Package: miaSim 1.13.0

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]

miaSim_1.13.0.tar.gz
miaSim_1.13.0.zip(r-4.5)miaSim_1.13.0.zip(r-4.4)miaSim_1.13.0.zip(r-4.3)
miaSim_1.13.0.tgz(r-4.4-any)miaSim_1.13.0.tgz(r-4.3-any)
miaSim_1.13.0.tar.gz(r-4.5-noble)miaSim_1.13.0.tar.gz(r-4.4-noble)
miaSim_1.13.0.tgz(r-4.4-emscripten)miaSim_1.13.0.tgz(r-4.3-emscripten)
miaSim.pdf |miaSim.html✨
miaSim/json (API)
NEWS

# 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-1.11.0(bioc 3.20)miaSim-1.10.0(bioc 3.19)

microbiome software sequencing dnaseq atacseq coverage network

6.59 score 18 stars 24 scripts 150 downloads 14 exports 71 dependencies

Last updated 24 days agofrom:667f35c367. Checks:OK: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 30 2024
R-4.5-win	OK	Oct 31 2024
R-4.5-linux	OK	Oct 30 2024
R-4.4-win	OK	Oct 31 2024
R-4.4-mac	OK	Oct 31 2024
R-4.3-win	OK	Oct 31 2024
R-4.3-mac	OK	Oct 31 2024

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

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

miaSim: Microbiome Data Simulation

miaSim authors

Rendered frommiaSim.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2023-06-02
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 a vector of times when events is happening	.eventTimes
Generate interactions according to five types of interactions and their weights	.getInteractions
check whether a number is a positive integer	.isPosInt
Generate dirichlet random deviates	.rdirichlet
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
Consumer-resource model simulation	simulateConsumerResource
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 1.13.0

miaSim: Microbiome Data Simulation

miaSim: Microbiome Data Simulation

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)