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0.2.0Package record

Multimodal Mediation Analysis

0packages depend
2.6Kdownloads / year
–test coverage
0/13flavors OK

Overview

About

Multimodal mediation analysis is an emerging problem in microbiome data analysis. Multimedia make advanced mediation analysis techniques easy to use, ensuring that all statistical components are transparent and adaptable to specific problem contexts. The package provides a uniform interface to direct and indirect effect estimation, synthetic null hypothesis testing, bootstrap confidence interval construction, and sensitivity analysis. More details are available in Jiang et al. (2024) "multimedia: Multimodal Mediation Analysis of Microbiome Data" doi:10.1101/2024.03.27.587024.

Changes in 0.2.0
  • Adds functions for sensitivity analysis: sensitivity(), sensitivity_pathwise(), and sensitivity_perturb().
  • Introduces test coverage and automated GitHub Actions.

From NEWS.md in the release

Install

Health

CRAN checks
4ERROR9NOTE
Check messages
ERRORtestsr-devel-windows-x86_64, r-oldrel-windows-x86_64, r-release-windows-x86_64

r-devel-windows-x86_64

Running 'testthat.R' [100s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(multimedia)
  Loading required package: brms
  Loading required package: Rcpp
  Loading 'brms' package (version 2.23.0). Useful instructions
  can be found by typing help('brms'). A more detailed introduction
  to the package is available through vignette('brms_overview').
  
  Attaching package: 'brms'
  
  The following object is masked from 'package:stats':
  
      ar
  
  Loading required package: glmnetUtils
  Loading required package: ranger
  Loading required package: tidyselect
  > 
  > test
...[truncated]...
eval2(call, envir = args, enclos = envir)
    8.             └─base::eval(expr, envir, ...)
    9.               └─base::eval(expr, envir, ...)
   10.                 └─brms (local) .fun(...)
   11.                   └─brms (local) .compile_model(model, ...)
   12.                     ├─brms:::eval_silent(...)
   13.                     │ └─base::eval(expr, envir)
   14.                     │   └─base::eval(expr, envir)
   15.                     └─brms::do_call(rstan::stan_model, args)
   16.                       └─brms:::eval2(call, envir = args, enclos = envir)
   17.                         └─base::eval(expr, envir, ...)
   18.                           └─base::eval(expr, envir, ...)
   19.                             └─rstan (local) .fun(model_code = .x1)
   20.                               └─rstan:::cxxfunctionplus(...)
   21.                                 └─base::sink(type = "output")
  
  [ FAIL 2 | WARN 11 | SKIP 0 | PASS 86 ]
  Error:
  ! Test failures.
  Execution halted

r-oldrel-windows-x86_64

Running 'testthat.R' [129s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(multimedia)
  Loading required package: brms
  Loading required package: Rcpp
  Loading 'brms' package (version 2.23.0). Useful instructions
  can be found by typing help('brms'). A more detailed introduction
  to the package is available through vignette('brms_overview').
  
  Attaching package: 'brms'
  
  The following object is masked from 'package:stats':
  
      ar
  
  Loading required package: glmnetUtils
  Loading required package: ranger
  Loading required package: tidyselect
  > 
  > test
...[truncated]...
:eval2(call, envir = args, enclos = envir)
    8.             └─base::eval(expr, envir, ...)
    9.               └─base::eval(expr, envir, ...)
   10.                 └─brms (local) .fun(...)
   11.                   └─brms (local) .compile_model(model, ...)
   12.                     ├─brms:::eval_silent(...)
   13.                     │ └─base::eval(expr, envir)
   14.                     │   └─base::eval(expr, envir)
   15.                     └─brms::do_call(rstan::stan_model, args)
   16.                       └─brms:::eval2(call, envir = args, enclos = envir)
   17.                         └─base::eval(expr, envir, ...)
   18.                           └─base::eval(expr, envir, ...)
   19.                             └─rstan (local) .fun(model_code = .x1)
   20.                               └─rstan:::cxxfunctionplus(...)
   21.                                 └─base::sink(type = "output")
  
  [ FAIL 2 | WARN 1 | SKIP 0 | PASS 86 ]
  Error:
  ! Test failures.
  Execution halted

r-release-windows-x86_64

Running 'testthat.R' [93s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(multimedia)
  Loading required package: brms
  Loading required package: Rcpp
  Loading 'brms' package (version 2.23.0). Useful instructions
  can be found by typing help('brms'). A more detailed introduction
  to the package is available through vignette('brms_overview').
  
