Groundfish CPUE Reports

Requires the following R packages:

pkgs <- c(
  "here", "glmmTMB", "ggplot2", "dplyr", "readr", "lubridate",
  "reshape2", "plyr", "purrr", "remotes"
)
install.packages(pkgs)

remotes::install_github("pbs-assess/gfplot")
remotes::install_github("pbs-assess/gfdata")

See examples in make.R to run a report.

Contact Sean Anderson for more details.

Parameter descriptions

• author: Character: author name. Whatever you want.
• species_proper: Character: common name of species.
• area: R code regular expression for groundfish areas to include. For example: !r c("^5A|^5B|^5C|^5D|^5E|^3C|^3D") would filter for 5A or 5B or 5C etc. Can be a vector where each element would be processed as a separate series.
• area_name: R code for names of areas specified in previous argument (same length). E.g. !r c("Coastwide").
• skip_single_variable_models: Logical: if FALSE, models with each individual predictor are run you understand their contributions. If TRUE, this is skipped to save time.
• era: Character: "modern" runs 1996 onwards. "historical" runs on data from gfdata::get_cpue_historical(), which includes data from min_year_historic--1995. The data go back to roughly 1955.
• use_alt_year: Logical: use alternative year starting date? If FALSE, uses January 1. If TRUE, uses alt_year_start_date.
• alt_year_start_date: Character: month and day of alternative year starting date. E.g. "02-21".
• min_year_historic: Numeric: minimum year to filter if using the historical data. E.g. 1956.
• discard_only: Logical: use only the discards for a discard-CPUE?
• parallel: Logical: parallel processing. Because the data are rather large you usually want to leave this as FALSE.
• min_positive_tows: Numeric: The minimum number of positive tows over all years. E.g. 140.
• min_positive_trips: Numeric: The minimum number of annual positive trips. E.g., 10.
• min_yrs_with_trips: Numeric: The number of years in which the min_positive_trips criteria needs to be met. E.g., 5.
• final_year: Numeric: Final year to include. E.g. 2021.
• final_date: Character representing the final day to include: "2021-12-31"
• depth_bin_quantiles: R code representing minimal and maximum depth quantiles beyond which to discard fishing events. E.g. !r c(0.001, 0.999). Set to !r c(0, 1) to not discard any fishing events based on extreme depths.
• lat_range: R code representing minimum and maximum values for latitude beyond which to discard fishing events. E.g. !r c(48, Inf).
• depth_range: R code representing minimum and maximum depth values beyond which to discard fishing events. E.g. !r c(-Inf, Inf) to do nothing. !r c(50, 350) would only include fishing events >= 50 and <= 350.