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 table contains VTR discard estimates, EM discard estimates for EM reviewed GF trips and delta model estimates for unreviewed EM trips from FY20 forward. From May 1, 2021 to December 31, 2021 VTR estimates were used until adequate data was available to fit the delta model. Discards from observer coverage take precedent over discard estimates from EM.

Description

OUTPUT TABLE: GF_EM_DELTA_VTR_DISCARD
YEARS: 2020+
RESOLUTION: Species discard estimate by VTRSERNO (subtrip)
DEVELOPMENT LANGUAGE: R
CODE: https://github.com/NOAA-Fisheries-Greater-Atlantic-Region/discaRd/tree/model_estimator/CAMS

Data Sources

nemis.NEMIS_TRIP_MV@nova nemis.NEMIS_HAUL_MV@nova nemis.NEMIS_CATCH_MV@nova noaa.document noaa.images

DiagrammeR::mermaid("
  graph LR
nemis.NEMIS_TRIP_MV --> GF_EM_DELTA_VTR_DISCARD
nemis.NEMIS_HAUL_MV --> GF_EM_DELTA_VTR_DISCARD
nemis.NEMIS_CATCH_MV --> GF_EM_DELTA_VTR_DISCARD
noaa.document --> GF_EM_DELTA_VTR_DISCARD
noaa.images --> GF_EM_DELTA_VTR_DISCARD
        ")

Approach

Criteria for EM data to be used to fit delta model: (ct_tot >= 30 AND fishnk_pct >= .1) THEN 'N' ELSE haul_observed

Delta model: EM_DISCARD ~ LOG_EVTR_DISCARD + (1+LOG_EVTR_DISCARD|SPECIES_ID) + (1+LOG_EVTR_DISCARD | PERMIT)

Data Dictionary

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

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)