indsp_calc: Computes Indicator Species Analysis for Count Data
In pmartR/pmartRseq: Analysis and Visualization of 16S Data

Description Usage Arguments Details Value Author(s) References Examples

This function is a wrapper for an indicator species analysis using the package indicspecies, studying the association between species patterns and combinations of group sites.

1	indsp_calc(omicsData, within = NULL, pval_thresh = 0.05)

`omicsData`	an object of the class 'seqData' created by `as.seqData`.
`within`	If desired, can run indicator species analysis between one effect and within another effect.
`pval_thresh`	P-value threshold for creating flags for significance. The default is 0.05.

This function uses the multipatt function in the package indicspecies to create combinations of input clusters and compare each combination with the species in e_data. Please refer to the multipatt function in the package indicspecies for more information.

An object of class indspRes (also a data.frame) containing the indicator species analysis of the data.

Allison Thompson

De Cáceres, M. and Legendre, P. 2009. Associations between species and groups of sites: indices and statistical inference. Ecology 90(12): 3566-3574.

## Not run: 
library(mintJansson)
data(rRNA_data)
rRNA_data <- group_designation(omicsData = rRNA_data, main_effects = c("site", "treatment"), time_course=NULL)

rRNA_indsp <- indsp_calc(omicsData = rRNA_data, within=NULL, pval_thresh=0.05)
head(rRNA_indsp)
summary(rRNA_indsp)
plot(rRNA_indsp)

## End(Not run)