Package: miaSim 1.19.0

Yagmur Simsek

miaSim: Microbiome Data Simulation

Microbiome time series simulation with generalized Lotka-Volterra model, Self-Organized Instability (SOI), and other models. Hubbell's Neutral model is used to determine the abundance matrix. The resulting abundance matrix is applied to (Tree)SummarizedExperiment objects.

Authors:Yagmur Simsek [cre, aut], Karoline Faust [aut], Yu Gao [aut], Emma Gheysen [aut], Daniel Rios Garza [aut], Tuomas Borman [aut], Leo Lahti [aut], Geraldson Muluh [ctb], Akewak Jeba [ctb]

miaSim_1.19.0.tar.gz
miaSim_1.19.0.zip(r-4.7)miaSim_1.19.0.zip(r-4.6)miaSim_1.19.0.zip(r-4.5)
miaSim_1.19.0.tgz(r-4.6-any)miaSim_1.19.0.tgz(r-4.5-any)
miaSim_1.19.0.tar.gz(r-4.7-any)miaSim_1.19.0.tar.gz(r-4.6-any)
miaSim_1.19.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
miaSim/json (API)

# Install 'miaSim' in R:

install.packages('miaSim', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/microbiome/miasim/issues

On BioConductor:miaSim-1.19.0(bioc 3.24)miaSim-1.18.0(bioc 3.23)

microbiome software sequencing dnaseq atacseq coverage network

7.09 score 22 stars 31 scripts 13 exports 62 dependencies

Last updated from:6f6c343112. Checks:1 NOTE, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	220
linux-devel-x86_64	OK	453
source / vignettes	OK	297
linux-release-x86_64	OK	458
macos-release-arm64	OK	308
macos-oldrel-arm64	OK	228
windows-devel	OK	282
windows-release	OK	327
windows-oldrel	OK	313
wasm-release	OK	206

Exports:.simulationTimes powerlawA randomA randomE rdirichlet simulateConsumerResource simulateEventTimes simulateGLV simulateHubbell simulateHubbellRates simulateRicker simulateSOI simulateStochasticLogistic

Dependencies:abind ape BH Biobase BiocGenerics BiocParallel Biostrings cli codetools cpp11 crayon DelayedArray deSolve digest dplyr formatR fs futile.logger futile.options generics GenomicRanges glue IRanges jsonlite lambda.r lattice lazyeval lifecycle magrittr Matrix MatrixGenerics matrixStats nlme pillar pkgconfig poweRlaw pracma purrr R6 rappdirs Rcpp rlang S4Arrays S4Vectors Seqinfo SingleCellExperiment snow SparseArray stringi stringr SummarizedExperiment tibble tidyr tidyselect tidytree treeio TreeSummarizedExperiment utf8 vctrs withr XVector yulab.utils

miaSim: Microbiome Data Simulation

Rendered frommiaSim.Rmdusingknitr::rmarkdown

Last update: 2025-07-01
Started: 2021-09-17

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Generate pairs of interactions according to interaction types	.applyInterType
Get the interspecies interaction matrix A using leave-one-out method	.estimateAFromSimulations
Generate interactions according to five types of interactions and their weights	.getInteractions
Check whether a number is a positive integer	.isPosInt
Replace one element with zero in a list	.replaceByZero
Interaction matrix with Power-Law network adjacency matrix	powerlawA
Generate random interaction matrix for GLV model	randomA
Generate random efficiency matrix	randomE
Generate dirichlet random deviates	rdirichlet
Consumer-resource model simulation	simulateConsumerResource
Generate a vector of event times	simulateEventTimes
Generalized Lotka-Volterra (gLV) simulation	simulateGLV
Hubbell's neutral model simulation	simulateHubbell
Hubbell's neutral model simulation applied to time series	simulateHubbellRates simulateHubbellRates,numeric-method simulateHubbellRates-numeric
Generate time series with the Ricker model	simulateRicker
Self-Organised Instability model (SOI) simulation	simulateSOI
Stochastic Logistic simulation	simulateStochasticLogistic

Package: miaSim 1.19.0

miaSim: Microbiome Data Simulation

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)