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

Mortality rates by area and gear from this discard estimation support table are based on values used in current stock assessments and quota monitoring. Discard mortality rates have been agreed upon by a CAMS discard working group.

Description

OUTPUT TABLE: CAMS_DISCARD_MORTALITY_STOCK
YEARS: N/A
RESOLUTION: Discard mortality rates by area and gear.
DEVELOPMENT LANGUAGE: N/A
CODE: N/A

DiagrammeR::mermaid("
  graph LR
  CAMS_DISCARD_MORTALITY_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_DISCARD_MORTALITY_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)