Tidy commercial PBS CPUE data

This function determines the qualifying "fleet" for CPUE analyses. It is meant to be used with modern data available at the fishing event level.

tidy_cpue_index(dat, species_common, year_range = c(1996,
  as.numeric(format(Sys.Date(), "%Y")) - 1),
  alt_year_start_date = "04-01", use_alt_year = FALSE,
  lat_range = c(48, Inf), min_positive_tows = 100,
  min_positive_trips = 5, min_yrs_with_trips = 5,
  area_grep_pattern = "5[CDE]+", lat_band_width = 0.1,
  depth_band_width = 25, clean_bins = TRUE,
  depth_bin_quantiles = c(0.001, 0.999), min_bin_prop = 0.001,
  lat_bin_quantiles = c(0, 1), gear = "bottom trawl")

Arguments

dat	An input data frame from get_cpue_index().
species_common	The species common name.
year_range	The range of years to include.
alt_year_start_date	Alternative year starting date specified as a month-day combination. E.g. "03-01" for March 1st. Can be used to create 'fishing years'.
use_alt_year	Should the alternate year (e.g. fishing year) column alt_year be used? If FALSE then the calendar year will be used. If this is set to TRUE then the year column will be replaced with the alt_year column.
lat_range	The range of latitudes to include.
min_positive_tows	The minimum number of positive tows over all years.
min_positive_trips	The minimum number of annual positive trips.
min_yrs_with_trips	The number of years in which the min_positive_trips criteria needs to be met.
area_grep_pattern	A regular expression to extract the management areas of interest.
lat_band_width	The latitude bandwidths in degrees.
depth_band_width	The depth band widths in m.
clean_bins	Logical. Should the depth and latitude bands be rounded to the nearest clean value as defined by lat_band_width or depth_band_width? Internally, these use, for example: gfplot:::round_down_even(lat_range[1], lat_band_width).
depth_bin_quantiles	Quantiles for the depth bands. If the cumulative proportion of positive fishing events within a given depth bin is less then the lower amount or greater than the upper amount then that depth bin will be dropped.
min_bin_prop	If the proportion of fishing events for any given factor level is less than this value then that factor level will be dropped.
lat_bin_quantiles	Quantiles for the latitude bands. Values above and below these quantiles will be discarded.
gear	One or more gear types as a character vector.

Examples

# NOT RUN {
d <- get_cpue_index(gear = "bottom trawl")
walleye <- tidy_cpue_index(d, "walleye pollock",
  area_grep_pattern = "5[CDE]+")
# }