This function calculates all (or a subset) of the Resource Potential 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.
allPotential(X, land, species.table, speciesinfo.table, resource.groups,
minTL = 0, TE = 0.1, base.start, base.end, years, raw = TRUE,
std = TRUE, glob.env = TRUE, export.path = NULL,
export.id = NULL)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).
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.
A table where the column names match the entries in
resource.groups. Column entries are the 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.
A table with columns SPECIES and the
corresponding TL_LAND (trophic level of landed species). Entries in
the SPECIES column should be the unique values of species codes in
land (or a subset thereof). Other columns will be ignored.
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.
The minimum trophic level of species to include to calculate FiB.
If minTL = NULL, FiB will not be calculated. Default is minTL =
0.
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.
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.
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.
A vector of years for which to calculate indicators.
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.
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.
Logical value indicating whether to return output to global
environment. Default is glob.env = TRUE.
File path indicating where to save a .csv file of
calculated indicators (named potential_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.
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 potential_export.id.csv. Default is
export.id = NULL.
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.
This function calculates the Resource Potential indicators: Abundance and Biomass of the community, Resource Potential of predefined species groups, and Fishing-in-Balance (FiB). 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.
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 resource potential indicators: fishingInBalance,
resourcePotential
# NOT RUN {
# Compile data
data(X)
data(land)
data(species.table)
data(species.info)
# Species groups of interest
resource.groups <- c("ALL", "CLUPEIDS", "FINFISH", "FLATFISH",
"FORAGE", "GADOIDS", "GROUNDFISH")
# Calculate standardized indicators
allPotential(X = X, land = land, species.table = species.table,
speciesinfo.table = species.info, resource.groups = resource.groups,
TE = 0.1, base.start = 2014, base.end = 2015, years = c(2014:2019),
raw = FALSE, std = TRUE)
# }
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