add.met: Reference specific Benthic Metric Calculation

In p-schaefer/BenthicAnalysistesting: Benthic Analysis with Test Site Anlysis

Reference specific Benthic Metric Calculation

Description

Calculation of a variety of metrics for determing impairment of Benthic Macroinvertebrate Communities, based on available Reference Condition information.

Usage

add.met(Test, Reference, original = F, tax.fields = 2)

Arguments

Test.taxa	Output of benth.met$Raw.Data for the test site
Reference.taxa	Output of benth.met$Raw.Data for the Reference site

Value

Indicator metrics caluclated from benth.met in addition to O:E ratios and Bray-Curtis Distance.

Examples

#load datasets
data(YKEnvData,envir = environment()) #Biological dataset
data(YKBioData,envir = environment()) #Environmental dataset

#Calculate indicator metrics from raw biological data
bio.data.test<-benth.met(YKBioData,2,2)

#standardize row names between datasets
rownames(YKEnvData)<-rownames(bio.data.test$Site.List)

#Match a test site (#201) to the nearest neighbour reference set
nn.sites<-site.match(YKEnvData[201,],YKEnvData[1:118,],k=NULL,adaptive=T)

#Extract the raw taxa data for additional metric calculation
taxa.data<-rbind(bio.data.test$Raw.Data[names(nn.sites$final.dist),],bio.data.test$Raw.Data[rownames(bio.data.test$Raw.Data[201,]),])

#Calculate additional metrics based on nearest neighbour reference sites
additional.metrics<-add.met(Test=bio.data.test$Raw.Data[rownames(bio.data.test$Raw.Data[201,]),],Reference=bio.data.test$Raw.Data[names(nn.sites$final.dist),])
additional.metrics

p-schaefer/BenthicAnalysistesting documentation built on Jan. 17, 2024, 7:24 p.m.