View source: R/tidy-cpue-index.R
tidy_cpue_index | R Documentation |
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",
return_raw_data = FALSE
)
dat |
An input data frame from |
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
|
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
|
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 |
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. |
## Not run:
d <- gfdata::get_cpue_index(gear = "bottom trawl")
walleye <- tidy_cpue_index(d, "walleye pollock",
area_grep_pattern = "5[CDE]+"
)
## End(Not run)
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