R Observatory: Metrics for spruce version 0.99.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

This package was removed from CRAN on 2022-12-05. Its history is shown below.

Reason: issues were not corrected despite reminders

Details below reflect version 0.99.1, its last release before removal.

spruce

0.99.1Package record

Spatial Random Effects Clustering of Single Cell Data

0packages depend

–downloads / year

–test coverage

–flavors OK

Overview

About

Maintained by Carter AllenCRAN page ↗

Allows for identification of cell sub-populations within tissue samples using Bayesian multivariate mixture models with spatial random effects to account for a wide range of spatial gene expression patterns, as described in Allen et. al, 2021 doi:10.1101/2021.06.23.449615. Bayesian inference is conducted using efficient Gibbs sampling implemented using 'Rcpp'.

Install

R (source archive)

url <- "https://cran.r-project.org/src/contrib/Archive/spruce/spruce_0.99.1.tar.gz"
pkgFile <- "spruce_0.99.1.tar.gz"
download.file(url, pkgFile)
install.packages(pkgFile, type = "source", repos = NULL)

This package is no longer on CRAN, so install.packages() cannot fetch it by name. This downloads the last archived source (0.99.1) and builds it locally. Install its dependencies first, and note that building from source needs the usual compiler toolchain.

Health

CRAN checks

CRAN check results are not tracked yet.

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.99.1

READMENoVignettesNoNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 24includes a package overview page
Examples that run: 11%2 run in a plain check · 16 only when donttest examples are enabled (R CMD check --as-cran) · 1 never run
Exported functions with examples: 95%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

How these are measured

Downloads

Releases R versions

Daily download trend is not available in this view yet.

Compare downloads with other packages →

Also on276 r2u5 autocran

How downloads are counted

Dependencies

Declared dependencies

15 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.0

Imports (14)

Rcpp mvtnorm BayesLogit truncnormstatsigraph MCMCpack patchwork tidyr dplyr ggplot2 tidyselect Seurat rlang

LinkingTo (2)

Rcpp RcppArmadillo

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

–indirect (not tracked)

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (2)

Carter Allen

Author, Maintainer since 0.99.1 (2022)

Dongjun Chung

Author

Releases (1)

R
R 4.3.0 released · 2023-04-21
archivedRemoved from CRAN
2022-12-05
issues were not corrected despite reminders
R
R 4.2.0 released · 2022-04-22
0.99.1
record
2022-02-21
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2022-02-21
Total releases: 1 / 4 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 4.0
Bundled data: 5.8 KB / 1 file

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("spruce")

Format

Allen, C., & Chung, D. (n.d.). spruce: Spatial Random Effects Clustering of Single Cell Data (Version 0.99.1) [Computer software]. Retrieved October 24, 2026, from https://CRAN.R-project.org/package=spruce

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for spruce version 0.99.1 [Data set]. HJJB, LLC. Data release v2026-10-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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