hill_test_rarperm_pq: Test multiple times effect of factor on Hill diversity with...

In MiscMetabar: Miscellaneous Functions for Metabarcoding Analysis

Test multiple times effect of factor on Hill diversity with different rarefaction even depth

Description

This reduce the risk of a random drawing of a exceptional situation of an unique rarefaction.

Usage

hill_test_rarperm_pq(
  physeq,
  fact,
  q = c(0, 1, 2),
  nperm = 99,
  sample.size = min(sample_sums(physeq)),
  verbose = FALSE,
  progress_bar = TRUE,
  p_val_signif = 0.05,
  type = "nonparametric",
  ...
)

Arguments

physeq	(required) a phyloseq-class object obtained using the phyloseq package.
fact	(required) Name of the factor in physeq@sam_data used to plot different lines
q	(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). Hill numbers are more appropriate in DNA metabarcoding studies when q > 0 (Alberdi & Gilbert, 2019; Calderón-Sanou et al., 2019).
nperm	(int) The number of permutations to perform.
sample.size	(int) A single integer value equal to the number of reads being simulated, also known as the depth. See phyloseq::rarefy_even_depth() and rarefy_even_depth_pq().
verbose	(logical). If TRUE, print additional information.
progress_bar	(logical, default TRUE) Do we print progress during the calculation?
p_val_signif	(float, ⁠[0:1]⁠) The mimimum value of p-value to count a test as significant int the prop_signif result.
type	A character specifying the type of statistical approach (See ggstatsplot::ggbetweenstats() for more details): "parametric" "nonparametric" "robust" "bayes"
...	Additional arguments passed on to ggstatsplot::ggbetweenstats() function

Value

A list of 6 components :

• method

• expressions

• plots

• pvals

• prop_signif

• statistics

Author(s)

Adrien Taudière

References

Alberdi, A., & Gilbert, M. T. P. (2019). A guide to the application of Hill numbers to DNA-based diversity analyses. Molecular Ecology Resources. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1111/1755-0998.13014")}

Calderón-Sanou, I., Münkemüller, T., Boyer, F., Zinger, L., & Thuiller, W. (2019). From environmental DNA sequences to ecological conclusions: How strong is the influence of methodological choices? Journal of Biogeography, 47. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1111/jbi.13681")}

See Also

ggstatsplot::ggbetweenstats(), hill_pq()

Examples

## Not run: 
if (requireNamespace("ggstatsplot")) {
  hill_test_rarperm_pq(data_fungi, "Time", nperm = 3)
  res <- hill_test_rarperm_pq(data_fungi, "Height",
    nperm = 3,
    p_val_signif = 0.9
  )
  patchwork::wrap_plots(res$plots[[1]])
  res$plots[[1]][[1]] + res$plots[[2]][[1]] + res$plots[[3]][[1]]
  res$prop_signif
  res_para <- hill_test_rarperm_pq(data_fungi, "Height",
    nperm = 3,
    type = "parametric"
  )
  res_para$plots[[1]][[1]] + res_para$plots[[2]][[1]] + res_para$plots[[3]][[1]]
  res_para$pvals
  res_para$method
  res_para$expressions[[1]]
}

## End(Not run)

MiscMetabar documentation built on June 8, 2026, 5:07 p.m.