Strength of species-group associations for a phyloseq object

A wrapper for the indicspecies::strassoc() function in the case of a physeq object. It computes the strength of the association between each taxon and the groups defined by fact, using one of the association indices provided by the indicspecies package (e.g. IndVal, the phi coefficient r, the specificity component A, or the fidelity component B). It complements multipatt_pq() which tests the statistical significance of those associations.

Usage

strassoc_pq(
  physeq,
  fact,
  func = "IndVal.g",
  nboot_ci = NULL,
  alpha_ci = 0.05,
  ...
)

Arguments

physeq

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

fact

(required) Name of the factor in physeq@sam_data defining the groups of samples.

func

(chr, default "IndVal.g") The association index to compute. See ?indicspecies::strassoc() for the full list. Common values are:

• "IndVal" / "IndVal.g": Dufrêne-Legendre indicator value (the .g variant equalizes group sizes),

• "r" / "r.g": the point-biserial / phi coefficient of association,

• "A": specificity (positive predictive value) component,

• "B": fidelity (sensitivity) component.

nboot_ci

(int, default NULL) Number of bootstrap replicates used to estimate confidence intervals. When NULL (default), no bootstrap is performed and a single estimate is returned per taxon and group.

alpha_ci

(float, default 0.05) Error level for the bootstrap confidence intervals (only used when nboot_ci is not NULL).

...

Additional arguments passed on to indicspecies::strassoc().

Value

• When nboot_ci is NULL: a tibble with one row per taxon, a taxon column and one column per group containing the association value.

• When nboot_ci is set: the list returned by indicspecies::strassoc() with the lowerCI, stat and upperCI matrices.

Details

This function is mainly a wrapper of the work of others. Please make a reference to indicspecies::strassoc() if you use this function.

See also

multipatt_pq(), indicspecies::strassoc()

Author

Adrien Taudière

Examples

# \donttest{
if (requireNamespace("indicspecies")) {
  strassoc_pq(
    subset_samples(data_fungi_mini, !is.na(Height)),
    fact = "Height",
    func = "IndVal.g"
  )
}
#> Taxa are now in columns.
#> # A tibble: 45 × 4
#>    taxon   High    Low  Middle
#>    <chr>  <dbl>  <dbl>   <dbl>
#>  1 ASV7  0.519  0.157  0.268  
#>  2 ASV8  0.553  0.239  0.474  
#>  3 ASV12 0.178  0.391  0.157  
#>  4 ASV18 0.508  0.0984 0.0939 
#>  5 ASV25 0.459  0.0229 0.0218 
#>  6 ASV26 0.0173 0.105  0.304  
#>  7 ASV27 0.0576 0.168  0.00346
#>  8 ASV29 0.0340 0.229  0.266  
#>  9 ASV32 0.266  0.0169 0      
#> 10 ASV34 0.154  0.266  0.387  
#> # ℹ 35 more rows
# }
if (FALSE) { # \dontrun{
if (requireNamespace("indicspecies")) {
  strassoc_pq(
    subset_samples(data_fungi_mini, !is.na(Height)),
    fact = "Height",
    func = "A"
  )
  strassoc_pq(
    subset_samples(data_fungi_mini, !is.na(Height)),
    fact = "Height",
    func = "IndVal.g",
    nboot_ci = 99
  )
}
} # }