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
NeedsCompilation: no
Packaged: 2026-10-27 08:40:32 UTC; stefano
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>
Repository: CRAN
Date/Publication: 2026-11-12 11:20:08 UTC
