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spatialFDA

Bioc current

A Tool for Spatial Multi-sample Comparisons

v1.4.0 · software · GPL (>= 3) + file LICENSE
View on Bioconductor ↗ Source ↗

Release Lineage

Entered 3.21 · Apr 16, 2025

Current · Requires R 4.6

1.0 In 3 of 49 releases 3.23

Description

spatialFDA is a package to calculate spatial statistics metrics. The package takes a SpatialExperiment object and calculates spatial statistics metrics using the package spatstat. Then it compares the resulting functions across samples/conditions using functional additive models as implemented in the package refund. Furthermore, it provides exploratory visualisations using functional principal component analysis, as well implemented in refund.

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

23 20 exported

Complexity

3.8 avg / 25 max

Call network

23 nodes / 14 edges

Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.

Call graph

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Lowest coverage

Per-function coverage is not measured for this package yet.

Code

Structure

Lines of code

4,810

Files

61

Compiled share

0%

Has compiled src

No

Language breakdown

R 1,972 (41%)Tests 675 (14%)Docs 1,334 (27.7%)Vignettes 829 (17.2%)

API

Exported functions

20

Internal functions

3

Recent export changes

v3.22+5 crossSpatialInference, extractCrossInferenceData, plotCrossHeatmap +2 more
v3.21+15 .dfToppp, .extractMetric, .loadExample +12 more

Testing & CI

Has tests

Yes

Test-to-code ratio

0.34

testthat edition

3

CI present

Yes

CI type

["github-actions"]

PR gated

Yes

Docs

Roxygen coverage

100%

Health & Security signals

Informational signals; not verdicts.

on.exit coverage

–

Unsafe pattern score

0

Dep constraint coverage

0%

Secret pattern count

0

Bundled 3rd-party code

2 items

Portability & License

Min R version

4.3.0

System requirements

–

C++ standard

–

License

GPL (>= 3) + file LICENSE

License flags

SPDX valid, OSI approved

History

Versions

3

First release

2025-04-15

Latest release

2026-04-28

Avg cadence

189 days

Cold removal rate

–

Dep drift

4

LOC over versions

v3.21: 2,913 LOCv3.22: 4,616 LOCv3.23: 4,810 LOC

Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.

Documentation

Documentation
READMEYes · 180 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo
Examples that run
100%
Documented parameters
98%
Return-value docs
100%
References docs
0%

Topics

Software
Software › Technology › Spatial
Software › ResearchField › Transcriptomics

Depended on by (1)

Bioconductor (1)

OSTA

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