  Attaching package: 'brms'
  
  The following object is masked from 'package:stats':
  
      ar
  
  Loading required package: glmnetUtils
  Loading required package: ranger
  Loading required package: tidyselect
  > 
  > test_
...[truncated]...
:eval2(call, envir = args, enclos = envir)
    8.             └─base::eval(expr, envir, ...)
    9.               └─base::eval(expr, envir, ...)
   10.                 └─brms (local) .fun(...)
   11.                   └─brms (local) .compile_model(model, ...)
   12.                     ├─brms:::eval_silent(...)
   13.                     │ └─base::eval(expr, envir)
   14.                     │   └─base::eval(expr, envir)
   15.                     └─brms::do_call(rstan::stan_model, args)
   16.                       └─brms:::eval2(call, envir = args, enclos = envir)
   17.                         └─base::eval(expr, envir, ...)
   18.                           └─base::eval(expr, envir, ...)
   19.                             └─rstan (local) .fun(model_code = .x1)
   20.                               └─rstan:::cxxfunctionplus(...)
   21.                                 └─base::sink(type = "output")
  
  [ FAIL 2 | WARN 1 | SKIP 0 | PASS 86 ]
  Error:
  ! Test failures.
  Execution halted
ERRORre-building of vignette outputsr-release-linux-x86_64
Error(s) in re-building vignettes:
  ...
--- re-building ‘illustration.Rmd’ using rmarkdown

Quitting from illustration.Rmd:133-138 [sensitivity_analysis]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[1m[34m<error/rlang_error>[39m[22m
[1m[33mError[39m:[22m
[33m![39m cannot open the connection
---
[1mBacktrace:[22m
[90m    [39m▆
[90m 1. [39m├─[1mreadr[22m::read_csv("https://go.wisc.edu/0xcyr1")
[90m 2. [39m│ [90m└─[1mvroom[22m::vroom(...)[39m
[90m 3. [39m│   [90m└─vroom:::vroom_(...)[39m
[90m 4. [39m└─vroom (local) `<fn>`(`<curl>`, "rb")
[90m 5. [39m  └─[1mbase[22m::tryCatch(...)
[90m 6. [39m    └─base (local) tryCatchList(expr, classes, parentenv, handlers)
[90m 7. [39m      └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
[90m 8. [39m        └─value[[3L]](cond)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'illustration.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘illustration.Rmd’

--- re-building ‘random.Rmd’ using rmarkdown
[WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead.
--- finished re-building ‘random.Rmd’

SUMMARY: processing the following file failed:
  ‘illustration.Rmd’

Error: Vignette re-building failed.
Execution halted
NOTEDESCRIPTION meta-informationr-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

r-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-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64

Missing dependency on R >= 4.2.0 because package code uses the pipe
  placeholder syntax added in R 4.2.0.
  File(s) using such syntax:
    ‘predict.R’ ‘sensitivity.R’ ‘treatment_profile.R’

r-devel-windows-x86_64, r-oldrel-windows-x86_64, r-release-windows-x86_64

Missing dependency on R >= 4.2.0 because package code uses the pipe
  placeholder syntax added in R 4.2.0.
  File(s) using such syntax:
    'predict.R' 'sensitivity.R' 'treatment_profile.R'

