Generalized Additive Model for Location, Scale and Shape (GAMLSS) with zero inflated beta (BEZI) family for analysis of microbiome relative abundance data (with various options for data transformation/normalization to address compositional effects) and random effects meta-analysis models for meta-analysis pooling estimates across microbiome studies are implemented. Random Forest model to predict microbiome age based on relative abundances of shared bacterial genera with the Bangladesh data (Subramanian et al 2014), comparison of multiple diversity indexes using linear/linear mixed effect models and some data display/visualization are also implemented. The reference paper is published by Ho NT, Li F, Wang S, Kuhn L (2019) <doi:10.1186/s12859-019-2744-2> .
| Version: | 1.2 |
| Depends: | R (≥ 4.0.0), gamlss |
| Imports: | meta, lme4, gdata, plyr, dplyr, tidyr, ggplot2, gridExtra, lmerTest, matrixStats, zCompositions, compositions |
| Suggests: | testthat, RCurl, httr, repmis, jsonlite, knitr, rmarkdown, grDevices, gplots, magrittr, tools, foreign, mgcv, reshape2, caret, randomForest, tsibble, RColorBrewer |
| Published: | 2020-11-09 |
| Author: | Nhan Ho [aut, cre] |
| Maintainer: | Nhan Ho <nhanhocumc at gmail.com> |
| BugReports: | https://github.com/nhanhocu/metamicrobiomeR/issues |
| License: | GPL-2 |
| URL: | https://github.com/nhanhocu/metamicrobiomeR |
| NeedsCompilation: | no |
| In views: | MetaAnalysis |
| CRAN checks: | metamicrobiomeR results |
| Reference manual: | metamicrobiomeR.pdf |
| Vignettes: |
metamicrobiomeR |
| Package source: | metamicrobiomeR_1.2.tar.gz |
| Windows binaries: | r-devel: metamicrobiomeR_1.2.zip, r-release: metamicrobiomeR_1.2.zip, r-oldrel: not available |
| macOS binaries: | r-release: metamicrobiomeR_1.2.tgz, r-oldrel: not available |
| Old sources: | metamicrobiomeR archive |
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