shannon: Calculates Shannon's Index of Diversity
In dempseydanielle/marindicators: Marine Ecosystem and Fishing Pressure Indicators

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

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

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

`X`	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).
`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.

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 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.

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.

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