Package: PathoFMPred
Type: Package
Title: Tumour Feature Models from Pathology Representations
Version: 0.1.0
URL: https://github.com/tkcaccia/PathoFMPred
BugReports: https://github.com/tkcaccia/PathoFMPred/issues
Authors@R: c(
    person("Aamilah", "Ismail", role = "aut"),
    person("Martin", "Ocharo", role = "aut"),
    person("Giulia", "Canarutto", role = "aut"),
    person("Moussa Kassim", "Mohamed", role = "aut", email = "moussa.kassim@icgeb.org"),
    person("Dalia", "Ahmed", role = "aut", email = "dalia.ahmed@icgeb.org"),
    person("Brendon", "Price", role = "aut"),
    person("Dupe", "Ojo", role = "aut", email = "dupe.ojo@icgeb.org"),
    person("Ekene Emmanuel", "Nweke", role = "aut"),
    person("Alessia", "Vignoli", role = "aut",
      email = "vignoli@cerm.unifi.it"),
    person("Silvano", "Piazza", role = "aut"),
    person("Dinesh", "Gupta", role = "aut"),
    person("Leonardo", "Tenori", role = "aut",
      email = "tenori@cerm.unifi.it"),
    person("Stefano", "Cacciatore", role = c("aut", "cre"),
      email = "tkcaccia@gmail.com")
  )
Description: Builds and applies portable cancer-specific partial least
        squares (PLS) regression and partial least squares with linear
        discriminant analysis (PLS-LDA) model collections from
        pathology foundation-model representations. Feature and outcome
        tables are linked by explicit patient identifiers, repeated
        slide rows are pooled at patient level, and model development
        uses nested cross-validation before final fitting. The source
        package contains no fitted foundation-model parameters,
        embeddings, patient-level data, or atlas registry. Users may
        download a separately licensed, checksum-verified Prov-GigaPath
        collection after installation, or load authorized collections
        from local files. Outputs are research estimates without
        external-validation or clinical-use claims. The methods build
        on Wold et al. (2001) <doi:10.1016/S0169-7439(01)00155-1> and
        Barker and Rayens (2003) <doi:10.1002/cem.785>.
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 4.6.0)
Imports: digest, fastPLS (>= 0.4), ggplot2, rmarkdown, stats, utils
Suggests: knitr, testthat (>= 3.0.0)
VignetteBuilder: knitr
Config/testthat/edition: 3
Config/roxygen2/version: 8.1.0
Config/pak/sysreqs: cmake make libuv1-dev
Repository: https://tkcaccia.r-universe.dev
Date/Publication: 2026-10-26 10:22:07 UTC
RemoteUrl: https://github.com/tkcaccia/pathofmpred
RemoteRef: HEAD
RemoteSha: 154d3df487e8efe13810bdabb4a8376332e7550a
NeedsCompilation: no
Packaged: 2026-11-13 15:15:11 UTC; root
Author: Aamilah Ismail [aut],
  Martin Ocharo [aut],
  Giulia Canarutto [aut],
  Moussa Kassim Mohamed [aut],
  Dalia Ahmed [aut],
  Brendon Price [aut],
  Dupe Ojo [aut],
  Ekene Emmanuel Nweke [aut],
  Alessia Vignoli [aut],
  Silvano Piazza [aut],
  Dinesh Gupta [aut],
  Leonardo Tenori [aut],
  Stefano Cacciatore [aut, cre]
Maintainer: Stefano Cacciatore <tkcaccia@gmail.com>