CRAN check page ↗

Slowest check: 20.0 min · r-oldrel-macos-x86_64
Status changes
  • ERROR9 NOTE, 4 ERRORNow
  • ERROR12 NOTE, 1 ERROR2026-09-04
  • NOTE13 NOTE2026-08-07
  • ERROR12 NOTE, 1 ERROR2026-08-06
  • NOTE13 NOTE2026-07-29
  • ERROR12 NOTE, 1 ERROR2026-07-27
Show 12 earlier changesHide 12 earlier changes
  • NOTE13 NOTE2026-06-09
  • ERROR12 NOTE, 1 ERROR2026-06-08
  • NOTE13 NOTE2026-05-30
  • ERROR12 NOTE, 1 ERROR2026-05-28
  • NOTE13 NOTE2026-05-10
  • ERROR12 NOTE, 1 ERROR2026-05-03
  • NOTE3 OK, 11 NOTE2026-04-22
  • ERROR3 OK, 10 NOTE, 1 ERROR2026-04-18
  • NOTE3 OK, 11 NOTE2026-03-16
  • ERROR3 OK, 10 NOTE, 1 ERROR2026-03-13
  • NOTE3 OK, 11 NOTE2026-03-12
  • ERROR3 OK, 10 NOTE, 1 ERROR2026-03-10
Advisories

none known

Documentation

In release 0.2.0
READMEYes · 1,127 wordsVignettesYes · 2 · dynamicNEWSYes · 100% structured · mentions 0.2.0Citation fileYes · cites a publicationWebsiteYes · pkgdown
Help pages
74
Examples that run
100%70 run in a plain check
Exported functions with examples
98%
Documented parameters
100%
Return-value docs
100%
Help pages citing references
0%

Downloads

2.6K
CRAN downloads in the past year
Rank #14,397 · ~7/day · ~219/mo
Daily download trend is not available in this view yet.
28130 days
83690 days
2.6K1 year
Compare downloads with other packages →
Also on73 r2u

Repository

4Stars
1Forks
3Open issues
0Open PRs
4Releases
358Commits
1Commit identities
causal-inferencemediation-analysismicrobiomedata-integration
License file reads as CC0-1.0 · 358 commits · Last activity 2026-07-20 · 0% stars, 30d · Default branch at 0.2.2, ahead of CRAN 0.2.0 (checked 2026-10-25)
Responsiveness
How these are sampled
PRs merged (all time)
100%
Median days to close, 50 most recently updated closed issues
28
Median days to close, 50 most recently updated closed PRs
0

Stars over time

2025-03-19 · 22026-08-20 · 4
PracticesBeta

6 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/krisrs1128/multimedia on 2026-10-25.

Continuous integration (2)
GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux

Docs source (3)
README.Rmdpkgdown

GitHub Pages site last deployed 2026-07-20

pkgdown site last built 2025-02-14

Coverage (1)
Coverage reporting
How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies
29 external dependencies (excludes base and recommended)

Installing multimedia adds 89 packages (41 with compiled code, 88 MB of source tarballs). Heaviest: BH 14 MB, stringi 11 MB, ggplot2 6.0 MB. 3 more not on CRAN are not measured.

Depends (5)
LinkingTo (0)
none
Enhances (0)
none
Reverse dependencies
0direct
0indirect

Nothing depends on this yet.

Datasets

People & History

People (2)
Author, Maintainer since 0.2.0 (2024)
Releases (1)
  • R
    R 4.6.0 released · 2026-04-24
  • R
    R 4.5.0 released · 2025-04-11
  • 0.2.0Latest
    2024-09-18 · current release
  • R
    R 4.4.0 released · 2024-04-24

Package metadata

First published
2024-09-18
Total releases
1 / 2 yrs
License
CC0
Minimum R
≥ 4.1.0
Bundled data
22 KB / 1 file
Download size
823 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("multimedia")

The package provides a citation file that builds its entry when R runs it. Run citation() to see it.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

APA

Balamuta, J. J. (2026). R Observatory: Metrics for multimedia version 0.2.0 [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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