R/get_survey.R
In Maritimes/Mar.datawrangling: A suite of tools for extracting, filtering and aggregating data from the Maritimes fisheries science databases
Defines functions
get_survey
Documented in
get_survey
#' @title get_survey
#' @description This function facilitates the extraction of particular survey from the rv database.
#' Within the groundfish data are a number of survey all mixed together. They are typically
#' differentiated via specific selections of 1) type; 2) date (i.e. month and year), and 3) strata.
#' Since this can be confusing, this function was written to help ensure that the extracted sets
#' match the survey they should.
#' @param db default is \code{NULL}. This identifies the dataset you are working
#' with.
#' @param survey default is \code{NULL}. This identifies which survey you want tto extract. Valid
#' values include the following:
#' \itemize{
#' \item \code{4X} - Type 1; Spring (i.e. months 1:4); 2008+; specific strata
#' \item \code{GEORGES} - Type 1; Spring (i.e. months 1:4); strata 5Z*
#' \item \code{SPRING} - Type 1; Spring (i.e. months 1:4); pre-2008; specific strata
#' \item \code{4VSW} - Type 1; Spring (i.e. months 1:4); 4VSW strata;
#' \item \code{SUMMER} - Type 1; Summer (i.e. months 5:8); specific strata
#' \item \code{FALL} - Type 1; Fall (i.e. months 9:12)
#' }
#' @param keepBadSets default is \code{FALSE}. This determines whether or not both type 1 and 3
#' sets are returned, or just type 1. Type 3 sets indicate an invalid tow.
#' @param data.dir The default is NULL. This should be a path to a folder containing your rdata files.
#' @param quiet default is \code{TRUE}. If TRUE, no output messages will be shown.
#' @param env This the the environment you want this function to work in. The
#' default value is \code{.GlobalEnv}.
#' @family dfo_extractions
#' @author Mike McMahon, \email{Mike.McMahon@@dfo-mpo.gc.ca}
#' @export
get_survey<- function(db=NULL, survey=NULL, keepBadSets = FALSE, data.dir = NULL, quiet=TRUE, env=.GlobalEnv){
setTypes = 1
if (keepBadSets) setTypes <- c(setTypes,3)
if (is.null(db))db = ds_all[[.GlobalEnv$db]]$db
if(db !='rv'){
cat(paste0("\n","This function currently only works for the rv database"))
return(NULL)
}
chooseSurvey <- function(db=NULL){
rvSurvs <- c("4X",
"GEORGES",
"SPRING",
"4VSW",
"SUMMER",
"FALL")
isdbSurvs <- c("<COMMERCIAL/OBSERVER>",
'4VN SENTINEL SURVEY',
'4VSW SENTINEL PROGRAM',
'4VWX HALIBUT PORT SAMPLE',
'4VWX SKATE SURVEY',
'4X MOBILE GEAR SURVEY',
'4X MONKFISH SURVEY',
'5Z FIXED GEAR SURVEY',
'FSRS - ECO - EXPERIMENTAL',
'GEAC JUV. AND FORAGE SURVEY',
'GULF RESEARCH SURVEY',
'HALIBUT LONGLINE SURVEY',
'LOBSTER SURVEY',
'LOBSTER TAG REPLACEMENT',
'N. ATL. BLUEFIN SURVEY',
'SCALLOP RESEARCH',
'SNOWCRAB SURVEY',
'FSRS - ECO - AT SEA SAMPLING')
thisSurv <- switch(db,
"rv" = rvSurvs,
"isdb" = isdbSurvs
)
survey = utils::select.list(thisSurv,
multiple = F,
graphics = T,
