kemptonQ: Calculates Kempton's Biodiversity Index
In marindicators: Marine Ecosystem and Fishing Pressure Indicators

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

This function calculates Kempton's Biodiversity index (Q) for j areas and i years.

1 2	kemptonQ(X, TL.table, percentiles = c(0.25, 0.75), minTL = 0, 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).
`TL.table`	A dataframe with columns `SPECIES` and the corresponding `TL` (trophic level). Entries in the `SPECIES` column should be the unique values of species codes in `X` (or a subset thereof). Other columns in `TL.table` are ignored.
`percentiles`	The percentiles used to determine R1 and R2. Default is `percentiles = c(0.25, 0.75)`.
`minTL`	Minimum trophic level for species included in the calculation. Default is `minTL = 0`.
`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.

Kempton's Biodiversity Index (Q) is a relative index of diversity calculated from the Kempton's Q75 index developed for expressing species diversity.

Q = S*(p_2 - p_1)*log(R_2/R_1)

S is the total number of species or functional groups, p_1 and p_2 are the lower and upper percentiles of interest and R_1 and R_2 are the corresponding lower and upper quartiles of the species abundance distribution. p_1 and p_2 are defaulted to 0.25 and 0.75, respectively (Kempton and Taylor, 1976).

Returns a dataframe with columns ID and YEAR, and a column KemptonQ_minTL_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

Ainsworth, C, Pitcher, T. 2006. Modifying Kempton's species diversity index for use with ecosystem simulation models. Ecological Indicators. 6. 623-630. 10.1016/j.ecolind.2005.08.024.

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.

Kempton R, Taylor L. 1976. Models and statistics for species diversity. Nature 262:818-820

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

# Compile data
data(X)
data(species.info)

# Calculate indicator
kemptonQ(X, TL.table = species.info, percentiles = c(.25, 0.75), minTL = 0,
   groups = "ALL", metric = "ABUNDANCE", years = c(2014:2019))

      ID YEAR KemptonQ_0_ALL
1  AREA1 2014       13.12902
2  AREA1 2015       15.15009
3  AREA1 2016       15.66883
4  AREA1 2017       15.71705
5  AREA1 2018       13.13195
6  AREA1 2019       16.62034
7  AREA2 2014       14.80901
8  AREA2 2015       13.31722
9  AREA2 2016       12.48471
10 AREA2 2017       10.57121
11 AREA2 2018       11.35864
12 AREA2 2019       13.33981