taxa.meansdn {metamicrobiomeR}

Summarize abundance by group

Description

This function summarizes taxa/pathway abundance tables to provide mean, sd, count by groups.

Usage

taxa.meansdn(
  taxtab,
  sumvar,
  groupvar,
  percent.filter = 0.05,
  relabund.filter = 5e-05,
  othervar = "none"
)

Arguments

taxtab

taxa/pathway abundance table from phylum to species or any preferred highest taxa level.

sumvar

main variable for summary

groupvar

variable to be stratified.

percent.filter

prevalence threshold (the percentage of number of samples the taxa/pathway available). Default is 0.05.

relabund.filter

relative abundance threshold (the minimum of the average relative abundance for a taxa/pathway to be retained). Default is 0.00005.

othervar

vector of variables that are not abundance variables to be summarized. Default is "none".

Value

table of mean, sd, count by group.

Examples

#Load summary tables of bacterial taxa relative abundance from Bangladesh data
data(taxtab6)
taxa.meansdn.rm<-taxa.meansdn(taxtab=taxtab6,sumvar="bf",groupvar="age.sample")