nEQR: nEQR

In BBI: Benthic Biotic Indices Calculation from Composition Data

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

Example output

Loading required package: vegan
Loading required package: permute
Loading required package: lattice
This is vegan 2.5-7
Processing : Siphonostomatoida - 0 match in database so far
   No match, trying exact match of the genus Siphonostomatoida
   No exact match, trying to match other species of the genus Siphonostomatoida
   Not found.
Processing : Placorhynchus octaculeatus - 0 match in database so far
   No match, trying exact match of the genus Placorhynchus
   No exact match, trying to match other species of the genus Placorhynchus
   Not found.
Processing : Acanthomacrostomum sp. - 0 match in database so far
   No match, trying exact match of the genus Acanthomacrostomum
   No exact match, trying to match other species of the genus Acanthomacrostomum
   Not found.
Processing : Paramphiascella fulvofasciata - 0 match in database so far
   No match, trying exact match of the genus Paramphiascella
   No exact match, trying to match other species of the genus Paramphiascella
   Not found.
Processing : Unassigned - 0 match in database so far
   No match, trying exact match of the genus Unassigned
   No exact match, trying to match other species of the genus Unassigned
   Not found.
Processing : Provortex balticus - 0 match in database so far
   No match, trying exact match of the genus Provortex
   No exact match, trying to match other species of the genus Provortex
   Not found.
Processing : Centropages - 0 match in database so far
   No match, trying exact match of the genus Centropages
   No exact match, trying to match other species of the genus Centropages
   Not found.
Processing : Promesostoma - 0 match in database so far
   No match, trying exact match of the genus Promesostoma
   No exact match, trying to match other species of the genus Promesostoma
   Not found.
Processing : Macrodasys - 0 match in database so far
   No match, trying exact match of the genus Macrodasys
   No exact match, trying to match other species of the genus Macrodasys
   Not found.
Processing : Capitella capitata - 1 match in database so far
   Found 1 matche for Capitella capitata
   Done - Capitella capitata AMBI: 5
Processing : Thyasira sarsi - 1 match in database so far
   Found 1 matche for Thyasira sarsi
   Done - Thyasira sarsi AMBI: 3
Processing : Misophriopsis - 0 match in database so far
   No match, trying exact match of the genus Misophriopsis
   No exact match, trying to match other species of the genus Misophriopsis
   Not found.
Processing : Unassigned - 0 match in database so far
   No match, trying exact match of the genus Unassigned
   No exact match, trying to match other species of the genus Unassigned
   Not found.
Processing : Spionida - 1 match in database so far
   Found 1 matche for Spionida
   Done - Spionida AMBI: 3
Processing : Hydrozoa - 1 match in database so far
   Found 1 matche for Hydrozoa
   Done - Hydrozoa AMBI: 1
Processing : Halomonhystera - 0 match in database so far
   No match, trying exact match of the genus Halomonhystera
   No exact match, trying to match other species of the genus Halomonhystera
   Not found.
Processing : Paracanthonchus caecus - 0 match in database so far
   No match, trying exact match of the genus Paracanthonchus
   No exact match, trying to match other species of the genus Paracanthonchus
   Not found.
Processing : Microstomum papillosum - 0 match in database so far
   No match, trying exact match of the genus Microstomum
   No exact match, trying to match other species of the genus Microstomum
   Not found.
Processing : Unassigned - 0 match in database so far
   No match, trying exact match of the genus Unassigned
   No exact match, trying to match other species of the genus Unassigned
   Not found.
Processing : Uncultured eukaryote - 0 match in database so far
   No match, trying exact match of the genus Uncultured
   No exact match, trying to match other species of the genus Uncultured
   Not found.
Processing : Uncultured Hydrozoa - 0 match in database so far
   No match, trying exact match of the genus Uncultured
   No exact match, trying to match other species of the genus Uncultured
   Not found.
Processing : Halomonhystera - 0 match in database so far
   No match, trying exact match of the genus Halomonhystera
   No exact match, trying to match other species of the genus Halomonhystera
   Not found.
Processing : uncultured eukaryote - 0 match in database so far
   No match, trying exact match of the genus uncultured
   No exact match, trying to match other species of the genus uncultured
   Not found.
Processing : Microstomum papillosum - 0 match in database so far
   No match, trying exact match of the genus Microstomum
   No exact match, trying to match other species of the genus Microstomum
   Not found.
Processing : Microstomum - 0 match in database so far
   No match, trying exact match of the genus Microstomum
   No exact match, trying to match other species of the genus Microstomum
   Not found.
==== Found match : 4  Not found : 21 ====
Processing : Capitella capitata - 1 match in database so far
   Found 1 matche for Capitella capitata
   Done - Capitella capitata AMBI: 5
Processing : Galathowenia oculata - 2 match in database so far
   Galathowenia oculata matched 2 entries in database. Trying exact match
   Found 1 match for Galathowenia oculata
   Done - Galathowenia oculata AMBI value 3
