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>.
| Version: | 0.1.0 |
| Depends: | R (≥ 4.6.0) |
| Imports: | digest, fastPLS (≥ 0.4), ggplot2, rmarkdown, stats, utils |
| Suggests: | knitr, testthat (≥ 3.0.0) |
| Published: | 2026-11-12 |
| DOI: | 10.32614/CRAN.package.PathoFMPred (may not be active yet) |
| 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 at gmail.com> |
| BugReports: | https://github.com/tkcaccia/PathoFMPred/issues |
| License: | MIT + file LICENSE |
| URL: | https://github.com/tkcaccia/PathoFMPred |
| NeedsCompilation: | no |
| Materials: | README, NEWS |
| CRAN checks: | PathoFMPred results |
| Reference manual: | PathoFMPred.html , PathoFMPred.pdf |
| Vignettes: |
PathoFMPred: building and using portable pathology models (source, R code) |
| Package source: | PathoFMPred_0.1.0.tar.gz |
| Windows binaries: | r-devel: not available, r-release: not available, r-oldrel: not available |
| macOS binaries: | r-release (arm64): not available, r-oldrel (arm64): not available, r-release (x86_64): not available, r-oldrel (x86_64): not available |
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