| Type: | Package |
| Title: | Benthic Biotic Indices Calculation from Composition Data |
| Version: | 0.3.0 |
| Author: | Tristan Cordier [aut, cre] |
| Maintainer: | Tristan Cordier <tristan.cordier@gmail.com> |
| Depends: | vegan |
| Description: | Set of functions to calculate Benthic Biotic Indices from composition data, obtained whether from morphotaxonomic inventories or sequencing data. Based on reference ecological weights publicly available for a set of commonly used marine biotic indices, such as AMBI (A Marine Biotic Index, Borja et al., 2000) <doi:10.1016/S0025-326X(00)00061-8> NSI (Norwegian Sensitivity Index) and ISI (Indicator Species Index) (Rygg 2013, <ISBN:978-82-577-6210-0>). It provides the ecological quality status of the samples based on each BBI as well as the normalized Ecological Quality Ratio. |
| License: | AGPL-3 | file LICENSE |
| Encoding: | UTF-8 |
| BugReports: | https://github.com/trtcrd/BBI/issues |
| URL: | https://github.com/trtcrd/BBI |
| NeedsCompilation: | no |
| Packaged: | 2018-10-17 13:02:12 UTC; tristan |
| Repository: | CRAN |
| Date/Publication: | 2018-10-17 13:40:02 UTC |
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., Pérez, 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, 1100–1114. 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
## 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
Subset of metabarcoding data
Description
The metab dataset is an example of OTU table produced from metabarcoding data.
OTUs are in rows and samples are in columns. It contains taxonomic assignements of OTUs in the first column.
These 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 the properly parse it.
Usage
data("metab")
Examples
## Loading the exemple data
data("metab")
## Computing BBI indices
BI_metab <- BBI(metab)
## And then computing nEQR
eqr <- nEQR(BI_metab$BBI)
## print nEQR values
eqr$nEQR
## print discrete status
eqr$nEQRclass
Subset of morphologic inventories data
Description
The morpho dataset is an example of morpho-taxonomic inventories table produced from microscopical analysis.
Taxa are in rows and samples are in columns. It contains taxonomic assignements of taxa in the first column.
Usage
data("morpho")
Examples
## Loading the exemple data
data("morpho")
## Computing BBI indices
BI_morpho <- BBI(morpho)
## And then computing nEQR
eqr <- nEQR(BI_morpho$BBI)
## print nEQR values
eqr$nEQR
## print discrete status
eqr$nEQRclass
nEQR
Description
The nEQR function compute the normalized Ecological Quality Ratio (nEQR).
Usage
nEQR(data)
Arguments
data |
A data frame containing samples as rows and BBI values as columns |
Value
Function nEQR returns a list containing :
nEQR |
The nEQR value. |
nEQR_class |
The dicrete ecological quality assessment. |
Examples
## Loading the exemple data
data("metab")
data("morpho")
## Computing BBI indices
BI_metab <- BBI(metab)
BI_morpho <- BBI(morpho)
## And then computing nEQR
eqr <- nEQR(BI_metab$BBI)
## print nEQR values
eqr$nEQR
## print discrete status
eqr$nEQRclass