ISPAT3D: Spatial Conditional Association Networks in Registered Tumor Volumes

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
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

Documentation:

Reference manual:	ISPAT3D.html , ISPAT3D.pdf
Vignettes:	Matched section-wise 2D networks (source, R code) A volumetric cell-density network (source, R code)

Downloads:

Package source:	ISPAT3D_0.3.1.tar.gz
Windows binaries:	r-devel: ISPAT3D_0.3.1.zip, r-release: ISPAT3D_0.3.1.zip, r-oldrel: ISPAT3D_0.3.1.zip
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

Linking:

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