data-raw/exampleData/TextBookExamples/BuildTextBookDataUpload_Pckg_SDAResources_coots_H1.R
In ices-tools-dev/icesRDBES: Functions for the ICES Regional Database and Estimation System (RDBES)
#======Prepares textbook data SDAResources::coots as H1 upload file===========
# Info:
# ?coots
# design is 2-stage cluster sampling with clusters of unequal sizes and Npsu not known
# clusters are clustches of eggs (nests) with at least 2 eggs.
# In each cluster, the volume of two eggs is measured
# clusters (psu) are unequal sized. In each cluster, 2 eggs are selected (ssus) and measured.
# total number of psus is not known (a drawback in this example). It is assumed very large (fpc negligible)
# table(coots$clutch)
# target variable is volume [others are available]
# how this example is placed in RDBES
# 1 DE row with DEstratumName == "Pckg_SDAResources_coots_H1"
# 1 child SD row
# 368 child rows in VS (the 368 eggs/psus observed)
# each associated to its cluster (clutch)
# VSnumberTotalClusters is not known (see page 59)
# VSnumberTotal is csize
# tables FT, FO, SS are just 1:1 links to the final data (in SA)
# in SA each volume is a SAsampleWeightMeasured
# ATT volumes are *100000000 to meet type requirement (integer)
rm(list=ls())
library(data.table)
# load textbook data
library(SDAResources)
data(coots)
dataset<-coots
target_var<-"volume"
# name your project (will be used in filenames for CS, SL and VD)
project_name_outputs <- "WGRDBES-EST_TEST_1_Pckg_SDAResources_coots_H1"
# select a year for upload
DEyear<-1965
SDinstitution <- 4484
DEsamplingScheme<-"WGRDBES-EST TEST 1"
DEstratumName <- "Pckg_SDAResources_coots_H1"
project_name_outputs <- gsub(" ","_", paste0(DEsamplingScheme,"_", DEstratumName))
baseDir <- "./data-raw/exampleData/TextBookExamples/"
baseDir <- ""
VD_base <- readRDS(paste0(baseDir,"aux_TextBookExamples/VD_base.rds"))
SL_base <- readRDS(paste0(baseDir,"aux_TextBookExamples/SL_base.rds"))
#nameof the directory where the outputs are saved currently
base_dir_outputs <- paste0(baseDir,"BuiltUploads")
if(!file.exists(base_dir_outputs)) dir.create(base_dir_outputs, recursive=T, showWarnings=FALSE)
#========Outline of Hierarchy 1================
# Design
# Sampling details
# Vessel Selection
# Fishing Trip
# Fishing Operation
# Species Selection
# Sample
# Length
# Biological variables
#===DE============
# 1 DEid [] - int
# 2 DErecordType [M] - string
# 3 DEsamplingScheme [M] - SamplingScheme
# 4 DEsamplingSchemeType [M] - SamplingSchemeType
# 5 DEyear [M] - Year
# 6 DEstratumName [M] - StringLength100
# 7 DEhierarchyCorrect [M] - YesNoFields
# 8 DEhierarchy [M] - RDBESUpperHierarchy
# 9 DEsampled [DV,M] - YesNoFields
# 10 DEreasonNotSampled [DV,O] - ReasonForNotSampling
# 11 DEnonResponseCollected [DV,O] - YesNoFields
# 12 DEauxiliaryVariableTotal [DV,O] - DecimalPrec3
# 13 DEauxiliaryVariableValue [DV,O] - DecimalPrec3
# 14 DEauxiliaryVariableName [DV,O] - AuxiliaryVariableName
# 15 DEauxiliaryVariableUnit[DV,O]-MUNIT
DE_df_base<-expand.grid(DEyear=DEyear,