Processing : Paramphinome jeffreysii - 1 match in database so far
   Found 1 matche for Paramphinome jeffreysii
   Done - Paramphinome jeffreysii AMBI: 3
Processing : Owenia sp. - 2 match in database so far
   Owenia sp. matched 2 entries in database. Trying exact match
   Found 1 match for Owenia sp.
   Done - Owenia sp. AMBI value 2
Processing : Thyasira sarsii - 0 match in database so far
   No match, trying exact match of the genus Thyasira
   Found 1 match for Thyasira. Taking the median values of 1 multiple values
   Done - Thyasira AMBI value 2
Processing : Praxillella praetermissa - 1 match in database so far
   Found 1 matche for Praxillella praetermissa
   Done - Praxillella praetermissa AMBI: 3
Processing : Maldane sarsi - 1 match in database so far
   Found 1 matche for Maldane sarsi
   Done - Maldane sarsi AMBI: 2
Processing : Ophiuroidea - 1 match in database so far
   Found 1 matche for Ophiuroidea
   Done - Ophiuroidea AMBI: 2
Processing : Yoldiella lucida - 1 match in database so far
   Found 1 matche for Yoldiella lucida
   Done - Yoldiella lucida AMBI: 1
Processing : Ophryotrocha lobifera - 1 match in database so far
   Found 1 matche for Ophryotrocha lobifera
   Done - Ophryotrocha lobifera AMBI: NA
Processing : Macoma calcarea - 1 match in database so far
   Found 1 matche for Macoma calcarea
   Done - Macoma calcarea AMBI: 2
Processing : Labidoplax buskii - 1 match in database so far
   Found 1 matche for Labidoplax buskii
   Done - Labidoplax buskii AMBI: 1
Processing : Spio limicola - 0 match in database so far
   No match, trying exact match of the genus Spio
   Found 1 match for Spio. Taking the median values of 1 multiple values
   Done - Spio AMBI value 3
Processing : Nephtys ciliata - 1 match in database so far
   Found 1 matche for Nephtys ciliata
   Done - Nephtys ciliata AMBI: 2
Processing : Mendicula sp. - 0 match in database so far
   No match, trying exact match of the genus Mendicula
   No exact match, trying to match other species of the genus Mendicula
   Found 2 match for Mendicula. Taking the median values of 2 multiple values
   Done - Mendicula AMBI value 2
Processing : Ennucula tenuis - 1 match in database so far
   Found 1 matche for Ennucula tenuis
   Done - Ennucula tenuis AMBI: 2
Processing : Chaetozone sp. - 2 match in database so far
   Chaetozone sp. matched 2 entries in database. Trying exact match
   Found 1 match for Chaetozone sp.
   Done - Chaetozone sp. AMBI value 4
Processing : Malacoceros fuliginosus - 1 match in database so far
   Found 1 matche for Malacoceros fuliginosus
   Done - Malacoceros fuliginosus AMBI: 5
Processing : Pholoe assimilis - 1 match in database so far
   Found 1 matche for Pholoe assimilis
   Done - Pholoe assimilis AMBI: 1
Processing : Thyasira dunbari - 0 match in database so far
   No match, trying exact match of the genus Thyasira
   Found 1 match for Thyasira. Taking the median values of 1 multiple values
   Done - Thyasira AMBI value 2
Processing : Leitoscoloplos mammosus - 1 match in database so far
   Found 1 matche for Leitoscoloplos mammosus
   Done - Leitoscoloplos mammosus AMBI: 4
Processing : Thyasira gouldi - 1 match in database so far
   Found 1 matche for Thyasira gouldi
   Done - Thyasira gouldi AMBI: 1
Processing : Rhodine gracilior - 1 match in database so far
   Found 1 matche for Rhodine gracilior
   Done - Rhodine gracilior AMBI: 1
Processing : Uncultured eukaryote - 0 match in database so far
   No match, trying exact match of the genus Uncultured
   No exact match, trying to match other species of the genus Uncultured
   Not found.
Processing : Scoloplos armiger - 1 match in database so far
   Found 1 matche for Scoloplos armiger
   Done - Scoloplos armiger AMBI: 3
Processing : Phascolion strombus - 1 match in database so far
   Found 1 matche for Phascolion strombus
   Done - Phascolion strombus AMBI: 1
Processing : Cylichnina sp. - 1 match in database so far
   Found 1 matche for Cylichnina sp.
   Done - Cylichnina sp. AMBI: 2
Processing : Yoldiella solidula - 1 match in database so far
   Found 1 matche for Yoldiella solidula
   Done - Yoldiella solidula AMBI: 1
==== Found match : 27  Not found : 1 ====
Bentix and ITI are being removed (if any), because not included in the nEQR assessment regulations
              nAMBI      nISI      nNSI     nNQI1  nShannon      nEQR
Sample_1  0.4927869 0.3334375 0.4978295 0.2706754 0.6133450 0.4416148
Sample_2  0.5760000 0.3334375 0.5249600 0.3297881 0.5860883 0.4700548
Sample_3  0.6207893 0.3334375 0.3841595 0.3207885 0.4202401 0.4158830
Sample_4  0.7415282 0.3334375 0.6493628 0.4466937 0.5127581 0.5367561
Sample_5  0.7035361 0.3334375 0.6120851 0.4028798 0.3478161 0.4799509
Sample_6  0.4194990 0.3334375 0.3011240 0.2326905 0.5749925 0.3723487
Sample_7  0.3807254 0.3334375 0.2864157 0.2177387 0.6177641 0.3672163
Sample_8  0.2734790 0.3334375 0.2235558 0.3117520 0.5852395 0.3454928
Sample_9  0.5628340 0.3334375 0.4435449 0.2982984 0.5804366 0.4437103
Sample_10 0.6838710 0.3334375 0.6678258 0.4068171 0.5226625 0.5229228
          nEQR                nEQR_class
Sample_1  "0.441614848846294" "moderate"
Sample_2  "0.470054780958598" "moderate"
Sample_3  "0.415882997907429" "moderate"
Sample_4  "0.536756069778151" "moderate"
Sample_5  "0.479950926757639" "moderate"
Sample_6  "0.372348702808717" "bad"     
Sample_7  "0.367216273665213" "bad"     
Sample_8  "0.345492767447628" "bad"     
Sample_9  "0.443710285994319" "moderate"
Sample_10 "0.522922777551736" "moderate"

BBI documentation built on May 1, 2019, 10:28 p.m.