Package: LDM 6.0.1

LDM: Testing Hypotheses About the Microbiome using the Linear Decomposition Model

A single analysis path that includes distance-based ordination, global tests of any effect of the microbiome, and tests of the effects of individual taxa with false-discovery-rate (FDR) control. It accommodates both continuous and discrete covariates as well as interaction terms to be tested either singly or in combination, allows for adjustment of confounding covariates, and uses permutation-based p-values that can control for sample correlations. It can be applied to transformed data, and an omnibus test can combine results from analyses conducted on different transformation scales. It can also be used for testing presence-absence associations based on infinite number of rarefaction replicates, testing mediation effects of the microbiome, analyzing censored time-to-event outcomes, and for compositional analysis by fitting linear models to centered-log-ratio taxa count data.

Authors:Yi-Juan Hu [aut, cre], Glen A Satten [aut]

LDM_6.0.1.tar.gz
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LDM.pdf |LDM.html✨
LDM/json (API)

# Install 'LDM' in R:
install.packages('LDM', repos = c('https://yijuanhu.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/yijuanhu/ldm/issues

Datasets:
  • sim.meta - Metadata of the simulated microbiome samples
  • sim.otu.tab - OTU count table of the simulated microbiome samples
  • sim.otu.tab5 - Filtered OTU count table of the simulated microbiome samples
  • throat.meta - Metadata of the throat microbiome samples
  • throat.otu.tab - OTU count table from 16S sequencing of the throat microbiome samples
  • throat.otu.tab5 - Filtered OTU count table from 16S sequencing of the throat microbiome samples
  • throat.tree - UPGMA tree of the OTUs from 16S sequencing of the throat microbiome samples

On CRAN:

6 exports 6 stars 1.26 score 73 dependencies 19 scripts 223 downloads

Last updated 1 years agofrom:7751ed69ba. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 01 2024
R-4.5-winOKSep 01 2024
R-4.5-linuxOKSep 01 2024
R-4.4-winOKSep 01 2024
R-4.4-macOKSep 01 2024
R-4.3-winOKSep 01 2024
R-4.3-macOKSep 01 2024

Exports:adjust.data.by.covariatesavgdist.squaredjaccard.meanldmpermanovaFLunifrac.mean

Dependencies:apeBHBiocParallelcastorcliclueclustercodetoolscolorspacecpp11digestdirmultfansifarverfastmatchfBasicsforeachformatRfutile.loggerfutile.optionsgenericsggplot2ggrepelgluegssgtableGUniFracigraphinlineisobanditeratorsjsonlitelabelinglambda.rlatticelifecyclemagrittrMASSMatrixmatrixStatsmgcvmodeestmunsellnaturalsortnlmepermutephangornpillarpkgconfigquadprogR6RColorBrewerRcppRcppEigenrlangrmutilrpartRSpectrascalessnowspatialstablestablediststatipstatmodtibbletimeDatetimeSeriesutf8vctrsveganviridisLitewithr

R packages: LDM

Rendered fromLDM.pdf.asisusingR.rsp::asison Sep 01 2024.

Last update: 2023-08-27
Started: 2023-08-27