distmat_stats: Run statistics on a distance matrix vs a categorical or...

In cmmr/rbiom: Read/Write, Analyze, and Visualize 'BIOM' Data

Run statistics on a distance matrix vs a categorical or numeric variable.

Description

Run statistics on a distance matrix vs a categorical or numeric variable.

Usage

distmat_stats(dm, groups, test = "adonis2", seed = 0, permutations = 999)

Arguments

dm	A dist-class distance matrix, as returned from bdiv_distmat() or stats::dist(). Required.
groups	A named vector of grouping values. The names should correspond to attr(dm, 'Labels'). Values can be either categorical or numeric. Required.
test	Permutational test for accessing significance. Options are: "adonis2" - Permutational MANOVA; vegan::adonis2(). "mrpp" - Multiple response permutation procedure; vegan::mrpp(). "none" - Don't run any statistics. Default: "adonis2" Abbreviations are allowed.
seed	Random seed for permutations. Default: 0
permutations	Number of random permutations to use. Default: 999

Value

A data.frame with summary statistics from vegan::permustats(). The columns are:

• .n - The size of the distance matrix.

• .stat - The observed statistic. For mrpp, this is the overall weighted mean of group mean distances.

• .z - The difference of observed statistic and mean of permutations divided by the standard deviation of permutations (also known as z-values). Evaluated from permuted values without observed statistic.

• .p.val - Probability calculated by test.

R commands for reproducing the results are in $code.

See Also

Other beta_diversity: bdiv_boxplot(), bdiv_corrplot(), bdiv_heatmap(), bdiv_ord_plot(), bdiv_ord_table(), bdiv_stats(), bdiv_table()

Other stats_tables: adiv_stats(), bdiv_stats(), stats_table(), taxa_stats()

Examples

    library(rbiom)
    
    hmp10        <- hmp50$clone()
    hmp10$counts <- hmp10$counts[,1:10]
    
    dm <- bdiv_distmat(hmp10, 'unifrac')
    
    distmat_stats(dm, groups = pull(hmp10, 'Body Site'))
    
    distmat_stats(dm, groups = pull(hmp10, 'Age'))
    
    # See the R code used to calculate these statistics:
    stats <- distmat_stats(dm, groups = pull(hmp10, 'Age'))
    stats$code

cmmr/rbiom documentation built on April 28, 2024, 6:38 a.m.