shannon: Calculates Shannon's Index of Diversity

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

View source: R/shannon.R


This function calculates Shannon's Index of Diversity for j areas and i years.


shannon(X, groups, species.table = NULL, metric = "ABUNDANCE", years)



A dataframe of fishery independent data derived from research vessel survey data or model output, with columns YEAR, ID, SPECIES, and ABUNDANCE. 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 is the corresponding abundance (stratified and corrected for catchability as required).


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.


Shannon's index of diversity (H'):

H' = -Σ p_i ln(p_i)

p_i is the proportion of the total sample contributed by the i(th) species and S is the number of species recorded in the sample. This index is sensitive to the number of species recorded in the sample (Magurran, 1988).


Returns a dataframe with columns ID and YEAR, and a column ShannonDiversity_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, 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.

Greenstreet SP, Rogers SI. 2006. Indicators of the health of the North Sea fish community: identifying reference levels for an ecosystem approach to management. ICES J Mar Sci J du Cons 63:573-593

Magurran, AE. 1988. Ecological Diversity and its Measurement. Chapman and Hall, London. 179 pp.

See Also

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


shannon(X, groups = c("ALL", "FINFISH"), metric = "ABUNDANCE", years = c(2014:2019))

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