title = paste("Select a standard survey")
)
return(survey)
}
if (is.null(survey)){
survey = chooseSurvey(db)
}
get_data(db=db, data.dir = data.dir, quiet=quiet, env=env)
if (db == 'rv'){
#ensure that we only resturn missions that had type 1 sets - don't want exploratory, etc
env$GSMISSIONS <- env$GSMISSIONS[env$GSMISSIONS$MISSION %in% unique(env$GSINF[env$GSINF$TYPE ==1, "MISSION"]),]
#US Stations
# env$GSMISSIONS = env$GSMISSIONS[env$GSMISSIONS$SEASON == 'SPRING',]
# env$GSINF = env$GSINF[env$GSINF$TYPE ==1 &
# env$GSINF$STRAT %in% c('551', '552', '553', '554', '555', '556', '557', '558', '559' ),]
do4X <-function(){
#4X
env$GSMISSIONS = env$GSMISSIONS[env$GSMISSIONS$SEASON == 'SPRING' & env$GSMISSIONS$YEAR >= 2008,]
env$GSINF = env$GSINF[env$GSINF$TYPE %in% setTypes &
env$GSINF$STRAT %in% c('434', '436', '437', '438', '439',
'440', '441', '442', '443', '444', '445', '446', '447', '448', '449',
'450', '451', '452', '453', '454', '455', '456', '457', '458', '459',
'460', '461', '462', '463', '464', '465', '466',
'470', '471', '472', '473', '474', '475', '476', '477', '478',
'480', '481', '482', '483', '484', '485',
'490', '491', '492', '493', '494', '495', '496', '497', '498',
'501', '502', '503', '504', '505', '557', '558', '559'),]
}
doGEORGES <-function(){
#GEORGES
env$GSMISSIONS = env$GSMISSIONS[env$GSMISSIONS$SEASON == 'SPRING',]
env$GSINF = env$GSINF[env$GSINF$TYPE %in% setTypes &
env$GSINF$STRAT %in% c("5Z1", "5Z2", "5Z3", "5Z4", "5Z5", "5Z6", "5Z7", "5Z8", "5Z9"),]
}
doSPRING <-function(){
#SPRING DATA (TYPE 1; MONTHS 1,2,3,4)
#i.e. not 4X, not US stations, and not 4VVSW
env$GSMISSIONS = env$GSMISSIONS[env$GSMISSIONS$SEASON == 'SPRING' & env$GSMISSIONS$YEAR < 2008,]
env$GSINF = env$GSINF[env$GSINF$TYPE %in% setTypes &
!grepl(pattern = "5Z", x = env$GSINF$STRAT) &
!(env$GSINF$STRAT %in% c('551', '552', '553', '554', '555', '556', '557', '558', '559')) &
!(env$GSINF$STRAT %in% c('396','397', '398', '399',
'400', '401', '402', '403', '404', '405', '406', '407', '408', '409',
'410', '411')),]
}
doSUMMER <-function(){
#SUMMER SURVEY (TYPE 1; MONTHS 5,6,7,8)
env$GSMISSIONS = env$GSMISSIONS[env$GSMISSIONS$SEASON == 'SUMMER',]
env$GSINF = env$GSINF[env$GSINF$TYPE %in% setTypes &
env$GSINF$STRAT %in% c("434", "436", "437", "438", "439", #1971 only, Gulf region
"440", "441", "442", "443", "444", "445", "446", "447", "448", "449",
"450", "451", "452", "453", "454", "455", "456", "457", "458", "459",
"460", "461", "462", "463", "464", "465", "466",
"470", "471", "472", "473", "474", "475", "476", "477", "478",
"480", "481", "482", "483", "484", "485",
"490", "491", "492", "493", "494", "495", "496", "497", "498",
"501", "502", "503", "504", "505", "557", "558", "559",
"5Z1", "5Z2", "5Z3", "5Z4", "5Z5", "5Z6", "5Z7", "5Z8", "5Z9"),]
}
doFALL <-function(){
#FALL
env$GSMISSIONS = env$GSMISSIONS[env$GSMISSIONS$SEASON == 'FALL',]
env$GSINF = env$GSINF[env$GSINF$TYPE %in% setTypes,]
}
