tina-matrix-method: Function for 'tina' dissimilarity calculation. Modified from...

In Guan06/mina: Microbial community dIversity and Network Analysis

Description

Function for 'tina' dissimilarity calculation. Modified from Schmidt et al., 2016. Person and Spearman could be used for correlation and weighted and unweighted Jaccard could be used for similarity calculation.

Usage

## S4 method for signature 'matrix'
tina(
  x,
  cor_method = "spearman",
  sim_method = "w_ja",
  threads = 80,
  nblocks = 400,
  ...
)

Arguments

x	A matrix for dissimilarity calculation.
cor_method	The method for correlation, "pearson" and "spearman" are available.
sim_method	The method for similarity, "w_ja" and "uw_ja" are available for weighted and unweighted Jaccard similarity respectively.
threads	The number of threads used for parallel running, 80 by default.
nblocks	The number of row and column for splitted sub-matrix, 400 by default.
...	Additional parameters.

Value

t The output 'tina' dissimilarity matrix.

Examples

## Not run: 
asv_norm <- norm_tab(maize_asv2, method = "raref", depth = 1000)
asv_dis <- com_dis(asv_norm, method = "bray")
asv_dis <- com_dis(asv_norm, method = "tina", threads = 8, nblocks = 40)
asv_tina <- tina(asv_norm, cor_method = "spearman", sim_method = "w_ja",
threads = 8, nblocks = 40)

## End(Not run)

Guan06/mina documentation built on Feb. 21, 2022, 11:56 a.m.