R/goa_rockfish.R

In afsc-assessments/afscdata: An R Package for Extraction of AFSC Fishery Data

#' raw data query for GOA northern rockfish
#'
#' @param year assessment year
#' @param off_yr if this is an off-year assessment change to TRUE
#'
#' @return a suite of raw data .csv files and a time stamp of when the query was done 
#' @export goa_nork
#'
#' @examples
#' \dontrun{
#' goa_nork(year = 2022, off_yr = FALSE)
#'}
goa_nork <- function(year, off_yr = FALSE){
  # globals 
  area = "GOA"
  species = "NORK"
  afsc_species = 30420
  norpac_species = 303
  
  akfin = connect()
  
  q_catch(year, species=species, area=area, db=akfin)
  q_fish_obs(year, species=norpac_species, area=area, db=akfin)
  q_bts_biomass(year, area=area, species=afsc_species, type='total', db=akfin) 
   
  if(isTRUE(off_yr)) {
    disconnect(akfin) 
  } else {
    q_fsh_specimen(year, species = norpac_species, area, db=akfin, print_sql=FALSE, save=TRUE)
    q_fsh_length(year, species = norpac_species, area, db=akfin, print_sql=FALSE, save=TRUE)  
    disconnect(akfin)  
    
    afsc = connect("afsc")
    q_bts_specimen(year, species=afsc_species, area, db=afsc)
    q_bts_length(year, species=afsc_species, area, db=afsc)  
    q_bts_agecomp(year = year, species = afsc_species, area = area, db = afsc)
    q_bts_sizecomp(year = year, species = afsc_species, area = area, db = afsc)
    disconnect(afsc)
  }
  
  # read in archived catch data
  afscdata::goa_nork_catch_1961_1992 %>%
    vroom::vroom_write(here::here(year, "data", "user_input", "goa_nork_catch_1961_1992.csv"), ",")
  
  # timestamp
  q_date(year)
}

#' raw data query for GOA dusky rockfish
#'
#' @param year assessment year
#' @param off_yr if this is an off-year assessment change to TRUE
#'
#' @return a suite of raw data .csv files and a time stamp of when the query was done 
#' @export goa_dusk
#'
#' @examples
#' \dontrun{
#' goa_dusk(year = 2022, off_yr = FALSE)
#'}
goa_dusk <- function(year, off_yr = FALSE){
  # globals 
  area = "GOA"
  species = c("PEL7", "PELS", "DUSK")
  afsc_species = c(30150, 30152)
  norpac_species = 330
  
  akfin = connect()
  
  q_catch(year=year, species=species, area=area, db=akfin)
  # commented functions are currently in development
  q_fish_obs(year=year, species=norpac_species, area=area, db=akfin)
  q_bts_biomass(year=year, area=area, species=afsc_species, type='total', db=akfin) 
  
  if(isTRUE(off_yr)) {
    disconnect(akfin) 
  } else {
    q_fsh_specimen(year=year, species=norpac_species, area=area, db=akfin)
    q_fsh_length(year=year, species=norpac_species, area=area, db=akfin)  
    disconnect(akfin)  
    
    afsc = connect("afsc")
    q_bts_specimen(year=year, species=afsc_species, area=area, db=afsc)
    q_bts_length(year=year, species=afsc_species, area=area, db=afsc)  
    q_bts_agecomp(year = year, species = afsc_species, area = area, db = afsc)
    q_bts_sizecomp(year = year, species = afsc_species, area = area, db = afsc)
    disconnect(afsc)
  }
  
  # read in archived catch data
  afscdata::goa_dusk_catch_1977_1990 %>%
    vroom::vroom_write(here::here(year, "data", "user_input", "goa_dusk_catch_1977_1990.csv"), ",")
  
  # timestamp
  q_date(year)
}

#' raw data query for GOA POP
#'
#' @param year assessment year
#' @param off_yr if this is an off-year assessment change to TRUE
#'
#' @return a suite of raw data .csv files and a time stamp of when the query was done 
#' @export goa_pop
#'
#' @examples
#' \dontrun{
#' goa_pop(year = 2022, off_yr = FALSE)
#'}
goa_pop <- function(year, off_yr = FALSE){
  
  # globals 
  species = "POPA"
  area = "GOA"
  afsc_species = 30060
  norpac_species = 301
  
  akfin = connect()
  
  q_catch(year = year, species = species, area = area, db = akfin)
  q_fish_obs(year = year, species = norpac_species, area = area, db = akfin)
  q_bts_biomass(year = year, area = area, species = afsc_species, type = 'total', db = akfin) 
  q_bts_biomass(year = year, area = area, species = afsc_species, type = 'area', db = akfin) 
  
  if(isTRUE(off_yr)) {
    disconnect(akfin) 
  } else {
    q_fsh_specimen(year = year, species = norpac_species, area = area, db = akfin)
    q_fsh_length(year = year, species = norpac_species, area = area, db = akfin) 
    disconnect(akfin)  
    
    afsc = connect("afsc")
    q_bts_specimen(year = year, species = afsc_species, area = area, db = afsc)
    q_bts_length(year = year, species = afsc_species, area = area, db = afsc)  
    q_bts_agecomp(year = year, species = afsc_species, area = area, db = afsc)
    q_bts_sizecomp(year = year, species = afsc_species, area = area, db = afsc)
    disconnect(afsc)
  }
  
