add.met | R Documentation |
Calculation of a variety of metrics for determing impairment of Benthic Macroinvertebrate Communities, based on available Reference Condition information.
add.met(Test, Reference, original = F, tax.fields = 2)
Test.taxa |
Output of |
Reference.taxa |
Output of |
Indicator metrics caluclated from benth.met
in addition to O:E ratios and Bray-Curtis Distance.
#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
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