mp_mantel-methods: Mantel and Partial Mantel Tests for MPSE or tbl_mpse Object

In YuLab-SMU/MicrobiotaProcess: A comprehensive R package for managing and analyzing microbiome and other ecological data within the tidy framework

Mantel and Partial Mantel Tests for MPSE or tbl_mpse Object

Description

Mantel and Partial Mantel Tests for MPSE or tbl_mpse Object

Usage

mp_mantel(
  .data,
  .abundance,
  .y.env,
  .z.env = NULL,
  distmethod = "bray",
  distmethod.y = "euclidean",
  distmethod.z = "euclidean",
  method = "pearson",
  permutations = 999,
  action = "get",
  seed = 123,
  scale.y = FALSE,
  scale.z = FALSE,
  ...
)

## S4 method for signature 'MPSE'
mp_mantel(
  .data,
  .abundance,
  .y.env,
  .z.env = NULL,
  distmethod = "bray",
  distmethod.y = "euclidean",
  distmethod.z = "euclidean",
  method = "pearson",
  permutations = 999,
  action = "get",
  seed = 123,
  scale.y = FALSE,
  scale.z = FALSE,
  ...
)

## S4 method for signature 'tbl_mpse'
mp_mantel(
  .data,
  .abundance,
  .y.env,
  .z.env = NULL,
  distmethod = "bray",
  distmethod.y = "euclidean",
  distmethod.z = "euclidean",
  method = "pearson",
  permutations = 999,
  action = "get",
  seed = 123,
  scale.y = FALSE,
  scale.z = FALSE,
  ...
)

## S4 method for signature 'grouped_df_mpse'
mp_mantel(
  .data,
  .abundance,
  .y.env,
  .z.env = NULL,
  distmethod = "bray",
  distmethod.y = "euclidean",
  distmethod.z = "euclidean",
  method = "pearson",
  permutations = 999,
  action = "get",
  seed = 123,
  scale.y = FALSE,
  scale.z = FALSE,
  ...
)

Arguments

.data	MPSE or tbl_mpse object
.abundance	the name of otu abundance to be calculated
.y.env	the column names of continuous environment factors to perform Mantel statistic, it is required.
.z.env	the column names of continuous environment factors to perform Partial Mantel statistic based on this, default is NULL.
distmethod	character the method to calculate distance based on .abundance.
distmethod.y	character the method to calculate distance based on .y.env.
distmethod.z	character the method of calculated distance based on .z.env
method	character Correlation method, options is "pearson", "spearman" or "kendall"
permutations	the number of permutations required, default is 999.
action	character, "add" joins the mantel result to the internal attributes of the object, "only" and "get" return 'mantel' or 'mantel.partial' (if .z.env is provided) object.
seed	a random seed to make the analysis reproducible, default is 123.
scale.y	logical whether scale the environment matrix (.y.env) before the distance is calculated, default is FALSE
scale.z	logical whether scale the environment matrix (.z.env) before the distance is calculated, default is FALSE
...	additional parameters, see also mantel.

Value

update object or tibble according the 'action'

See Also

mantel

Examples

library(vegan)
data(varespec, varechem)
mpse <- MPSE(assays=list(Abundance=t(varespec)), colData=varechem)
mpse %>% mp_mantel(.abundance=Abundance, 
                   .y.env=colnames(varechem),
                   distmethod.y="euclidean",
                   scale.y = TRUE
                   )

YuLab-SMU/MicrobiotaProcess documentation built on Nov. 8, 2024, 4:37 p.m.