R Observatory: Metrics for SPCompute version 1.0.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

SPCompute

1.0.3Package record

Compute Power or Sample Size for GWAS with Covariate Effect

0packages depend

2.8Kdownloads / year

9.5%test coverage

11/13flavors OK

Overview

About

Maintained by Ziang ZhangCRAN page ↗

Fast computation of the required sample size or the achieved power, for GWAS studies with different types of covariate effects and different types of covariate-gene dependency structure. For the detailed description of the methodology, see Zhang (2022) "Power and Sample Size Computation for Genetic Association Studies of Binary Traits: Accounting for Covariate Effects" arXiv:2203.15641.

Changes in 1.0.3

Updated the power (sample size) computation functions to accommodate conditional dependency between covariates.

From NEWS.md in the release

Install

R (CRAN)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("SPCompute", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-spcompute

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-SPCompute

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-SPCompute

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

2NOTE11OK

Check messages

NOTECRAN incoming feasibilityr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Maintainer: ‘Ziang Zhang <aguero.zhang@mail.utoronto.ca>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Ziang",
                      family = "Zhang",
                      role = c("aut", "cre"),
                      email = "aguero.zhang@mail.utoronto.ca"),
               person(given = "Lei",
                      family = "Sun",
                      role = "aut"))
as necessary.

The Description field contains
  Accounting for Covariate Effects" <arXiv:2203.15641>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.

CRAN check page ↗

Slowest check: 4.5 min · r-oldrel-windows-x86_64

Status changes

NOTE11 OK, 2 NOTENow
NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.3

READMEYes · 111 wordsVignettesYes · 1 · dynamicNEWSYes · 67% structured · mentions 1.0.3Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 6
Examples that run: 100%6 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

SPCompute HTML

How these are measured

Downloads

2.8K

CRAN downloads in the past year

Rank #18,895 · ~8/day · ~232/mo

Releases R versions

Daily download trend is not available in this view yet.

31430 days

70190 days

2.8K1 year

Compare downloads with other packages →

Also on69 r2u5 autocran

How downloads are counted

Dependencies

Declared dependencies

3 external dependencies (excludes base and recommended)

Installing SPCompute adds no packages beyond those that come with R.

Depends (0)

none

Imports (2)

Matrixstats

LinkingTo (0)

none

Suggests (3)

knitr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (from the free-text Author field) (2)

Ziang Zhang

Lei Sun

· added in 1.0.2

Maintainer since 1.0.1 (2022)

Releases (3)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
1.0.3Latest
record
2023-01-24 · current release · diff ↗
1.0.2
record
2022-09-05 · diff ↗ ·
added 3 exports
Compute_Power_multi, Compute_Size_multi, convert_preva_to_intercept
R
R 4.2.0 released · 2022-04-22
1.0.1
record
2022-04-01
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2022-04-01
Total releases: 3 / 4 yrs
License: GPL (>= 3) OSI
Download size: 42 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("SPCompute")

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 SPCompute version 1.0.3 [Data set]. HJJB, LLC. Data release v2026-10-26. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-26, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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