get_NRI_NTI {MicrobiotaProcess} | R Documentation |
calculate NRT and NTI of sample. It is a wrapper method of picante::ses.mpd and picante::ses.mntd
get_NRI_NTI(obj, ...) ## S4 method for signature 'matrix' get_NRI_NTI( obj, mindepth, sampleda, tree, abundance.weighted = TRUE, force = FALSE, seed = 123, ... ) ## S4 method for signature 'data.frame' get_NRI_NTI(obj, mindepth, sampleda, tree, abundance.weighted = TRUE, ...) ## S4 method for signature 'phyloseq' get_NRI_NTI(obj, mindepth, abundance.weighted = TRUE, ...)
obj |
object, data.frame of (nrow sample * ncol taxonomy(feature)) or phyloseq. |
... |
additional arguments see also "ses.mpd" and "ses.mntd" of "picante". |
mindepth |
numeric, Subsample size for rarefying community. |
sampleda |
data.frame, sample information, row sample * column factors. |
tree |
tree object, it can be phylo object or treedata object. |
abundance.weighted |
logical, whether calculate mean nearest taxon distances for each species weighted by species abundance, default is TRUE. |
force |
logical whether calculate the index even the count of otu is not rarefied, default is FALSE. If it is TRUE, meaning the rarefaction is not be performed automatically. |
seed |
integer a random seed to make the result reproducible, default is 123. |
alphasample object contained NRT and NTI.
Shuangbin Xu