BBI (version 0.3.0)

BBI: BBI

Description

The BBI function searches the taxa of the composition data in the reference table for match. The taxonomic assignement usually includes previous taxonomic ranks, e.g. Kingdom;Phylum;Class;Order;Family;Genus;species. The taxonomic path must be separated by a semicolon ';' in order properly parsed by the function. The BBI function then compute benthic biotic indices. The function BBI returns a list of containing.

Usage

BBI(data, log = FALSE)

Arguments

data

A data frame containing samples as columns and taxa as rows, with species (or last taxonomic rank) in the first column

log

Whether or not keeping the history of match searching in a separate file in the workinf directory. Default = F

Value

Function BBI returns a list containing :

found

The amount of taxa that matched an entry in the database and the amount that did not.

BBI

The BBI values per sample.

table

The subset of composition data that contains only taxa with at least a match in one of the BBI.

taxa

The list of taxa that matched an entry and the correspondant OTU, if from metabarcoding data data.

References

Borja, A., Franco, J., P<U+00E9>rez, V., 2000. A Marine Biotic Index to Establish the Ecological Quality of Soft-Bottom Benthos Within European Estuarine and Coastal Environments. Mar. Pollut. Bull. 40, 1100<U+2013>1114. doi:10.1016/S0025-326X(00)00061-8

Rygg, B., 2013. Norwegian Sensitivity Index (NSI) for marine macroinvertebrates, and an update of Indicator Species Index (ISI). Norwegian Institute for Water Research

Rygg, B., 2002. Indicator species index for assessing benthic ecological quality in marine waters of Norway. Norwegian Institute for Water Research

Examples

# NOT RUN {
## Loading the exemple data
data("metab")
data("morpho")
## Computing BBI indices
BI_metab <- BBI(metab)
BI_morpho <- BBI(morpho)
## print values
BI_metab$BBI
## print classes
BI_metab$BBIclass
# }