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Calculate hill number and compute Tuckey post-hoc test

Source: R/alpha_div_test.R
hill_tuckey_pq.Rd

[Maturing] Note that, by default, this function use a sqrt of the read numbers in the linear model in order to correct for uneven sampling depth.

Usage

hill_tuckey_pq(
  physeq,
  modality,
  hill_scales = c(0, 1, 2),
  silent = TRUE,
  correction_for_sample_size = TRUE
)

Arguments

physeq

(required): a phyloseq-class object obtained using the phyloseq package.

modality

(required) the variable to test

hill_scales

(a vector of integer) The list of q values to compute the hill number H^q. If Null, no hill number are computed. Default value compute the Hill number 0 (Species richness), the Hill number 1 (exponential of Shannon Index) and the Hill number 2 (inverse of Simpson Index).

silent

(logical) If TRUE, no message are printing.

correction_for_sample_size

(logical, default TRUE) This function use a sqrt of the read numbers in the linear model in order to correct for uneven sampling depth.

Value

A ggplot2 object

Author

Adrien Taudière

Examples

data("GlobalPatterns", package = "phyloseq")
GlobalPatterns@sam_data[, "Soil_logical"] <-
  ifelse(GlobalPatterns@sam_data[, "SampleType"] == "Soil", "Soil", "Not Soil")
hill_tuckey_pq(GlobalPatterns, "Soil_logical")
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘RNeXML’ ‘tidytree’
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘RNeXML’ ‘tidytree’

hill_tuckey_pq(GlobalPatterns, "Soil_logical", hill_scales = 1:2)
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘RNeXML’ ‘tidytree’
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘RNeXML’ ‘tidytree’