alphadat {metamicrobiomeR}

Alpha diversity data.

Description

Alpha diversity data from alpha_rarefaction output from QIIME.

Usage

data(alphadat)

Format

A list of 4 dataframes for four indexes: Chao1, Observed_species, PD_whole_tree, Shannon.

Source

Gordon Lab

References

Subramanian et al. Nature. 2014 Jun 19; 510(7505): 417–421. (PubMed)

Examples

data(alphadat)
# Load covariate data
data(covar.rm)
covar.rm$sampleid<-tolower(covar.rm$sampleid)
#comparison of standardized alpha diversity indexes between genders adjusting for
#breastfeeding and infant age at sample collection in infants <=6 months of age
alphacom<-alpha.compare(datlist=alphadat,depth=3,mapfile=covar.rm,
mapsampleid="sampleid", comvar="gender",adjustvar=c("age.sample","bf"),
longitudinal="yes", age.limit=6,standardize=TRUE)
alphacom$alphasum[,1:5]