc or pcalg::fci.

Additionally, the package contains all functions required for replicating the analyses in Foraita et al. (2020).

Installation

Install the packages graph and RBGL from Bioconductor. Make sure that rtools is installed on your computer. Then, simply type in R to install micd

R devtools::install_github("bips-hb/micd") (Note: The latest micd was created using R 4.2.1)

References

Foraita R, Friemel J, Günther K, Behrens T, Bullerdiek J, Nimzyk R, Ahrens W, Didelez V (2020). Causal discovery of gene regulation with incomplete data. Journal of the Royal Statistical Society: Series A (Statistics in Society), 183(4), 1747-1775. URL https://rss.onlinelibrary.wiley.com/doi/10.1111/rssa.12565.

Foraita R, Witte J, Börnhorst C, Gwozdz W, Pala V, Lissner L, Lauria F, Reisch L, Molnár D, De Henauw S, Moreno L, Veidebaum T, Tornaritis M, Pigeot I, Didelez V. A longitudinal causal graph analysis investigating modifiable risk factors and obesity in a European cohort of children and adolescents. 2022; medRxiv 2022.05.18.22275036.

Witte J, Foraita R, Didelez V (2022). Multiple imputation and test-wise deletion for causal discovery with incomplete cohort data. Statistics in Medicine, https://doi.org/10.1002/sim.9535.

References for pcalg

Markus Kalisch, Martin Mächler, Diego Colombo, Marloes H. Maathuis, Peter Bühlmann (2012). Causal Inference Using Graphical Models with the R Package pcalg. Journal of Statistical Software, 47(11), 1-26. URL www.jstatsoft.org/v47/i11/.

Alain Hauser, Peter Bühlmann (2012). Characterization and greedy learning of interventional Markov equivalence classes of directed acyclic graphs. Journal of Machine Learning Research, 13, 2409-2464. URL https://www.jmlr.org/papers/v13/hauser12a.html.

Owner

  • Name: BIPS
  • Login: bips-hb
  • Kind: organization
  • Location: Bremen, Germany

Leibniz Institute for Prevention Research and Epidemiology

GitHub Events

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  • Watch event: 2
Last Year
  • Watch event: 2

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 1
  • Total pull requests: 5
  • Average time to close issues: 3 days
  • Average time to close pull requests: about 20 hours
  • Total issue authors: 1
  • Total pull request authors: 1
  • Average comments per issue: 2.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 5
  • 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
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Top Authors
Issue Authors
  • MichielBosma (1)
Pull Request Authors
  • jawitte (5)
Top Labels
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Packages

  • Total packages: 1
  • Total downloads:
    • cran 277 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 2
  • Total maintainers: 1
cran.r-project.org: micd

Multiple Imputation in Causal Graph Discovery

  • Versions: 2
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 277 Last month
Rankings
Stargazers count: 28.5%
Forks count: 28.8%
Dependent packages count: 29.8%
Average: 34.9%
Dependent repos count: 35.5%
Downloads: 51.9%
Maintainers (1)
foraita@leibniz-bips.de
Last synced: 6 months ago

Dependencies

DESCRIPTION cran
  • R >= 3.0.2 depends
  • mice * depends
  • pcalg * depends
  • RBGL * imports
  • Rfast * imports
  • methods * imports
  • stats * imports
  • utils * imports
  • Rgraphviz * suggests
  • nnet * suggests
  • ranger * suggests
  • testthat >= 3.0.0 suggests