The function can create trip level historical CPUE for index standardization or an "arithmetic" CPUE where the catch and effort are summed each year and divided.
tidy_cpue_historical(dat, species_common, year_range = c(1956, 1995), area_grep_pattern = c("3[CD]+", "5[ABCDE]+"), use_alt_year = FALSE, depth_band_width = 25, depth_bin_quantiles = c(0.001, 0.999), min_bin_prop = 0.001, type = c("trip-level-data", "arithmetic-cpue"), max_fe_hours = 5)
| dat | Data from |
|---|---|
| species_common | A species common name in lowercase. |
| year_range | A range of years to include. Can go up to current year but note the management changes, particularly in 1996. |
| area_grep_pattern | A major statistical area as a regular expression. |
| use_alt_year | Should the alternate year (e.g. fishing year) column
|
| depth_band_width | The depth band widths in m. |
| 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. |
| type | Should the trip-level data be returned (for possible future index standardization) or should the arithmetic CPUE be returned (species specific catch and all effort is summed each year and then divided.) |
| max_fe_hours | The maximum number of allowable hours per fishing event (e.g. per trawl). Fishing events that are longer than this will be removed. This can be used to remove erroneous fishing events. Only affects data in 1991 and after when the data are recorded as fishing events. |
A (tibble) data frame.
Note that fishing events prior to 1991 are 'rolled up' in the databases to locality-specific trips. This function well aggregate fishing events into trips in 1991 and after to create a consistent form of data.
get_cpue_historical(end_year = 2016) %>% tidy_cpue_historical(species_common = "pacific cod", area_grep_pattern = "5[CD]+")#> Error: nanodbc/nanodbc.cpp:950: 01000: [unixODBC][Driver Manager]Can't open lib 'SQL Server' : file not found