Fits tumor-zone-specific conditional cell-density networks from registered three-dimensional multiplex imaging. An anisotropic Matern-3/2 Gaussian process is estimated per variable and zone using a Vecchia likelihood on spatially balanced anchors; predictions at all selected cells yield residual covariance sufficient statistics. Gaussian maximum likelihood then fits a shared-plus-zone factor covariance model. A matched section-wise planar fit uses the same selected cells and covariance estimator. This extends the spatially informed cell-density analysis of Bhadury et al. (2026) <doi:10.1038/s41598-026-35341-8>.
| Version: | 0.3.1 |
| Imports: | gpboost, graphics, stats, utils |
| Suggests: | data.table, knitr, rmarkdown, testthat (≥ 3.0.0) |
| Published: | 2026-09-27 |
| DOI: | 10.32614/CRAN.package.ISPAT3D (may not be active yet) |
| Author: | Sagnik Bhadury [aut, cre] |
| Maintainer: | Sagnik Bhadury <bhadury at umich.edu> |
| BugReports: | https://github.com/sagnikbhadury/ISPAT-3D/issues |
| License: | MIT + file LICENSE |
| URL: | https://github.com/sagnikbhadury/ISPAT-3D |
| NeedsCompilation: | no |
| Materials: | README |
| CRAN checks: | ISPAT3D results |
| Reference manual: | ISPAT3D.html , ISPAT3D.pdf |
| Vignettes: |
Matched section-wise 2D networks (source, R code) A volumetric cell-density network (source, R code) |
| Package source: | ISPAT3D_0.3.1.tar.gz |
| Windows binaries: | r-devel: not available, r-release: not available, r-oldrel: not available |
| macOS binaries: | r-release (arm64): ISPAT3D_0.3.1.tgz, r-oldrel (arm64): ISPAT3D_0.3.1.tgz, r-release (x86_64): ISPAT3D_0.3.1.tgz, r-oldrel (x86_64): ISPAT3D_0.3.1.tgz |
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