speciesrichness: Calculates Species Richness of the community or the Diversity...
In dempseydanielle/marindicators: Marine Ecosystem and Fishing Pressure Indicators

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

This function counts the number of species recorded in fishery independent survey data or commercial landings data for i years and j areas.

1	speciesRichness(X, groups, species.table = NULL, metric, years)

`X`	A dataframe of fishery independent data derived from research vessel survey data or model output, OR commercial landings data. Fishery independent survey data has columns `YEAR`, `ID`, `SPECIES`, and `ABUNDANCE` and/or `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 `ABUNDANCE`/`BIOMASS` is the corresponding abundance/biomass (stratified and corrected for catchability as required). Similarly, commercial landings data should have columns `YEAR`, `ID`, `SPECIES` are as above, and `CATCH` is the corresponding landed weight.
`groups`	A vector indicating the species group(s) for which to calculate the indicator. If `groups = "ALL"`, all species will be included; otherwise, each entry must be a character string matching the name of a column in `species.table`.
`species.table`	A table where the column names match the entries in `groups`. Column entries are species codes indicating the species from `X` included in each group. `species.table` may also include columns for other species groups; these will be ignored. If `groups = "ALL"`, this table is not required. Default is `species.table = NULL`.
`metric`	A character string indicating which column in `X` to use to calculate the indicator. Default is `metric = "ABUNDANCE"`.
`years`	A vector of years for which to calculate indicator.

Two useful species richness indicators are: "Species Richness" (S) of the surveyed community in an area and "Diversity of the Target Species" (TS) in the commercial fishery, which is a measure of the distribution of fishing pressure.

Species richness (S_y) is the count of the number of species recorded in all research vessel trawl surveys collected in year y for a given area (Hurlbert, 1971).

The diversity of the target species for year y (TS_y) is the count of the number of target species recorded in all trawl catches collected in that year for a given area.

Returns a dataframe with columns ID and YEAR, and if metric = "ABUNDANCE", a column SpeciesRichness_group for each entry in groups OR if metric = "CATCH", a column DiversityTargetSpp_group for each entry in groups.

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

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

Hurlbert SH. 1971. The non-concept of species diversity: a critique and alternative parameters. Ecology, 52, 577-86.

Other biodiversity indicators: allBiodiversity(), heips(), hillN1(), hillN2(), kemptonQ(), margalef(), pielouEvenness(), shannon()

Other fishing pressure indicators: allPressure(), fishingPressure(), landings(), meanTLLandings()

# Calculate species richness (community)
data(X)
speciesRichness(X, groups = "ALL", metric = "BIOMASS", years = c(2014:2019))

# Calculate diversity of target species
data(land)
speciesRichness(land, groups = "ALL", metric = "CATCH",  years = c(2014:2019))