biomassRatio: Calculates the biomass ratio between two species groups
In marindicators: Marine Ecosystem and Fishing Pressure Indicators

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

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

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

`X`	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).
`ratio.groups`	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"`.
`species.table`	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`.
`metric`	A character string indicating which column in `X` to use to calculate indicator. Default is `metric = "BIOMASS"`.
`years`	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:

B_{invertebrates}/B_{demersal}

and

B_{pelagic}/B_{demersal}

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 Danielle.Dempsey@dfo-mpo.gc.ca, 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

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

# Compile data
data(X)
data(species.table)

# 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))