R Observatory: Metrics for GMMAT version 1.5.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

GMMAT

1.5.0Package record

Generalized Linear Mixed Model Association Tests

2packages dependsuggested by 1

15Kdownloads / year

30.4%test coverage

12/13flavors OK

Overview

About

Maintained by Han ChenCRAN page ↗

Perform association tests using generalized linear mixed models (GLMMs) in genome-wide association studies (GWAS) and sequencing association studies. First, GMMAT fits a GLMM with covariate adjustment and random effects to account for population structure and familial or cryptic relatedness. For GWAS, GMMAT performs score tests for each genetic variant as proposed in Chen et al. (2016) DOI:10.1016/j.ajhg.2016.02.012. For candidate gene studies, GMMAT can also perform Wald tests to get the effect size estimate for each genetic variant. For rare variant analysis from sequencing association studies, GMMAT performs the variant Set Mixed Model Association Tests (SMMAT) as proposed in Chen et al. (2019) DOI:10.1016/j.ajhg.2018.12.012, including the burden test, the sequence kernel association test (SKAT), SKAT-O and an efficient hybrid test of the burden test and SKAT, based on user-defined variant sets.

Install

R (CRAN)Ubuntu (r2u)

install.packages("GMMAT", 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-gmmat

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

Health

CRAN checks

1ERROR12OK

Check messages

ERRORtestsr-oldrel-macos-arm64

Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(GMMAT)
  > Sys.setenv(MKL_NUM_THREADS = 1)
  > 
  > test_check("GMMAT")
  
   *** caught segfault ***
  address 0x110, cause 'invalid permissions'
  
   *** caught segfault ***
  address 0x110, cause 'invalid permissions'
  
  Traceback:
   1: eval(c.expr, envir = args, enclos = envir)
   2: eval(c.expr, envir = args, enclos = envir)
   3: doTryCatch(return(expr), name, parentenv, handler)
   4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
   5: tryCatchList(expr, classes, parentenv, handlers)
   6: tryCatch(eval(c.expr, envir = args, enclos = envir), error = function(e) e)
   7: FUN(X[[i]], ...)
   8: lapply(X = S, FUN = FUN, ...)
   9: doTryCatch(return(expr), name, parentenv, handler)
  10: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  11: tryCatchList(expr, classes, parentenv, handlers)
  12: tryCatch(expr, error = function(e) {    call <- c
...[truncated]...
   'test_SMMAT.meta.R:165:2', 'test_glmm.score.R:317:2',
    'test_glmm.score.R:616:2', 'test_glmm.score.R:914:2',
    'test_glmm.score.R:1213:2', 'test_glmm.score.R:1505:2',
    'test_glmm.score.R:1797:2', 'test_glmm.wald.R:2:2', 'test_glmm.wald.R:805:2',
    'test_glmm.wald.R:1609:2', 'test_glmm.wald.R:1761:2', 'test_glmmkin.R:2:2',
    'test_glmmkin.R:82:2', 'test_glmmkin.R:163:2', 'test_glmmkin.R:245:2',
    'test_glmmkin.R:328:2', 'test_glmmkin.R:362:2', 'test_glmmkin.R:396:2'
  • {SeqArray} is not installed (2): 'test_SMMAT.R:2:9', 'test_SMMAT.meta.R:2:2'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_glmm.score.R:37:2'): cross-sectional id le 400 binomial ────────
  Error in `file(outfile, "w")`: cannot open the connection
  Backtrace:
      ▆
   1. └─GMMAT::glmm.score(...) at test_glmm.score.R:37:9
   2.   └─base::file(outfile, "w")
  
  [ FAIL 1 | WARN 2 | SKIP 30 | PASS 3 ]
  Error:
  ! Test failures.
  Execution halted

CRAN check page ↗

Slowest check: 9.9 min · r-oldrel-macos-x86_64

Status changes

ERROR12 OK, 1 ERRORNow
ERROR9 OK, 3 NOTE, 2 ERROR2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.5.0

READMENoVignettesYes · 1 · dynamicNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 8includes a package overview page
Examples that run: 17%1 run in a plain check · 5 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 100%
Documented parameters: 92%
Return-value docs: 100%
Help pages citing references: 75%

Vignettes (1)

GMMAT PDF

How these are measured

Downloads

15K

CRAN downloads in the past year

Rank #4,934 · ~41/day · ~1.2K/mo

Releases R versions

Daily download trend is not available in this view yet.

68030 days

1.7K90 days

15K1 year

Compare downloads with other packages →

Also on445 r2u

How downloads are counted

Dependencies

Declared dependencies

10 external dependencies (excludes base and recommended)

Installing GMMAT adds 6 packages (4 with compiled code, 8.9 MB of source tarballs). Heaviest: data.table 5.7 MB, Rcpp 1.8 MB, RcppArmadillo 1.0 MB.

Depends (1)

R >= 3.2.0

Imports (7)

Rcpp CompQuadForm foreachparallelMatrixmethodsdata.table

LinkingTo (2)

Rcpp RcppArmadillo

Suggests (4)

doMC SeqArray SeqVarTools testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

2direct

0indirect

Imports 2

Suggested by 1

Depends, Imports or LinkingTo, most downloaded first

MAGEE RsqMed

Suggests, most downloaded first

gaawr2

How these are counted

Code & Tests

Datasets

People & History

People (11)

Han Chen

Author, Maintainer since 1.0.3 (2019)

Matthew Conomos

Author · added in 1.4.0

Duy Pham

Author · added in 1.4.0

The R Core Team