do4VSW <-function(){
#4VSW
env$GSMISSIONS = env$GSMISSIONS[env$GSMISSIONS$SEASON == 'SPRING',]
env$GSINF = env$GSINF[env$GSINF$TYPE %in% setTypes &
env$GSINF$STRAT %in% c('396','397', '398', '399', '400',
'401', '402', '403', '404', '405', '406', '407', '408', '409',
'410', '411'),]
}
switch(survey,
"4X" = do4X(),
"GEORGES" = doGEORGES(),
"SPRING" = doSPRING(),
"4VSW" = do4VSW(),
"SUMMER" = doSUMMER(),
"FALL" = doFALL()
)
# } else if (db=='isdb'){
# doCOMM <- function(){
# env$ISTRIPTYPECODES[env$ISTRIPTYPECODES$TRIPCD_ID <7010 | obs_TRIPS_all$TRIPCD_ID == 7099,]
# }
# do4VN <- function(){
# env$ISTRIPTYPECODES[env$ISTRIPTYPECODES$TRIPCD_ID==7052,]
# }
# do4VSW <- function(){
# env$ISTRIPTYPECODES[env$ISTRIPTYPECODES$TRIPCD_ID==7050,]
# }
# do4VWXHAL <- function(){
# env$ISTRIPTYPECODES[env$ISTRIPTYPECODES$TRIPCD_ID==7058,]
# }
# do4VWXSKAT <- function(){
# env$ISTRIPTYPECODES[env$ISTRIPTYPECODES$TRIPCD_ID==7054,]
# }
# do4XMOB <- function(){
# env$ISTRIPTYPECODES[env$ISTRIPTYPECODES$TRIPCD_ID==7051,]
# }
# do4XMONK <- function(){
# env$ISTRIPTYPECODES[env$ISTRIPTYPECODES$TRIPCD_ID==7053,]
# }
# do5Z <- function(){
# env$ISTRIPTYPECODES[env$ISTRIPTYPECODES$TRIPCD_ID==7055,]
# }
# doATSEA <- function(){
# env$ISTRIPTYPECODES[env$ISTRIPTYPECODES$TRIPCD_ID==7010,]
# }
# doEXP <- function(){
# env$ISTRIPTYPECODES[env$ISTRIPTYPECODES$TRIPCD_ID==7011,]
# }
# doGEAC <- function(){
# env$ISTRIPTYPECODES[env$ISTRIPTYPECODES$TRIPCD_ID==7060,]
# }
# doGULF <- function(){
# env$ISTRIPTYPECODES[env$ISTRIPTYPECODES$TRIPCD_ID==8998,]
# }
# doHAL <- function(){
# env$ISTRIPTYPECODES[env$ISTRIPTYPECODES$TRIPCD_ID==7057,]
# }
# doLOBS <- function(){
# env$ISTRIPTYPECODES[env$ISTRIPTYPECODES$TRIPCD_ID==7065,]
# }
# doLOBSTAG <- function(){
# env$ISTRIPTYPECODES[env$ISTRIPTYPECODES$TRIPCD_ID==7068,]
# }
# doBLUEFIN <- function(){
# env$ISTRIPTYPECODES[env$ISTRIPTYPECODES$TRIPCD_ID==7059,]
# }
# doSCALL <- function(){
# env$ISTRIPTYPECODES[env$ISTRIPTYPECODES$TRIPCD_ID==7062,]
# }
# doSNOWCRAB <- function(){
# env$ISTRIPTYPECODES[env$ISTRIPTYPECODES$TRIPCD_ID==7061,]
# }
# switch(survey,
# '<COMMERCIAL/OBSERVER>'= doCOMM(),
# '4VN SENTINEL SURVEY'= do4VN(),
# '4VSW SENTINEL PROGRAM'= do4VSW(),
# '4VWX HALIBUT PORT SAMPLE'= do4VWXHAL(),
# '4VWX SKATE SURVEY'= do4VWXSKAT(),
# '4X MOBILE GEAR SURVEY'= do4XMOB(),
# '4X MONKFISH SURVEY'= do4XMONK(),
# '5Z FIXED GEAR SURVEY'= do5Z(),
# 'FSRS - ECO - AT SEA SAMPLING'= doATSEA(),
# 'FSRS - ECO - EXPERIMENTAL'= doEXP(),
# 'GEAC JUV. AND FORAGE SURVEY'= doGEAC(),
# 'GULF RESEARCH SURVEY'= doGULF(),
# 'HALIBUT LONGLINE SURVEY'= doHAL(),
# 'LOBSTER SURVEY'= doLOBS(),
# 'LOBSTER TAG REPLACEMENT'= doLOBSTAG(),
# 'N. ATL. BLUEFIN SURVEY'= doBLUEFIN(),
# 'SCALLOP RESEARCH'= doSCALL(),
# 'SNOWCRAB SURVEY'= doSNOWCRAB()
# )
}
self_filter(db = ds_all[[.GlobalEnv$db]]$db, quiet=quiet, env=env)
}
Maritimes/Mar.datawrangling documentation built on Feb. 6, 2024, 3:25 a.m.
