Calculate hill number and compute Tuckey post-hoc test

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,
  q = c(0, 1, 2),
  hill_scales = lifecycle::deprecated(),
  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

q

(numeric vector) Hill diversity orders to compute (q values). Default computes Hill number 0 (species richness), Hill number 1 (exponential of Shannon index) and Hill number 2 (inverse of Simpson index). Formerly hill_scales. Hill numbers are more appropriate in DNA metabarcoding studies when q > 0 (Alberdi & Gilbert, 2019; Calderón-Sanou et al., 2019).

hill_scales

Use q instead.

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.

...

Additional arguments passed to divent_hill_matrix_pq() and hence to divent::div_hill() (e.g. estimator = "naive" to match vegan-style results).

Value

A ggplot2 object

References

Alberdi, A., & Gilbert, M. T. P. (2019). A guide to the application of Hill numbers to DNA-based diversity analyses. Molecular Ecology Resources. 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. doi:10.1111/jbi.13681

Author

Adrien Taudière

Examples

hill_tuckey_pq(data_fungi_mini, "Height")