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 stat areas to species stock areas used for discard stratification based on area stratifications used in current stock assessments and quota monitoring. Species specific area stratifications have agreed upon by a discard working group.

Description

OUTPUT TABLE: CAMS_STATAREA_STOCK
YEARS: N/A
RESOLUTION: N/A
DEVELOPMENT LANGUAGE: N/A
CODE: https://github.com/NOAA-Fisheries-Greater-Atlantic-Region/discaRd/tree/model_estimator/CAMS

DiagrammeR::mermaid("
  graph LR
  CAMS_STATAREA_STOCK --> 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_STATAREA_STOCK'")

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)