Multimodal Mediation Analysis
Overview
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.
- Adds functions for sensitivity analysis:
sensitivity(),sensitivity_pathwise(), andsensitivity_perturb(). - Introduces test coverage and automated GitHub Actions.
From NEWS.md in the release
Install
Health
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 haltedr-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 haltedr-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 haltedERRORre-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 haltedNOTEDESCRIPTION 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'- 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
Documentation
- 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
Repository
- 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
Forks over time
Releases over time
Issues over time
Commits over time
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.
The R CMD check workflow runs on Linux
GitHub Pages site last deployed 2026-07-20
pkgdown site last built 2025-02-14
Dependencies
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.
Code & Tests
Datasets
People & History
- RR 4.6.0 released · 2026-04-24
- RR 4.5.0 released · 2025-04-11
- 0.2.0Latest2024-09-18 · current release
- RR 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.
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.