Package: NetSurvProx
Type: Package
Title: 'NetSurvProx': Network-Based Survival Analysis via Proximal
        Methods
Version: 1.0.0
Authors@R: c(
  person("Maura", "Mecchi", , "maura.mecchi@unibas.it", c("aut", "cre")),
  person("Antonella", "Iuliano", , "antonella.iuliano@unibas.it", c("aut")))
Maintainer: Maura Mecchi <maura.mecchi@unibas.it>
Description: Introduces a novel network-constrained survival
    analysis framework for variable selection and parameter estimation in
    penalized survival models with convex penalties. The package extends two
    classical survival models, the Cox Proportional Hazards (PH) model and the
    Accelerated Failure Time (AFT) model, by incorporating prior biological
    knowledge from curated interaction networks (e.g., KEGG) into a
    double-penalty framework. The first penalty enforces variable selection
    through a LASSO penalty, while the second preserves gene-gene correlations
    by incorporating Laplacian-based constraints, ensuring that biologically
    relevant network structures are maintained. Using censored survival data,
    the method enables the identification of predictive biomarkers and pathways
    with potential relevance for target therapies. Model estimation is
    performed via proximal optimization algorithms combined with
    cross-validation for reliable tuning. To enhance interpretability,
    dedicated utility functions are implemented to consolidate results,
    yielding biologically coherent insights that can support personalized
    medicine and contribute to improved patient outcomes.
Depends: R (>= 4.3)
Imports: AnnotationDbi, curl, cvTools, dplyr, flexsurv, foreach,
        ggplot2, ggpubr, glmnet, grDevices, Hmisc, httr, igraph, magic,
        openxlsx, RColorBrewer, rmarkdown, survAUC, survival,
        survminer,
Suggests: knitr, org.Hs.eg.db, plotly, scales, sessioninfo, stringr,
        visNetwork
VignetteBuilder: knitr
License: GPL (>= 3)
Encoding: UTF-8
RoxygenNote: 7.3.3
LazyData: true
LazyDataCompression: bzip2
NeedsCompilation: no
Packaged: 2026-06-03 12:02:58 UTC; maura
Author: Maura Mecchi [aut, cre],
  Antonella Iuliano [aut]
Repository: CRAN
Date/Publication: 2026-06-09 06:50:02 UTC
Built: R 4.6.0; ; 2026-06-09 11:01:54 UTC; unix
