extractAll: Calculates indicators from all attributes
In marindicators: Marine Ecosystem and Fishing Pressure Indicators

Description Usage Arguments Details Value Author(s) Examples

This function calculates all of the indicators described in this package. 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.

extractAll(X, X_length, land, speciesinfo.table, species.table, years,
  metric.bio = "ABUNDANCE", group.bio = "ALL", percentiles = c(0.25,
  0.75), minTL.bio = 0, LSI.group, max.length = 85, LFI.group,
  large.fish = 35, LenWt.table, guild.groups, condition.groups,
  ratio.groups, maxlength.group, TL.grouping = 1, wind = 5,
  negative = FALSE, resource.groups, minTL.FiB = 0, TE = 0.1,
  base.start, base.end, landings.groups, FP.groups, minTL.FP = c(0,
  3.25), 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 `ABUNDANCE` is the corresponding abundance (stratified and corrected for catchability as required).
`X_length`	A dataframe of fishery independent data derived from research vessel survey data or model output, with columns `YEAR`, `ID`, `SPECIES`, `LENGTH`, `BIOMASS` and `ABUNDANCE`. `YEAR` indicates the year the observation was recorded, `ID` is an area code indicating where the observation was recorded, and `SPECIES` is a numeric code indicating the species sampled. `LENGTH` is the length class (cm) and `ABUNDANCE` is the corresponding abundance at length (stratified and corrected for catchability as required). Species for which there are no length data should be assigned `LENGTH = -99`. These observations are removed by the function.
`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. If `land = NULL`, the landings-based indicators will not be calculated.
`speciesinfo.table`	A table with columns `SPECIES` and the corresponding `TL`, `MAXLENGTH`, `MAXAGE`, `IVI`, and `TL_LAND` (trophic level, maximum recorded age, maximum recorded length, intrinsic vulnerability index, and trophic level of the landings). Entries in the `SPECIES` column should be the unique values of species codes in `X`/`X_length` (or a subset thereof). If there are different species codes in `X` and `land`, the Fishing-in-Balance, Intrinsic Vulnerability Index of Landings, Mean Trophic Level of the Landings, and Marine Trophic Index should be calculated using their respective single functions (see manual or vignette).
`species.table`	A table where the column names match the entries in `condition.groups`, `FP.groups`, `group.bio`, `guild.groups`, `landings.group`, `LFI.group`, `LSI.group`, `maxlength.group`, `ratio.groups`, and `resource.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.
`years`	A vector of years for which to calculate indicators.
`metric.bio`	A character string indicating which column in `X` to use to calculate the biodiversity indicators. Default is `metric = "ABUNDANCE"`.
`group.bio`	A character string indicating which species to include in the calculation of the Biodiversity indicators. If `group = "ALL"`, all species will be included; otherwise, `group.bio` should match a column name in `species.table`. Default is `group.bio = "ALL"`.
`percentiles`	The percentiles used to determine R1 and R2 for calculating Kempton's Q. Default is `percentiles = c(0.25, 0.75)`.
`minTL.bio`	Minimum trophic level for species included to calculate Kempton's Q. Default is `minTL.bio = 0`.
`LSI.group`	A character string indicating the species group for which to calculate the Large Species Indicator. Must be set to `"ALL"` or match a column name in `species.table`. If `LSI.group = NULL`, the Large Species Indicator will not be calculated.
`max.length`	The threshold for large species (cm). Default is `max.length = 85` (i.e., large species are those with `MAXLENGTH` >= 85 cm).
`LFI.group`	A character string indicating the species group for which to calculate the Large Fish Indicator. Must be set to `"ALL"` or match a column name in `species.table`. If `LFI.group = NULL`, the Large Fish Indicator will not be calculated.
`large.fish`	Threshold for large fish (cm). Default is `large.fish = 35` (i.e., large fish are those with `X_length$LENGTH` >= 35 cm).
`LenWt.table`	A table of annual length at weight data with 5 columns. `YEAR`, `ID`, and `SPECIES` are as described in `X_length`. `LENGTH` is fish length at the corresponding `WEIGHT` (fish weight).
`guild.groups`	A vector indicating the species groups for which to calculate the resource potential. Each entry must be a character string matching the name of a column in `species.table`. If `guild.groups = NULL`, these indicators will not be calculated.
`condition.groups`	A vector indicating the species groups for which to calculate Fulton's community condition factor. Each entry must be a character string matching the name of a column in `species.table`. If `condition.groups = NULL`, the community condition indicators will not be calculated.
`ratio.groups`	A dataframe with two columns, which must be named `group1` and `group2`. Each row holds the group names for one biomass ratio, with the numerator in column `group1` and the denominator in column `group2`. Each entry must be a character string matching the name of a column in `species.table` or `"ALL"`. If `ratio.groups = NULL`, biomass ratio indicators will not be calculated.
`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.
`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 and the Intrinsic Vulnerability Index of the Landings will be multiplied by -1 so that their expected response is to decrease with increasing fishing pressure. Default is `negative = FALSE`.
`resource.groups`	A vector indicating the species groups for which to calculate the resource potential. Each entry must be a character string matching the name of a column in `species.table`. If `resource.groups = NULL`, these indicators will not be calculated.
`minTL.FiB`	The minimum trophic level of species to include to calculate Fishing-in-Balance.
`TE`	Trophic efficiency, used to calculate FiB. Default is `TE = 0.1`, i.e., a trophic efficiency of 10%. If `TE = NULL`, FiB will not be calculated.
`base.start`	Year indicating the beginning of the baseline period for calculating FiB. The average landings and average mean trophic level of the landings over the baseline period are used as baseline values to calculate FiB. `land` must include data for the baseline period. If `base.start = NULL`, FiB will not be calculated.
`base.end`	Year indicating the end of the baseline period for calculating FiB. The average landings and average mean trophic level of the landings over the baseline period are used as baseline values to calculate FiB. `land` must include data for the baseline period. If `base.end = NULL`, FiB will not be calculated.
`landings.groups`	A vector indicating the species groups for which to calculate the landings. Each entry must be a character string matching the name of a column in `species.table`. If `landings.groups = NULL`, no Landings indicators will be calculated.
`FP.groups`	A dataframe with two columns, which must be named `group.land` and `group.X`. Each row holds the group names to calculate the fishing pressure on a target group, with the numerator in column `group.land` and the denominator in column `group.X`. Each entry must be a character string matching the name of a column in `species.table`. If `FP.groups = NULL`, no fishing pressure indicators will be calculated.
`minTL.FP`	A vector containing minimum trophic level to include when calculating the mean trophic level of the landings. Default is `minTL = c(0, 3.25)`, which will return the mean trophic level of the landings and the marine trophic index.
`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 allIndicators_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 allIndicators_export.id.csv. Default is `export.id = NULL`.

