Package: cglasso 2.0.7

cglasso: Conditional Graphical LASSO for Gaussian Graphical Models with Censored and Missing Values

Conditional graphical lasso estimator is an extension of the graphical lasso proposed to estimate the conditional dependence structure of a set of p response variables given q predictors. This package provides suitable extensions developed to study datasets with censored and/or missing values. Standard conditional graphical lasso is available as a special case. Furthermore, the package provides an integrated set of core routines for visualization, analysis, and simulation of datasets with censored and/or missing values drawn from a Gaussian graphical model. Details about the implemented models can be found in Augugliaro et al. (2023) <doi:10.18637/jss.v105.i01>, Augugliaro et al. (2020b) <doi:10.1007/s11222-020-09945-7>, Augugliaro et al. (2020a) <doi:10.1093/biostatistics/kxy043>, Yin et al. (2001) <doi:10.1214/11-AOAS494> and Stadler et al. (2012) <doi:10.1007/s11222-010-9219-7>.

Authors:Luigi Augugliaro [aut, cre], Gianluca Sottile [aut], Ernst C. Wit [aut], Veronica Vinciotti [aut]

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cglasso.pdf |cglasso.html
cglasso/json (API)

# Install 'cglasso' in R:
install.packages('cglasso', repos = c('https://luigiaugugliaro.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Uses libs:
  • openblas– Optimized BLAS
  • fortran– Runtime library for GNU Fortran applications
Datasets:
  • MKMEP - Megakaryocyte-Erythroid Progenitors
  • MKMEP.Sim - Simulated data for the cglasso vignette
  • MM - The Rule of miRNA in Multiple Myeloma
  • MM.Sim - Simulated data for the cglasso vignette

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

1.32 score 21 scripts 375 downloads 29 exports 12 dependencies

Last updated 9 months agofrom:59a2f69c2a. Checks:OK: 9. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 17 2024
R-4.5-win-x86_64OKNov 17 2024
R-4.5-linux-x86_64OKNov 17 2024
R-4.4-win-x86_64OKNov 17 2024
R-4.4-mac-x86_64OKNov 17 2024
R-4.4-mac-aarch64OKNov 17 2024
R-4.3-win-x86_64OKNov 17 2024
R-4.3-mac-x86_64OKNov 17 2024
R-4.3-mac-aarch64OKNov 17 2024

Exports:cggmcggm.fitcglassocglasso.fitColMeanscolNamescolNames<-ColVarsdatacggmeventfit_matrixfunction2xygetGraphgetMatriximputeis.cglasso2igraphis.datacggmlowernprednrespQFunqqcnormrcggmrowNamesrowNames<-select_cglassoShowStructureto_graphupper

Dependencies:clicpp11glueigraphlatticelifecyclemagrittrMASSMatrixpkgconfigrlangvctrs

Readme and manuals

Help Manual

Help pageTopics
Conditional Graphical LASSO for Gaussian Graphical Models with Censored and Missing Valuescglasso-package
Akaike Information CriterionAIC AIC.cglasso
Bayesian Information CriterionBIC BIC.cglasso
Post-Hoc Maximum Likelihood Refitting of a Conditional Graphical Lassocggm
Conditional Graphical Lasso Estimatorcglasso
Extract Model Coefficientscoef coef.cglasso
Calculate Column Means and Vars of a "datacggm" ObjectColMeans ColVars
Create a Dataset from a Conditional Gaussian Graphical Model with Censored and/or Missing Valuesdatacggm
Dimensions of a "datacggm" Objectdim dim.datacggm
Dimnames of a "datacggm" Objectdimnames dimnames.datacggm dimnames<-.datacggm
Status Indicator Matrix from a ''datacggm'' Objectevent
Simulated data for the cglasso vignetteExample MKMEP.Sim MM.Sim
Extract Model Fitted Valuesfitted fitted.cglasso
Retrieve Graphs from a ''cglasso2igraph'' ObjectgetGraph
Retrieve Matrices ''Y'' and ''X'' from a ''datacggm'' ObjectgetMatrix
Histogram for a 'datacggm' Objecthist hist.datacggm
Imputation of Missing and Censored Valuesimpute
Is an Object of Class 'cglasso2igraph'?is.cglasso2igraph
Is an Object of Class 'datacggm'?is.datacggm
Lower and Upper Limits from a "datacggm" Objectlower upper
Megakaryocyte-Erythroid ProgenitorsMKMEP
The Rule of miRNA in Multiple MyelomaMM
Extract the Number of Observations/Responses/Predictors from a datacggm Objectnobs nobs.datacggm npred npred.datacggm nresp nresp.datacggm
Plot Method for a ''cggm'' Objectplot.cggm
Plot Method for ''cglasso'' Objectplot.cglasso
Plot Method for a cglasso2igraph Object"plot.cglasso2igraph
Plot for ''GoF'' Objectplot.GoF
Predict Method for cglasso and cggm Fitspredict predict.cggm predict.cglasso
Extract Q-FunctionQFun
Quantile-Quantile Plots for a 'datacggm' Objectqqcnorm
Simulate Data from a Conditional Gaussian Graphical Model with Censored and/or Missing Valuesrcggm
Extract Model Residualsresiduals residuals.cglasso
Row and Column Names of a "datacggm" ObjectcolNames colNames<- rowNames rowNames<-
Model Selection for the Conditional Graphical Lasso Estimatorselect_cglasso
Show Package StructureShowStructure
Summarizing cglasso and cggm Fitssummary.cglasso
Summarizing Objects of Class ''datacggm''summary.datacggm
Create Graphs from cglasso or cggm Objectsto_graph