allBiodiversity: Calculates all Biodiversity indicators
In dempseydanielle/marindicators: Marine Ecosystem and Fishing Pressure Indicators

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

This function calculates all (or a subset) of the Biodiversity indicators for j areas and i years. The user can choose whether the function returns the indicator dataframe to the global environment, exports the dataframe to a csv file, or both. The user can also choose whether the function returns the raw indicator values, the standardized (z-score) values, or both.

allBiodiversity(
  X,
  metric = "ABUNDANCE",
  groups = "ALL",
  species.table = NULL,
  TL.table,
  percentiles = c(0.25, 0.75),
  minTL = 0,
  years,
  raw = TRUE,
  std = TRUE,
  glob.env = TRUE,
  export.path = NULL,
  export.id = NULL
)

`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).
`metric`	A character string indicating which column in `X` to use to calculate the indicators. Default is `metric = "ABUNDANCE"`.
`groups`	A vector indicating the species group(s) for which to calculate the indicators. 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`. Default is `groups = "ALL"`.
`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`.
`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. If `TL.table = NULL`, Kempton's Q will not be calculated.
`percentiles`	The percentiles used to determine R1 and R2 for calculating Kempton's Q. Default is `percentiles = c(0.25, 0.75)`.
`minTL`	Minimum trophic level for species included to calculate Kempton's Q. Default is `minTL = 0`.
`years`	A vector of years for which to calculate indicators.
`raw`	A logical value. If `raw = TRUE`, the raw indicator values are returned by the function. If `raw = FALSE`, the raw indicator values are not returned. Default is `raw = TRUE`. Either `raw` or `std` must be `TRUE`.
`std`	A logical value. If `std = TRUE`, the standardized indicator values for each area `ID` are returned by the function. Indicators are standardized using z-scores, i.e., by subtracting the mean and dividing by the standard deviation (ignoring `NA` values). If `std = FALSE`, the standardized indicator values are not returned. Default is `std = TRUE`. Either `raw` or `std` must be `TRUE`.
`glob.env`	Logical value indicating whether to return output to global environment. Default is `glob.env = TRUE`.
`export.path`	File path indicating where to save a .csv file of calculated indicators (named biodiversity_export.id.csv; see below). If `export.file = NULL`, the indicator dataframe will not be exported as a .csv file. Default is `export.path = NULL`.
`export.id`	Character string to modify the name of the .csv file (if export.path is specified), for example an area name or date of analysis. The exported .csv file is named biodiversity_export.id.csv. Default is `export.id = NULL`.

This function calculates the Biodiversity indicators: Species Richness, Shannon's Index of Diversity, Margalef's Species Richness, Pielou's Species Evenness, Hill's N1, Hill's N2, Heip's Evenness Index, and Kempton's Q. If trophic level data are not available to calculate Kempton's Q, the remaining Biodiversity indicators will be returned. See the help file for the individual functions for information on how each indicator is calculated.

Notes on indicator calculations: In the individual functions, the user generally has control over which metric (e.g., "BIOMASS" or "ABUNDANCE") and group (e.g., "ALL" or "GROUNDFISH") are used to calculate the indicator. Here, the same metric and group are used to calculate each indicator. Defaults are metric = "ABUNDANCE" and group = "ALL".

Returns a dataframe with columns ID, YEAR, and indicators corresponding to the arguments supplied to the function. Standardized indicators are noted with _s in the name.

Danielle Dempsey, Adam Cook Adam.Cook@dfo-mpo.gc.ca, Catalina Gomez, Alida Bundy

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

data(X)

# Calculate raw and standardized indicators
allBiodiversity(X = X, metric = "ABUNDANCE", groups = "ALL", TL.table = species.info,
   percentiles = c(.25, 0.75), minTL = 0, years = c(2014:2019), raw = TRUE, std = TRUE)