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions get_survey
Documented in get_survey
#' @title get_survey
#' @description This function facilitates the extraction of particular survey from the rv database.
#' Within the groundfish data are a number of survey all mixed together. They are typically
#' differentiated via specific selections of 1) type; 2) date (i.e. month and year), and 3) strata.
#' Since this can be confusing, this function was written to help ensure that the extracted sets
#' match the survey they should.
#' @param db default is \code{NULL}. This identifies the dataset you are working
#' with.
#' @param survey default is \code{NULL}. This identifies which survey you want tto extract. Valid
#' values include the following:
#' \itemize{
#' \item \code{4X} - Type 1; Spring (i.e. months 1:4); 2008+; specific strata
#' \item \code{GEORGES} - Type 1; Spring (i.e. months 1:4); strata 5Z*
#' \item \code{SPRING} - Type 1; Spring (i.e. months 1:4); pre-2008; specific strata
#' \item \code{4VSW} - Type 1; Spring (i.e. months 1:4); 4VSW strata;
#' \item \code{SUMMER} - Type 1; Summer (i.e. months 5:8); specific strata
#' \item \code{FALL} - Type 1; Fall (i.e. months 9:12)
#' }
#' @param keepBadSets default is \code{FALSE}. This determines whether or not both type 1 and 3
#' sets are returned, or just type 1. Type 3 sets indicate an invalid tow.
#' @param data.dir The default is NULL. This should be a path to a folder containing your rdata files.
#' @param quiet default is \code{TRUE}. If TRUE, no output messages will be shown.
#' @param env This the the environment you want this function to work in. The
#' default value is \code{.GlobalEnv}.
#' @family dfo_extractions
#' @author Mike McMahon, \email{Mike.McMahon@@dfo-mpo.gc.ca}
#' @export
get_survey<- function(db=NULL, survey=NULL, keepBadSets = FALSE, data.dir = NULL, quiet=TRUE, env=.GlobalEnv){
setTypes = 1
if (keepBadSets) setTypes <- c(setTypes,3)
if (is.null(db))db = ds_all[[.GlobalEnv$db]]$db
if(db !='rv'){
cat(paste0("\n","This function currently only works for the rv database"))
return(NULL)
}
chooseSurvey <- function(db=NULL){
rvSurvs <- c("4X",
"GEORGES",
"SPRING",
"4VSW",
"SUMMER",
"FALL")
isdbSurvs <- c("<COMMERCIAL/OBSERVER>",
'4VN SENTINEL SURVEY',
'4VSW SENTINEL PROGRAM',
'4VWX HALIBUT PORT SAMPLE',
'4VWX SKATE SURVEY',
'4X MOBILE GEAR SURVEY',
'4X MONKFISH SURVEY',
'5Z FIXED GEAR SURVEY',
'FSRS - ECO - EXPERIMENTAL',
'GEAC JUV. AND FORAGE SURVEY',
'GULF RESEARCH SURVEY',
'HALIBUT LONGLINE SURVEY',
'LOBSTER SURVEY',
'LOBSTER TAG REPLACEMENT',
'N. ATL. BLUEFIN SURVEY',
'SCALLOP RESEARCH',
'SNOWCRAB SURVEY',
'FSRS - ECO - AT SEA SAMPLING')
thisSurv <- switch(db,
"rv" = rvSurvs,
"isdb" = isdbSurvs
)
survey = utils::select.list(thisSurv,
multiple = F,
graphics = T,
title = paste("Select a standard survey")
)
return(survey)
}
if (is.null(survey)){
