biomassRatio: Calculates the biomass ratio between two species groups

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

View source: R/biomassRatio.R


This function calculates the biomass ratio between two pre-defined species groups for j areas and i years.


biomassRatio(X, ratio.groups, species.table, metric = "BIOMASS", years)



A dataframe of fishery independent data derived from research vessel survey data or model output, with columns YEAR, ID, SPECIES, and BIOMASS. YEAR indicates the year the observation was recorded, ID is an area code indicating where the observation was recorded, SPECIES is a numeric code indicating the species sampled, and BIOMASS is the corresponding biomass (stratified and corrected for catchability as required).


A dataframe with two columns, which must be named group1 and group2. Each row holds the group names for one biomass ratio, with the numerator in column group1 and the denominator in column group2. Each entry must be a character string matching the name of a column in species.table or "ALL".


A table with column names that match the entries of ratio.groups. The entries in each column are the species codes from X indicating which species are included that group. species.table may also include columns for other species groups; these will be ignored. Note that an entry in ratio.groups could be "ALL". In this case, a column in species.table named "ALL" is not required; the function will automatically include all species in X.


A character string indicating which column in X to use to calculate indicator. Default is metric = "BIOMASS".


A vector of years for which to calculate indicator.


One useful biomass ratio is the proportion of predatory fish in the community, which is estimated by:

PropPred = Biomass of Predatory Fish Surveyed/Total Biomass Surveyed

Predatory fish species are defined as all surveyed fish species that are not largely planktivorous, ie., fish that are piscivorous, or that feed on invertebrates larger than the macrozooplankton category (0.2 cm; Shin et al. 2010). Phytoplankton, zooplankton and detritus feeders should be excluded. This indicator captures changes in the trophic structure and changes in the functional diversity of fish in the ecosystem.

Other useful biomass (B) ratios indicators include:





Returns a dataframe with columns ID and YEAR, and a column for each biomass ratio, named after the entries in ratio.groups, e.g. group1_group2.

If there is no data for spatial scale j in year i, indicator values is assigned NA.


Danielle Dempsey, Adam Cook, Catalina Gomez, Alida Bundy


Bundy A, Gomez C, Cook AM. 2017. Guidance framework for the selection and evaluation of ecological indicators. Can. Tech. Rep. Fish. Aquat. Sci. 3232: xii + 212 p.

Bundy A, Heymans JJ, Morissette L, Savenkoff C (2009) Seals, cod and forage fish: A comparative exploration of variations in the theme of stock collapse and ecosystem change in four Northwest Atlantic ecosystems. Prog Oceanogr 81:188 206

Shin YJ, Shannon LJ, Bundy A, Coll M, Aydin K, Bez N, Blanchard JL, Borges, MF, Diallo I, Diaz E, Heymans JJ, Hill L, Johannesen E, Jouffre D, Kifani S, Labrosse P, Link JS, Mackinson S, Masski H, Möllmann C, Neira S, Ojaveer H, Abdallahi KM, Perry I, Thiao D, Yemane D, and Cury PM. 2010. Using indicators for evaluating, comparing and communicating the ecological status of exploited marine ecosystems. Part 2: Setting the scene. ICES Journal of Marine Science, 67: 692-716

See Also

Other ecosystem structure and function indicators: allStructure, communityCondition, largeFishIndicator, largeSpeciesIndicator, meanTLCommunity


# Compile data

# Species groups of interest
ratio.groups <- data.frame(rbind(c("PELAGIC", "GROUNDFISH"), c("PREDATORS", "ALL")))
names(ratio.groups) <- c("group1", "group2")

# Calculate indicators
biomassRatio(X, ratio.groups = ratio.groups, species.table = species.table,
   metric = "BIOMASS", years = c(2014:2019))

marindicators documentation built on Nov. 12, 2019, 5:07 p.m.