dist_bdisp: Wrapper for vegan::betadisper()

In david-barnett/microViz: Microbiome Data Analysis and Visualization

Wrapper for vegan::betadisper()

Description

Takes the output of dist_calc function. Or use with the result of the permanova function to ensure the results correspond to exactly the same input data. Runs betadisper for all categorical variables in variables argument. See help('betadisper', package = 'vegan').

Usage

dist_bdisp(
  data,
  variables,
  method = c("centroid", "median")[[1]],
  complete_cases = TRUE,
  verbose = TRUE
)

Arguments

data	psExtra output from dist_calc
variables	list of variables to use as group
method	centroid or median
complete_cases	drop samples with NAs in any of the variables listed
verbose	sends messages about progress if true

Value

psExtra containing betadisper results

Examples

library(phyloseq)
library(vegan)
data("dietswap", package = "microbiome")

# add some missings to demonstrate automated removal
sample_data(dietswap)$sex[3:6] <- NA
# create a numeric variable to show it will be skipped with a warning
dietswap <- ps_mutate(dietswap, timepoint = as.numeric(timepoint))

# straight to the betadisp
bd1 <- dietswap %>%
  tax_agg("Genus") %>%
  dist_calc("aitchison") %>%
  dist_bdisp(variables = c("sex", "bmi_group", "timepoint")) %>%
  bdisp_get()
bd1$sex
# quick vegan plotting methods
plot(bd1$sex$model, label.cex = 0.5)
boxplot(bd1$sex$model)

# compute distance and use for both permanova and dist_bdisp
testDist <- dietswap %>%
  tax_agg("Genus") %>%
  dist_calc("bray")

PERM <- testDist %>%
  dist_permanova(
    variables = c("sex", "bmi_group"),
    n_processes = 1, n_perms = 99
  )
str(PERM, max.level = 1)

bd <- PERM %>% dist_bdisp(variables = c("sex", "bmi_group"))
bd

david-barnett/microViz documentation built on April 17, 2025, 4:25 a.m.