diff --git a/R/get_comdisc_raw_data.R b/R/get_comdisc_raw_data.R index 6f90a6b..4152a02 100644 --- a/R/get_comdisc_raw_data.R +++ b/R/get_comdisc_raw_data.R @@ -41,14 +41,14 @@ get_comdisc_raw_data <- function(channel, filterByYear){ ob.qry <- paste0("select year, month, area, negear, nespp4, hailwt, catdisp, drflag, tripid, haulnum, lathbeg, lonhbeg, link3 - from OBSPP + from obdbs.OBSPP where obsrflag = 1 and program not in ('127', '900', '250', '160') and year ", years, "\n union select year, month, area, negear, nespp4, hailwt, catdisp, drflag, tripid, haulnum, lathbeg, lonhbeg, link3 - from ASMSPP + from obdbs.ASMSPP where obsrflag = 1 and program not in ('127', '900', '250', '160') and year ", years) @@ -60,14 +60,14 @@ get_comdisc_raw_data <- function(channel, filterByYear){ mammal.qry <- paste0("select distinct a.year, a.month, b.area, b.negear, a.nespp4, 1 as hailwt, 0 as catdisp, 1 as drflag, a.tripid, a.haulnum, b.lathbeg, b.lonhbeg, a.link3 - from obinc a, obspp b + from obdbs.obinc a, obdbs.obspp b where a.tripid = b.tripid and a.year ", years, "\n union select distinct a.year, a.month, b.area, b.negear, a.nespp4, 1 as hailwt, 0 as catdisp, 1 as drflag, a.tripid, a.haulnum, b.lathbeg, b.lonhbeg, a.link3 - from asminc a, asmspp b + from obdbs.asminc a, obdbs.asmspp b where a.tripid = b.tripid and a.year ", years) @@ -78,7 +78,7 @@ get_comdisc_raw_data <- function(channel, filterByYear){ #Grab otter trawl gear tables to get mesh size for small verses large mesh mesh.qry <- paste0("select link3, codmsize - from OBOTGH + from obdbs.OBOTGH where year ", years) mesh <- data.table::as.data.table(DBI::dbGetQuery(channel, mesh.qry)) sql <- c(sql, mesh.qry) @@ -113,7 +113,7 @@ get_comdisc_raw_data <- function(channel, filterByYear){ #Convert weights convert.qry <- "select nespp4_obs, catdisp_code, drflag_code, cf_lndlb_livlb, cf_rptqty_lndlb - from obspecconv" + from obdbs.obspecconv" convert <- data.table::as.data.table(DBI::dbGetQuery(channel, convert.qry)) sql <- c(sql, convert.qry) @@ -136,7 +136,7 @@ get_comdisc_raw_data <- function(channel, filterByYear){ #Grab PR flags prflag.qry <- "select NESPP4, cetacean, turtle, pinniped - from obspec" + from obdbs.obspec" prflag <- data.table::as.data.table(DBI::dbGetQuery(channel, prflag.qry)) sql <- c(sql, prflag.qry) @@ -162,11 +162,11 @@ get_comdisc_raw_data <- function(channel, filterByYear){ #drop extra columns NESPP4 comdisc[, c('DRFLAG', 'CF_LNDLB_LIVLB', 'CF_RPTQTY_LNDLB', 'HAILWT', 'C.HAILWT', 'NESPP4') := NULL] - + #Convert number fields from chr to num numberCols <- c('YEAR', 'MONTH', 'NEGEAR', 'NESPP3', 'AREA', 'MKTCAT') comdisc[, (numberCols):= lapply(.SD, as.numeric), .SDcols = numberCols][] - + return(list(comdisc = comdisc[], sql = sql)) }