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ALLSPICER

ALLelic Spectrum of Pleiotropy Informed Correlated Effects

v0.1.9 · Oct 16, 2024 · MIT + file LICENSE

Description

Provides statistical tools to analyze heterogeneous effects of rare variants within genes that are associated with multiple traits. The package implements methods for assessing pleiotropic effects and identifying allelic heterogeneity, which can be useful in large-scale genetic studies. Methods include likelihood-based statistical tests to assess these effects. For more details, see Lu et al. (2024) <doi:10.1101/2024.10.01.614806>.

Downloads

CRAN

237

Last 30 days

21115th

651

Last 90 days

2.9K

Last year

Trend: +40.2% (30d vs prior 30d)

r2u CRAN

0

Last 30 days

25

Last 90 days

174

Last year

Trend: -100% (30d vs prior 30d)

autoCRAN

11

Last 7 days

32

Last 30 days

1

All-time

autoCRAN-only: this name is served only by autoCRAN, so the count is exact.

CRAN Check Status

13 OK
Show all 13 flavors
Flavor Status
r-devel-linux-x86_64-debian-clang OK
r-devel-linux-x86_64-debian-gcc OK
r-devel-linux-x86_64-fedora-clang OK
r-devel-linux-x86_64-fedora-gcc OK
r-devel-windows-x86_64 OK
r-oldrel-macos-arm64 OK
r-oldrel-macos-x86_64 OK
r-oldrel-windows-x86_64 OK
r-patched-linux-x86_64 OK
r-release-linux-x86_64 OK
r-release-macos-arm64 OK
r-release-macos-x86_64 OK
r-release-windows-x86_64 OK

Check History

OK 14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 12, 2026
WARNING 13 OK · 0 NOTE · 1 WARNING · 0 ERROR · 0 FAILURE Mar 11, 2026
WARNING r-devel-linux-x86_64-fedora-gcc

for code/documentation mismatches

shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory
shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory
shell-init: error 
...[truncated]...
 file or directory
shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory
shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory
OK 14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 10, 2026

Line coverage

Expression

Tests / Examples

Functions

13 13 exported

Complexity

1.5 avg / 3 max

Call network

13 nodes / 12 edges

Loading call graph…

Lowest coverage

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

Code

Structure

Lines of code

767

Files

20

Compiled share

0%

Has compiled src

No

Language breakdown

R 369 (48.1%)Docs 398 (51.9%)

API

Exported functions

13

Internal functions

0

Recent export changes

v0.1.9+13 ALLSPICE, ALLSPICE_simulation, format_ALLSPICE_data +10 more

Testing & CI

Has tests

No

Test-to-code ratio

0.00

testthat edition

3

CI present

No

CI type

[]

PR gated

No

Docs

Return-value doc rate

100%

\dontrun example ratio

0%

Roxygen coverage

100%

Has pkgdown

No

NEWS present

No

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

System requirements

C++ standard

License

MIT + file LICENSE

License flags

SPDX valid, OSI approved

History

Versions

1

First release

2024-10-16

Latest release

2024-10-16

Avg cadence

Cold removal rate

Dep drift

0

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

Dependency Network

Dependencies Reverse dependencies dplyr magrittr readr mvtnorm ALLSPICER

Version History

1 tracked
new 0.1.9 Mar 10, 2026

R Observatory began tracking this package on Mar 10, 2026; it first appeared on CRAN Oct 16, 2024. Releases before tracking aren’t shown.