diff --git a/R/queries.R b/R/queries.R index a7d8dbb..f54b016 100644 --- a/R/queries.R +++ b/R/queries.R @@ -238,6 +238,110 @@ q_bts_biomass <- function(year, species, area, type='total', db, print_sql=FALSE } +#' query GAP products bottom trawl survey biomass +#' note: pay attention to the 'design_year' column, particularly for region or depth queries as there may be data duplicates +#' +#' six areas are available to query from +#' bs = bering sea + northwest 1987-present (includes nw stations) - recommended +#' bsslope = bering sea slope +#' nbs = northern bering sea +#' ai = aleutian islands +#' goa = gulf of alaska +#' old_bs = bering sea standard 1982-present (minus ~20 stations in nw) - not recommended +#' +#' @param year max year to retrieve data from, and default folder location +#' @param area options are bs (the bs+nw), bsslope, nbs, ai, goa, old_bs (was called "standard") - can only call a single area +#' @param species 5 digit afsc species code(s) e.g., 79210 or c(79210, 90210) +#' @param type the goa and ai have: region, regulatory_area, stat_area, stratum, inpfc, inpfc_depth, depth, (ai only: reg_area_depth); the bs has: region, subarea, stratum, depth; the bsslope has: region, subarea, stratum; the nbs hasregion, stratum - can only use a single type (default: "region") +#' @param db the database to query (akfin) +#' @param print_sql outputs the sql query instead of calling the data (default: false) +#' @param save save the file in designated folder, if FALSE outputs to global environment +#' +#' @return saves bts biomass data as data/raw/(area)_(type)_bts_biomass_data.csv or outputs to the global environment, also saves a copy of the SQL code used for the query and stores it in the data/sql folder. +#' @export q_bts_biomass +#' +#' @examples +#' \dontrun{ +#' db <- afscdata::connect() +#' q_bts_biomass(year=2024, species=10110, area="bs", type="region", db=db) +#' } +q_gap_biomass <- function(year = 2024, species = 10110, area ='bs', type = 'region', db, print_sql=FALSE, save=TRUE) { + + if(area=='bsslope' | area=='BSSLOPE') area = 'BSS' + type = dplyr::case_when(type=='regulatory_area' ~ 'REGULATORY AREA', + type=='stat_area' ~ 'NMFS STATISTICAL AREA', + type=='inpfc_depth' ~ 'INPFC BY DEPTH', + type=='reg_area_depth' ~ 'REGULATORY AREA BY DEPTH', + TRUE ~ toupper(type)) + + # adjust filters + yr = year + area = tolower(area) + ar = toupper(area) + type = toupper(type) + tl = tolower(type) + + # message center + if(area=='ebs') stop("area must be 'bs', 'bss', 'nbs', or 'old_bs'") + + data.frame(id = c('AI', 'GOA', 'BS', 'OLD_BS', 'BSS', 'NBS'), + srv_id = c(52, 47, 98, 98, 78, 143), + aid = c(99904, 99903, 99900, 99901, 99905, 99902)) -> dat + + if(ar=='BS') { + an = "Standard Plus NW" + } else if(ar == 'OLD_BS') { + an = "Standard" + } + dat %>% + dplyr::filter(id %in% ar) %>% + dplyr::pull(srv_id) -> srv_id # survey_definition_id + + dat %>% + dplyr::filter(id %in% ar) %>% + dplyr::pull(aid) -> aid # survey_definition_id + + if(type=='REGION') { + dplyr::tbl(db, dplyr::sql('gap_products.akfin_area')) %>% + dplyr::rename_all(tolower) %>% + dplyr::filter(survey_definition_id %in% srv_id, + area_id==aid) %>% + dplyr::collect() -> dat1 + } else { + dplyr::tbl(db, dplyr::sql('gap_products.akfin_area')) %>% + dplyr::rename_all(tolower) %>% + dplyr::filter(survey_definition_id %in% srv_id, + area_type==type) %>% + dplyr::collect() -> dat1 + } + + dat1 %>% + as.data.frame() %>% + dplyr::left_join(dplyr::tbl(db, dplyr::sql('gap_products.akfin_biomass')) %>% + dplyr::rename_all(tolower) %>% + dplyr::filter(species_code %in% species, + year <= yr) %>% + as.data.frame()) %>% + dplyr::collect() -> table + + # prefix area and type to file name + id = paste0(area, "_", tl, "_") + if(isTRUE(save)){ + dplyr::collect(table) %>% + vroom::vroom_write(here::here(year, "data", "raw", paste0(id, "bts_biomass_data.csv")), + delim = ",") + capture.output(dplyr::show_query(table), + file = here::here(year, "data", "sql", paste0(id, "bts_biomass_sql.txt"))) + + message("bottom trawl survey biomass data can be found in the data/raw folder") + } else if (isFALSE(save) & isFALSE(print_sql)) { + dplyr::collect(table) + } else { + dplyr::show_query(table) + message("this sql code is passed to the server") + } +} + #' query bottom trawl survey agecomps #' #'