survey = chooseSurvey(db)
}
get_data(db=db, data.dir = data.dir, quiet=quiet, env=env)
if (db == 'rv'){
#ensure that we only resturn missions that had type 1 sets - don't want exploratory, etc
env$GSMISSIONS <- env$GSMISSIONS[env$GSMISSIONS$MISSION %in% unique(env$GSINF[env$GSINF$TYPE ==1, "MISSION"]),]
#US Stations
# env$GSMISSIONS = env$GSMISSIONS[env$GSMISSIONS$SEASON == 'SPRING',]
# env$GSINF = env$GSINF[env$GSINF$TYPE ==1 &
# env$GSINF$STRAT %in% c('551', '552', '553', '554', '555', '556', '557', '558', '559' ),]
do4X <-function(){
#4X
env$GSMISSIONS = env$GSMISSIONS[env$GSMISSIONS$SEASON == 'SPRING' & env$GSMISSIONS$YEAR >= 2008,]
env$GSINF = env$GSINF[env$GSINF$TYPE %in% setTypes &
env$GSINF$STRAT %in% c('434', '436', '437', '438', '439',
'440', '441', '442', '443', '444', '445', '446', '447', '448', '449',
'450', '451', '452', '453', '454', '455', '456', '457', '458', '459',
'460', '461', '462', '463', '464', '465', '466',
'470', '471', '472', '473', '474', '475', '476', '477', '478',
'480', '481', '482', '483', '484', '485',
'490', '491', '492', '493', '494', '495', '496', '497', '498',
'501', '502', '503', '504', '505', '557', '558', '559'),]
}
doGEORGES <-function(){
#GEORGES
env$GSMISSIONS = env$GSMISSIONS[env$GSMISSIONS$SEASON == 'SPRING',]
env$GSINF = env$GSINF[env$GSINF$TYPE %in% setTypes &
env$GSINF$STRAT %in% c("5Z1", "5Z2", "5Z3", "5Z4", "5Z5", "5Z6", "5Z7", "5Z8", "5Z9"),]
}
doSPRING <-function(){
#SPRING DATA (TYPE 1; MONTHS 1,2,3,4)
#i.e. not 4X, not US stations, and not 4VVSW
env$GSMISSIONS = env$GSMISSIONS[env$GSMISSIONS$SEASON == 'SPRING' & env$GSMISSIONS$YEAR < 2008,]
env$GSINF = env$GSINF[env$GSINF$TYPE %in% setTypes &
!grepl(pattern = "5Z", x = env$GSINF$STRAT) &
!(env$GSINF$STRAT %in% c('551', '552', '553', '554', '555', '556', '557', '558', '559')) &
!(env$GSINF$STRAT %in% c('396','397', '398', '399',
'400', '401', '402', '403', '404', '405', '406', '407', '408', '409',
'410', '411')),]
}
doSUMMER <-function(){
#SUMMER SURVEY (TYPE 1; MONTHS 5,6,7,8)
env$GSMISSIONS = env$GSMISSIONS[env$GSMISSIONS$SEASON == 'SUMMER',]
env$GSINF = env$GSINF[env$GSINF$TYPE %in% setTypes &
env$GSINF$STRAT %in% c("434", "436", "437", "438", "439", #1971 only, Gulf region
"440", "441", "442", "443", "444", "445", "446", "447", "448", "449",
"450", "451", "452", "453", "454", "455", "456", "457", "458", "459",
"460", "461", "462", "463", "464", "465", "466",
"470", "471", "472", "473", "474", "475", "476", "477", "478",
"480", "481", "482", "483", "484", "485",
"490", "491", "492", "493", "494", "495", "496", "497", "498",
"501", "502", "503", "504", "505", "557", "558", "559",
"5Z1", "5Z2", "5Z3", "5Z4", "5Z5", "5Z6", "5Z7", "5Z8", "5Z9"),]
}
doFALL <-function(){
#FALL
env$GSMISSIONS = env$GSMISSIONS[env$GSMISSIONS$SEASON == 'FALL',]
env$GSINF = env$GSINF[env$GSINF$TYPE %in% setTypes,]
}
do4VSW <-function(){
#4VSW
