Hill numbers are the number of equiprobable species giving the same diversity value as the observed distribution.

Note that contrary to `hill_pq()`

, this function does not take into
account for difference in the number of sequences per samples/modalities.
You may use rarefy_by_sample = TRUE if the mean number of sequences per
samples differs among modalities.

## Usage

```
psmelt_samples_pq(
physeq,
hill_scales = c(0, 1, 2),
filter_zero = TRUE,
rarefy_by_sample = FALSE,
taxa_ranks = NULL
)
```

## Arguments

- physeq
(required): a

`phyloseq-class`

object obtained using the`phyloseq`

package.- 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).

- filter_zero
(logical, default TRUE) Do we filter non present OTU from samples ? For the moment, this has no effect on the result because the dataframe is grouped by samples with abundance summed across OTU.

- rarefy_by_sample
(logical, default FALSE) If TRUE, rarefy samples using

`phyloseq::rarefy_even_depth()`

function.- taxa_ranks
A vector of taxonomic ranks. For examples c("Family","Genus"). If taxa ranks is not set (default value = NULL), taxonomic information are not present in the resulting tibble.

## Value

A tibble with a row for each sample. Columns provide information
from `sam_data`

slot as well as hill numbers, Abundance (nb of sequences),
and Abundance_log10 (*log10(1+Abundance)*).

## Examples

```
if (requireNamespace("ggstatsplot")) {
psm_tib <- psmelt_samples_pq(data_fungi_mini, hill_scales = c(0, 2, 7))
ggstatsplot::ggbetweenstats(psm_tib, Height, Hill_0)
ggstatsplot::ggbetweenstats(psm_tib, Height, Hill_7)
psm_tib_tax <- psmelt_samples_pq(data_fungi_mini, taxa_ranks = c("Class", "Family"))
ggplot(filter(psm_tib_tax, Abundance > 2000), aes(y = Family, x = Abundance, fill = Time)) +
geom_bar(stat = "identity") +
facet_wrap(~Height)
}
#> Joining with `by = join_by(Sample)`
#> Joining with `by = join_by(Sample)`
```