allStability: Calculates all Stability and Resistance indicators
In marindicators: Marine Ecosystem and Fishing Pressure Indicators

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

This function calculates all (or a subset) of the Stability and Resistance 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.

allStability(X, land, maxlength.group, species.table, speciesinfo.table,
  TL.grouping = 1, wind = 5, negative = FALSE, 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`, `BIOMASS`, 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 `BIOMASS`/`ABUNDANCE` is the corresponding biomass/abundance (stratified and corrected for catchability as required).
`land`	A dataframe of commercial landings data with columns `YEAR`, `ID`, `SPECIES` and `CATCH`. `YEAR` indicates the year the landing was recorded, `ID` is an area code indicating where the landing was recorded, `SPECIES` is a numeric code indicating the species landed, and `CATCH` is the corresponding landed weight.
`maxlength.group`	A character string indicating the species group for which to calculate the mean maximum length of fish in the community. Must be set to `"ALL"` or match a column name in `species.table`. If `maxlength.group = NULL`, the mean maximum length will not be calculated.
`species.table`	A table where the column names match the entries in `resource.groups`, `ratio.groups`, and/or `condition.groups`. Column entries are the species codes indicating the species from `X` (or `X_length`) included in each group. `species.table` may also include columns for other species groups; these will be ignored.
`speciesinfo.table`	A table with columns `SPECIES` and the corresponding `TL`, `MAXLENGTH`, `MAXAGE`, and `IVI` (trophic level, maximum recorded age, maximum recorded length, and intrinsic vulnerability index). Entries in the `SPECIES` column should be the unique values of species codes in `X` (or a subset thereof). If there are different species codes in `X` and `land`, the Intrinsic Vulnerability Index of the Landings indicator should be calculated separately using the function `IVILandings()`.
`TL.grouping`	Size of the trophic level bin for which to aggregate biomass when calculating Biomass per Trophic Level. For example, if `TL.grouping = 1`, trophic levels are binned from 1.00 - 1.99, 2.00 - 2.99, etc. If TL.grouping = 0.5, trophic levels are binned from 1.00 - 1.49, 1.50 - 1.99, 2.00 - 2.49, 2.50 - 2.99, etc. Default is `TL.grouping = 1` so that biomass is aggregated over discrete trophic levels.
`wind`	Window for the moving average used to calculate the Coefficient of Variation of the Biomass. The first and last `floor(wind/2)` values of the indicator are assigned `NA` to account for the moving average. Default is `wind = 5` years.
`negative`	If `negative = TRUE`, the Coefficient of Variation of the Biomass will be multiplied by -1 so that the expected response is to decrease with increasing fishing pressure. Default is `negative = FALSE`.
`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 stability_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 stability_export.id.csv. Default is `export.id = NULL`.

This function calculates the Stability and Resistance indicators: Biomass per Trophic Level, Intrinsic Vulnerability Index, Coefficient of Variation of the Biomass, Mean Lifespan, and Mean Maximum Length (weighted by biomass and abundance). If data are not available to calculate one or more of these indicators, a subset 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) is used to calculate the indicator. Here, BIOMASS is used to calculate Coefficient of Variation of the Biomass, Mean Lifespan, Biomass per Trophic Level, and Mean Maximum Length weighted by biomass. ABUNDANCE is used to calculate Mean Maximum Length weighted by abundance. See individual functions for more flexibility.

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 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.

Other stability and resistance indicators: CVBiomass, IVILandings, biomassPerTL, meanMaxAge, meanMaxLength

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

# Calculate raw and standardized indicators
allStability(X = X, land = land, maxlength.group = "FINFISH",
   species.table = species.table, speciesinfo.table = species.info,TL.grouping = 1,
   wind = 5, negative = FALSE, years = c(2014:2019), raw = TRUE, std = TRUE)