In noaa-garfo/discaRd: Cochran bycatch estimation

knitr::opts_chunk$set(echo = TRUE)

library(tidyverse)
library(odbc)
library(ROracle)
library(dplyr, warn.conflicts = FALSE)

# # unlock keyring
# keyring::keyring_unlock("apsd_ma")
# 
# # local run
# # dw_apsd <- config::get(value = "apsd", file = "K:/R_DEV/config.yml")
# 
# # if on server..
# # dw_apsd <- config::get(value = "maps", file = "~/config.yml")
# 
# 
# # connect to MAPS
# 
# con_maps = apsdFuns::roracle_login(key_name = 'apsd_ma', key_service = 'maps')

Sys.setenv(TZ = "America/New_York")
Sys.setenv(ORA_SDTZ = "America/New_York")

if(file.exists(here::here("vignettes/articles", "pw.csv"))) {
  pw_df <- readr::read_csv(here::here("vignettes/articles", "pw.csv"), col_types = "c")
  pw <- pw_df$pw
} else {
  pw <- rstudioapi::askForPassword("Enter keyring password")
}

keyring::keyring_unlock("apsd_ma", password = pw) # will prompt for password
con_maps <- apsdFuns::roracle_login(key_name = 'apsd_ma', key_service = 'maps')

Summary

This discard support table translates species VTR gear code to the CAMS gear code used for discard stratification based on gear stratification used in current stock assessments and quota monitoring. Species specific gear stratifications have been agreed upon by a discards working group.

Description

OUTPUT TABLE: CAMS_GEARCODE_STRATA
YEARS: N/A
RESOLUTION: Gearcode translation from VTR gear code to cams_gear_group by species
DEVELOPMENT LANGUAGE: N/A
CODE: N/A

DiagrammeR::mermaid("
  graph LR
  CAMS_GEARCODE_STRATA --> GF_and_Non_GF_Discard_Modules
        ")

Data Dictionary

comments <- ROracle::dbGetQuery(con_maps, "SELECT * FROM all_col_comments WHERE owner = 'MAPS' AND table_name = 'CAMS_GEARCODE_STRATA'")

comments %>%
dplyr::select(
COLUMN = COLUMN_NAME,
DESCRIPTION = COMMENTS) %>%
knitr::kable(booktabs = TRUE) %>%
kableExtra::kable_styling(bootstrap_options = c("striped", 
"hover", "condensed", "responsive"),full_width = FALSE,position = "left", fixed_thead = TRUE,
font_size = 10)