R Observatory: Metrics for SIMICO version 0.2.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

SIMICO

0.2.0Package record

Set-Based Inference for Multiple Interval-Censored Outcomes

0packages depend

2.3Kdownloads / year

–test coverage

0/13flavors OK

Overview

About

Maintained by Jaihee ChoiCRAN page ↗

Contains tests for association between a set of genetic variants and multiple correlated outcomes that are interval censored. Interval-censored data arises when the exact time of the onset of an outcome of interest is unknown but known to fall between two time points.

Changes in 0.2.0

Added a vignette

From NEWS.md in the release

Install

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

install.packages("SIMICO", 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-simico

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-SIMICO

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-SIMICO

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

13NOTE

Check messages

NOTERd filesr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64

checkRd: (-1) fd_term.Rd:4: Lost braces; missing escapes or markup?
     4 | d/d_{theta_l}
       |     ^
checkRd: (-1) gamma_fd.Rd:4: Lost braces; missing escapes or markup?
     4 | d/d_{gamma_l}
       |     ^
checkRd: (-1) gamma_off.Rd:4: Lost braces; missing escapes or markup?
     4 | d^2/d_{gamma_l}d{gamma_m}
       |       ^
checkRd: (-1) gamma_off.Rd:4: Lost braces
     4 | d^2/d_{gamma_l}d{gamma_m}
       |                 ^
checkRd: (-1) gamma_off.Rd:7: Lost braces; missing escapes or markup?
     7 | Calculates the [off-diagonal] Information matrix term for I_{gamma gamma} with respect to outcome l and outcome m.
       |                                                             ^
checkRd: (-1) gamma_on.Rd:4: Lost braces; missing escapes or markup?
     4 | d^2/d_{gamma_l}d{gamma_l}
       |       ^
checkRd: (-1) gamma_on.Rd:4: Lost braces
     4 | d^2/d_{gamma_l}d{gamma_l}
       |                 ^
checkRd: (-1) gamma_on.Rd:7: Lost braces; missing escapes or markup?
   
...[truncated]...
           ^
checkRd: (-1) surv_diff.Rd:4: Lost braces; missing escapes or markup?
     4 | S_{ik}(L_{ik}) - S_{ik}(R_{ik})
       |   ^
checkRd: (-1) surv_diff.Rd:4: Lost braces; missing escapes or markup?
     4 | S_{ik}(L_{ik}) - S_{ik}(R_{ik})
       |          ^
checkRd: (-1) surv_diff.Rd:4: Lost braces; missing escapes or markup?
     4 | S_{ik}(L_{ik}) - S_{ik}(R_{ik})
       |                    ^
checkRd: (-1) surv_diff.Rd:4: Lost braces; missing escapes or markup?
     4 | S_{ik}(L_{ik}) - S_{ik}(R_{ik})
       |                           ^
checkRd: (-1) surv_left.Rd:4: Lost braces; missing escapes or markup?
     4 | S_{ik}(L_{ik})
       |   ^
checkRd: (-1) surv_left.Rd:4: Lost braces; missing escapes or markup?
     4 | S_{ik}(L_{ik})
       |          ^
checkRd: (-1) surv_right.Rd:4: Lost braces; missing escapes or markup?
     4 | S_{ik}(R_{ik})
       |   ^
checkRd: (-1) surv_right.Rd:4: Lost braces; missing escapes or markup?
     4 | S_{ik}(R_{ik})
       |          ^

CRAN check page ↗

Slowest check: 7.8 min · r-oldrel-windows-x86_64

Status changes

NOTE13 NOTENow
NOTE14 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.2.0

READMENoVignettesYes · 1 · dynamicNEWSYes · 67% structured · mentions 0.2.0Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 25
Examples that run: 100%4 run in a plain check
Exported functions with examples: 16%
Documented parameters: not tracked
Return-value docs: not tracked
Help pages citing references: 0%

Vignettes (1)

SIMICO Vignette HTML

How these are measured

Downloads

2.3K

CRAN downloads in the past year

Rank #22,286 · ~6/day · ~191/mo

Releases R versions

Daily download trend is not available in this view yet.

21430 days

59390 days

2.3K1 year

Compare downloads with other packages →

Also on63 r2u2 autocran

How downloads are counted

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Installing SIMICO adds 26 packages (19 with compiled code, 11 MB of source tarballs). Heaviest: Rcpp 1.8 MB, RcppEigen 1.7 MB, mvtnorm 1.0 MB.

Depends (0)

none

Imports (5)

bindata fastGHQuad CompQuadFormstatsICSKAT

LinkingTo (0)

none

Suggests (2)

knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (2)

Jaihee Choi

Author, Maintainer since 0.1.0 (2022)

Ryan Sun

Author

Releases (2)

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
0.2.0Latest
record
2022-11-26 · current release · diff ↗
0.1.0
record
2022-11-07
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2022-11-07
Total releases: 2 / 4 yrs
License: GPL-3 OSI
Download size: 28 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("SIMICO")

Format

Choi, J., & Sun, R. (2022). SIMICO: Set-Based Inference for Multiple Interval-Censored Outcomes (Version 0.2.0) [Computer software]. https://doi.org/10.32614/CRAN.package.SIMICO

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 SIMICO version 0.2.0 [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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