env$GSMISSIONS = env$GSMISSIONS[env$GSMISSIONS$SEASON == 'SPRING',]
env$GSINF = env$GSINF[env$GSINF$TYPE %in% setTypes &
env$GSINF$STRAT %in% c('396','397', '398', '399', '400',
'401', '402', '403', '404', '405', '406', '407', '408', '409',
'410', '411'),]
}
switch(survey,
"4X" = do4X(),
"GEORGES" = doGEORGES(),
"SPRING" = doSPRING(),
"4VSW" = do4VSW(),
"SUMMER" = doSUMMER(),
"FALL" = doFALL()
)
# } else if (db=='isdb'){
# doCOMM <- function(){
# env$ISTRIPTYPECODES[env$ISTRIPTYPECODES$TRIPCD_ID <7010 | obs_TRIPS_all$TRIPCD_ID == 7099,]
# }
# do4VN <- function(){
# env$ISTRIPTYPECODES[env$ISTRIPTYPECODES$TRIPCD_ID==7052,]
# }
# do4VSW <- function(){
# env$ISTRIPTYPECODES[env$ISTRIPTYPECODES$TRIPCD_ID==7050,]
# }
# do4VWXHAL <- function(){
# env$ISTRIPTYPECODES[env$ISTRIPTYPECODES$TRIPCD_ID==7058,]
# }
# do4VWXSKAT <- function(){
# env$ISTRIPTYPECODES[env$ISTRIPTYPECODES$TRIPCD_ID==7054,]
# }
# do4XMOB <- function(){
# env$ISTRIPTYPECODES[env$ISTRIPTYPECODES$TRIPCD_ID==7051,]
# }
# do4XMONK <- function(){
# env$ISTRIPTYPECODES[env$ISTRIPTYPECODES$TRIPCD_ID==7053,]
# }
# do5Z <- function(){
# env$ISTRIPTYPECODES[env$ISTRIPTYPECODES$TRIPCD_ID==7055,]
# }
# doATSEA <- function(){
# env$ISTRIPTYPECODES[env$ISTRIPTYPECODES$TRIPCD_ID==7010,]
# }
# doEXP <- function(){
# env$ISTRIPTYPECODES[env$ISTRIPTYPECODES$TRIPCD_ID==7011,]
# }
# doGEAC <- function(){
# env$ISTRIPTYPECODES[env$ISTRIPTYPECODES$TRIPCD_ID==7060,]
# }
# doGULF <- function(){
# env$ISTRIPTYPECODES[env$ISTRIPTYPECODES$TRIPCD_ID==8998,]
# }
# doHAL <- function(){
# env$ISTRIPTYPECODES[env$ISTRIPTYPECODES$TRIPCD_ID==7057,]
# }
# doLOBS <- function(){
# env$ISTRIPTYPECODES[env$ISTRIPTYPECODES$TRIPCD_ID==7065,]
# }
# doLOBSTAG <- function(){
# env$ISTRIPTYPECODES[env$ISTRIPTYPECODES$TRIPCD_ID==7068,]
# }
# doBLUEFIN <- function(){
# env$ISTRIPTYPECODES[env$ISTRIPTYPECODES$TRIPCD_ID==7059,]
# }
# doSCALL <- function(){
# env$ISTRIPTYPECODES[env$ISTRIPTYPECODES$TRIPCD_ID==7062,]
# }
# doSNOWCRAB <- function(){
# env$ISTRIPTYPECODES[env$ISTRIPTYPECODES$TRIPCD_ID==7061,]
# }
# switch(survey,
# '<COMMERCIAL/OBSERVER>'= doCOMM(),
# '4VN SENTINEL SURVEY'= do4VN(),
# '4VSW SENTINEL PROGRAM'= do4VSW(),
# '4VWX HALIBUT PORT SAMPLE'= do4VWXHAL(),
# '4VWX SKATE SURVEY'= do4VWXSKAT(),
# '4X MOBILE GEAR SURVEY'= do4XMOB(),
# '4X MONKFISH SURVEY'= do4XMONK(),
# '5Z FIXED GEAR SURVEY'= do5Z(),
# 'FSRS - ECO - AT SEA SAMPLING'= doATSEA(),
# 'FSRS - ECO - EXPERIMENTAL'= doEXP(),
# 'GEAC JUV. AND FORAGE SURVEY'= doGEAC(),
# 'GULF RESEARCH SURVEY'= doGULF(),
# 'HALIBUT LONGLINE SURVEY'= doHAL(),
# 'LOBSTER SURVEY'= doLOBS(),
# 'LOBSTER TAG REPLACEMENT'= doLOBSTAG(),
# 'N. ATL. BLUEFIN SURVEY'= doBLUEFIN(),
# 'SCALLOP RESEARCH'= doSCALL(),
# 'SNOWCRAB SURVEY'= doSNOWCRAB()
# )
}
self_filter(db = ds_all[[.GlobalEnv$db]]$db, quiet=quiet, env=env)
}
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