marindicators (version 1.0.0)

kemptonQ: Calculates Kempton's Biodiversity Index

Description

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

Usage

kemptonQ(X, TL.table, percentiles = c(0.25, 0.75), minTL = 0, groups,
  species.table = NULL, metric = "ABUNDANCE", years)

Arguments

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.

Value

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.

Details

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).

References

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

See Also

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

Examples

# NOT RUN {
# 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))
# }