mp_cal_NRI_NTI {MicrobiotaProcess} | R Documentation |
Calculating NRI (Nearest Relative Index) and NTI (Nearest Taxon Index) with MPSE or tbl_mpse object
mp_cal_NRI_NTI( .data, .abundance, action = "add", abundance.weighted = TRUE, force = FALSE, seed = 123, ... ) ## S4 method for signature 'MPSE' mp_cal_NRI_NTI( .data, .abundance, action = "add", abundance.weighted = TRUE, force = FALSE, seed = 123, ... ) ## S4 method for signature 'tbl_mpse' mp_cal_NRI_NTI( .data, .abundance, action = "add", abundance.weighted = TRUE, force = FALSE, seed = 123, ... ) ## S4 method for signature 'grouped_df_mpse' mp_cal_NRI_NTI( .data, .abundance, action = "add", abundance.weighted = TRUE, force = FALSE, seed = 123, ... )
.data |
object, MPSE or tbl_mpse object |
.abundance |
The column name of OTU abundance column to be calculate. |
action |
character it has three options, "add" joins the new information to the input tbl (default), "only" return a non-redundant tibble with the just new information, ang 'get' return a 'alphasample' 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 alpha index even the '.abundance' is not rarefied, default is FALSE. |
seed |
integer a random seed to make the result reproducible, default is 123. |
... |
additional arguments see also "ses.mpd" and "ses.mntd" of "picante". |
update object.
Shuangbin Xu