BenthicPB: Calculation of macrobenthic invertebrate productivity
In HenrikeAndresen/BenthicPro: Benthic Energy Flow

Description Usage Arguments Details Value Author(s) References See Also Examples

Predicts production to biomass ratio (P/B) of macrobenthic invertebrate populations. Takes a data frame with mean body mass in Joule, mean annual temperature, water depth, and taxonomic and lifestyle information. Returns mean production to biomass ratio per year, with 95% confidence limits. This is the translation to R of the Excel spreadsheet "ProductivityANN01" from the "Virtual Handbook on Population Dynamics" http://www.thomas-brey.de/science/virtualhandbook/navlog/index.html.

1	BenthicPB(data)

data

A data frame which must contain the following twenty columns: "Bodymass" (individual body mass or mean individual body mass in Joule. For taxon specific body mass conversions to Joule refer to the conversion data bank on http://www.thomas-brey.de/science/virtualhandbook/navlog/index.html); "Temperature" (mean annual bottom water temperature in Celsius); "Depth" (water depth in m); "Mollusca", "Annelida", "Crustacea", "Echinodermata", and "Insecta" (taxon coded as 1 and 0, must sum to 1 per row, other taxa must be assigned to one of these); "Infauna" (environmental position coded as 1 for infauna or 0 for epifauna); "Sessile", "Crawler", and "FacultativeSwimmer" (movement traits coded as 0 or 1, must sum to 1); "Herbivore", "Omnivore", and "Carnivore" (diet coded as 0 or 1, must sum to 1); "Lake", "River", and "Marine" (habitat coded as 0 or 1, must sum to 1); "Subtidal" (0 or 1, must be 1 if depth > 1 m), "Exploited" (0 or 1, 1 refers to fished populations, usually set to 0).

Data may contain additional columns, typically scientific name, sample ID, number of individuals per sample, total biomass, conversion factors, sample area etc.

Returns data frame with the columns annual.PtoB, lowerCI and upperCI.

Henrike Andresen <henrike.andresen@awi.de> and Thomas Brey

Brey, Thomas (2012) A multi-parameter artificial neural network model to estimate macrobenthic invertebrate productivity and production. Limnol. Oceanogr.: Methods 10, 2012, 581-589. DOI 10.4319/lom.2012.10.581

BenthicProdExampleData for an example data set.

# productivity of average individual per species and sample
data("BenthProdExampleData")
individualPB<-BenthicPB(BenthProdExampleData)
PBresults<-cbind(BenthProdExampleData,individualPB)

# annual secondary production in Joule per species and sample
productionJ<-PBresults$annual.PtoB*PBresults$Bodymass*PBresults$Count

# conversion from Joule to gram carbon
productionC<-productionJ/(PBresults$ConFac_j2mgc*1000)
biomassC<-PBresults$Bodymass*PBresults$Count/(PBresults$ConFac_j2mgc*1000)

# summation over all species per sample and conversion to squaremeter
ProductionGramCperSqm<-aggregate(productionC/PBresults$Sample.area, by=list(SampleID=PBresults$SampleID), FUN=sum)
BiomassGramCperSqm<-aggregate(biomassC/PBresults$Sample.area, by=list(SampleID=PBresults$SampleID), FUN=sum)

# annual carbon productivity
summarized.results<-cbind(BiomassGramCperSqm$SampleID,BiomassGramCperSqm$x, ProductionGramCperSqm$x, ProductionGramCperSqm$x/BiomassGramCperSqm$x)
colnames(summarized.results)=c("SampleID", "Biomass.gC/m^2", "Production.gC/m^2", "Carbon.Productivity")
summarized.results