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DESCRIPTION
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DESCRIPTION
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Package: metamicrobiomeR
Title: an R package for analysis of microbiome relative abundance data using zero inflated beta GAMLSS and meta-analysis across studies using random effect model
Version: 1.1
YEAR: 2019
Authors@R: person("Nhan", "Ho", email = "nhanhocumc@gmail.com",
role = c("aut", "cre"))
Description: The metamicrobiomeR package implements 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 effect meta-analysis models for meta-analysis pooling estimates across microbiome studies.
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.
Depends: R (>= 3.4.2)
License: GPL-2
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1.9000
Imports:
gdata,
plyr,
dplyr,
ggplot2,
gridExtra,
RColorBrewer,
lme4,
lmerTest,
mgcv,
meta,
gamlss,
reshape2,
caret,
randomForest,
grDevices,
gplots,
magrittr,
tools,
sas7bdat,
foreign,
knitr,
rmarkdown,
zCompositions,
compositions,
matrixStats,
RCurl,
httr,
repmis,
jsonlite
Suggests: knitr,
rmarkdown
VignetteBuilder: knitr
URL: https://github.com/nhanhocu/metamicrobiomeR
BugReports: https://github.com/nhanhocu/metamicrobiomeR/issues