margalef: Calculates Margalef's Species Richness
In marindicators: Marine Ecosystem and Fishing Pressure Indicators

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

This function calculates Margalef's Species Richness for j areas and i years.

1	margalef(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.

Margalef's Species Richness:

S_{Marg} = (S_y - 1)/log(F_y)

S_y is the count of the number of species recorded in all trawl catches collected in year y. F is the total count of all individuals caught in year y (Margalef, 1958).

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

Margalef R. 1958. Information theory in ecology. General Systems 3, 36–71.

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

1 2	data(X) margalef(X, groups = c("ALL", "GROUNDFISH"), metric= "ABUNDANCE", years = c(2014:2019))

      ID YEAR MargalefRichness_ALL MargalefRichness_GROUNDFISH
1  AREA1 2014             6.197670                          NA
2  AREA1 2015             7.702378                          NA
3  AREA1 2016             7.717426                          NA
4  AREA1 2017             8.265226                          NA
5  AREA1 2018             7.754668                          NA
6  AREA1 2019             7.842566                          NA
7  AREA2 2014             6.726931                          NA
8  AREA2 2015             6.420818                          NA
9  AREA2 2016             6.376422                          NA
10 AREA2 2017             6.143174                          NA
11 AREA2 2018             5.850146                          NA
12 AREA2 2019             6.054704                          NA