speciesRichness: Calculates Species Richness of the community or the Diversity...

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

View source: R/speciesRichness.R


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


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



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.


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.


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.


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


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 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.

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

See Also

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

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


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

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

Example output

      ID YEAR SpeciesRichness_ALL
1  AREA1 2014                 153
2  AREA1 2015                 190
3  AREA1 2016                 191
4  AREA1 2017                 200
5  AREA1 2018                 187
6  AREA1 2019                 196
7  AREA2 2014                 161
8  AREA2 2015                 150
9  AREA2 2016                 151
10 AREA2 2017                 143
11 AREA2 2018                 140
12 AREA2 2019                 141
      ID YEAR DiversityTargetSpp_ALL
1  AREA1 2014                     51
2  AREA1 2015                     51
3  AREA1 2016                     51
4  AREA1 2017                     51
5  AREA1 2018                     51
6  AREA1 2019                     51
7  AREA2 2014                     51
8  AREA2 2015                     51
9  AREA2 2016                     51
10 AREA2 2017                     51
11 AREA2 2018                     51
12 AREA2 2019                     51

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