  # read in archived catch data
  afscdata::goa_pop_catch_1960_1990 %>%
    vroom::vroom_write(here::here(year, "data", "user_input", "goa_pop_catch_1960_1990.csv"), ",")
  
  afscdata::goa_pop_fixed_fish_length_comp %>%
    vroom::vroom_write(here::here(year, "data", "user_input", "goa_pop_fixed_fish_length_comp.csv"))
  
  afscdata::saa_pop_60 %>%
    vroom::vroom_write(here::here(year, "data", "user_input", "saa_pop_60.csv"))
 
   # timestamp
  q_date(year)
 
}

#' raw data query for GOA rougheye/blackspotted rockfish
#'
#' @param year assessment year
#' @param off_yr if this is an off-year assessment change to TRUE
#'
#' @return a suite of raw data .csv files and a time stamp of when the query was done 
#' @export goa_rebs
#'
#' @examples
#' \dontrun{
#' goa_rebs(year = 2021, off_yr = FALSE)
#'}
goa_rebs <- function(year, off_yr = FALSE){
  
  # globals 
  area = "GOA"
  species = c("REYE")
  afsc_species = c(30050,30051,30052)
  norpac_species = c(307, 357)
  
  akfin = afscdata::connect()
  
  q_catch(year=year, species=species, area=area, db=akfin)
  q_fish_obs(year=year, species=norpac_species, area=area, db=akfin)
  q_bts_biomass(year=year, area=area, species=afsc_species, type='area', db=akfin) 
  q_lls_rpn(year=year, area=area, species=afsc_species, by='fmpsubarea', db=akfin)
  
  if(isTRUE(off_yr)) {
    disconnect(akfin) 
  } else {
    q_fsh_specimen(year=year, species=norpac_species, area=area, db=akfin)
    q_fsh_length(year=year, species=norpac_species, area=area, db=akfin)
    q_lls_rpn_length(year=year, species=afsc_species, area=area, by='fmpsubarea', db=akfin)
    disconnect(akfin)  
    
    afsc = connect("afsc")
    q_bts_specimen(year=year, species=afsc_species, area=area, db=afsc)
    q_bts_length(year=year, species=afsc_species, area=area, db=afsc)  
    q_bts_agecomp(year = year, species = afsc_species, area = area, db = afsc)
    q_bts_sizecomp(year = year, species = afsc_species, area = area, db = afsc)
    disconnect(afsc)
  }
  
  # read in archived catch data
  afscdata::goa_rebs_catch_1977_2004 %>%
    vroom::vroom_write(here::here(year, "data", "user_input", "goa_rebs_catch_1977_2004.csv"), ",")
  
  # timestamp
  q_date(year)
}

#' raw data query for GOA thorynhead rockfish
#'
#' @param year assessment year
#' @param off_yr if this is an off-year assessment change to TRUE
#' @param catch_report is this a catch report year, default FALSE
#'
#' @return a suite of raw data .csv files and a time stamp of when the query was done 
#' @export goa_thornyhead
#'
#' @examples
#' \dontrun{
#' goa_thornyhead(year = 2022, off_yr = FALSE)
#'}
goa_thornyhead <- function(year, off_yr = FALSE, catch_report = FALSE){
  # globals 
  area = "GOA"
  norpac_species = c(349, 350, 352)
  
  
  akfin = connect()
  
  if(isTRUE(catch_report)) {
    q_catch(year, species=species, area=area, db=akfin)
  } else {
    q_catch(year, species=species, area=area, db=akfin)
    q_fish_obs(year, species=norpac_species, area=area, db=akfin)
    q_bts_biomass(year, area=area, species=afsc_species, type='total', db=akfin) 
  }
  
  if(isTRUE(off_yr) | isTRUE(catch_report)) {
    disconnect(akfin) 
  } else {
    q_fsh_specimen(year, species=norpac_species, area, db=akfin, print_sql=FALSE, save=TRUE)
    q_fsh_length(year, species=norpac_species, area, db=akfin, print_sql=FALSE, save=TRUE)  
    disconnect(akfin)  
    
    afsc = connect("afsc")
    q_bts_specimen(year, species=afsc_species, area, db=afsc)
    q_bts_length(year, species=afsc_species, area, db=afsc)  
    q_bts_agecomp(year = year, species = afsc_species, area = area, db = afsc)
    q_bts_sizecomp(year = year, species = afsc_species, area = area, db = afsc)
    disconnect(afsc)
  }
  
  # read in archived catch data
  # afscdata::goa_nork_catch_1961_1992 %>%
  #   vroom::vroom_write(here::here(year, "data", "user_input", "goa_nork_catch_1961_1992.csv"), ",")
  
  # timestamp
  q_date(year)
}