This function calculates the indicators for each attribute and pressure: Biodiversity, Structure and Functioning, Stability and Resistance, Resource Potential, and Fishing Pressure.

See the help file for the individual functions for information on how each indicator is calculated.

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

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

# Species groups of interest
trophicguild.groups <- c("LBENTHIVORE", "MBENTHIVORE", "PISCIVORE", "PLANKTIVORE",
   "ZOOPISCIVORE")
condition.groups <- c("FINFISH", "PISCIVORE", "PLANKTIVORE", "ZOOPISCIVORE")
resource.groups <- c("ALL", "CLUPEIDS", "FINFISH", "FLATFISH", "FORAGE",
   "GADOIDS", "GROUNDFISH", "PELAGIC", "SKATES")
ratio.groups <- data.frame(rbind(c("PELAGIC", "GROUNDFISH"), c("PREDATORS", "ALL")))
names(ratio.groups) <- c("group1", "group2")

landings.groups <- c("ALL", "CLUPEIDS.L", "FLATFISH.L", "GROUNDFISH.L")
FP.groups <- data.frame(rbind(c("ALL", "ALL"),
    c("CLUPEIDS", "CLUPEIDS.L"),
    c("FLATFISH", "FLATFISH.L"),
    c("GROUNDFISH", "GROUNDFISH.L")))
names(FP.groups) <- c("group.X", "group.land")

# Calculate raw and standardized indicators
extractAll(X = X, X_length = X_length, land = land,
    speciesinfo.table = species.info, species.table = species.table, years = c(2014:2019),
    LSI.group = "ALL", LFI.group = "ALL", LenWt.table = Length_Weight,
    guild.groups = trophicguild.groups, condition.groups = condition.groups,
    ratio.groups = ratio.groups,
    maxlength.group = "FINFISH",
    resource.groups = resource.groups,
    minTL.FiB = 0, base.start = 2014, base.end = 2015,
    landings.groups = landings.groups, FP.groups = FP.groups,
    raw = TRUE, std = TRUE, export.path = NULL)