DEstratumName="U",stringsAsFactors=F)
DE_df<-data.frame(
DEid = 1:nrow(DE_df_base),
DErecordType = "DE",
DEsamplingScheme = DEsamplingScheme,
DEsamplingSchemeType = "NatRouCF",
DEyear = as.integer(DEyear),
DEstratumName = DEstratumName,
DEhierarchyCorrect = "Y",
DEhierarchy = 1,
DEsampled = "Y",
DEreasonNotSampled = "",
DEnonResponseCollected = "Y",
DEauxiliaryVariableTotal = "",
DEauxiliaryVariableValue = "",
DEauxiliaryVariableName = "",
DEauxiliaryVariableUnit = "",
stringsAsFactors=FALSE
)
#===SD============
# x
# 1 SDid [M] - int
# 2 DEid [M] - int
# 3 SDrecordType [M] - string
# 4 SDcountry [M] - ISO_3166
# 5 SDinstitution [M] - EDMO
SD_df<-data.frame(
SDid=DE_df$DEid,
DEid=DE_df$DEid,
SDrecordType="SD",
SDcountry="ZW",
SDinstitution=as.integer(SDinstitution),
stringsAsFactors=FALSE
)
#===VS============
# x
# 1 VSid [M] - int
# 2 SDid [M] - int
# 3 VDid [M] - int
# 4 TEid [M/O] - int
# 5 VSrecordType [M] - string
# 6 VSsequenceNumber [M] - int
# 7 VSencryptedVesselCode [M] - StringLength100
# 8 VSstratification [DV,M] - YesNoFields
# 9 VSstratumName [DV,M] - StringLength100
# 10 VSclustering [DV,M] - Clustering
# 11 VSclusterName [DV,M] - StringLength100
# 12 VSsampler [O] - Sampler
# 13 VSnumberTotal [DV,O] - int
# 14 VSnumberSampled [DV,O] - int
# 15 VSselectionProb [DV,O] - Decimal0.0000000000000001-1
# 16 VSinclusionProb [DV,O] - Decimal0.0000000000000001-1
# 17 VSselectionMethod [DV,M] - SelectionMethod
# 18 VSunitName [DV,M] - StringLength100
# 19 VSselectionMethodCluster [DV,O] - SelectionMethod
# 20 VSnumberTotalClusters [DV,O] - int
# 21 VSnumberSampledClusters [DV,O] - int
# 22 VSselectionProbCluster [DV,O] - Decimal0.0000000000000001-1
# 23 VSinclusionProbCluster [DV,O] - Decimal0.0000000000000001-1
# 24 VSsampled [DV,M] - YesNoFields
# 25 VSreasonNotSampled [DV,O] - ReasonForNotSampling
# 26 VSnonResponseCollected [DV,O] - YesNoFields
# 27 VSauxiliaryVariableTotal [DV,O] - DecimalPrec3
# 28 VSauxiliaryVariableValue [DV,O] - DecimalPrec3
# 29 VSauxiliaryVariableName [DV,O] - AuxiliaryVariableName
# 30 VSauxiliaryVariableUnit [DV,O] - MUNIT
#check_All_fields("VS")
# adds VSid to dataset
dataset$VSid <- 1:nrow(dataset)
VS_base<-as.data.table(dataset)[,list(N="",n=.N),clutch]
# creates a dummyVD and adds dataset
# restricts VD_base to what is needed
VD_base <- VD_base[1:nrow(VS_base),]
VS_base$VSencryptedVesselCode<-VD_base$VDencryptedVesselCode
# should be 0
test<-sum(duplicated(VS_base$VSencryptedVesselCode))==0
if(!test) stop( "duplicated VSencryptedVesselCode")
VS_df <- data.frame(
VSid = dataset$VSid,
SDid = as.integer(1),
VDid = "",
TEid = "",
VSrecordType = 'VS',
VSsequenceNumber = rep(1:2,184),# M
VSencryptedVesselCode = VS_base$VSencryptedVesselCode, #M
VSstratification = "N",
VSstratumName = "U", #M
VSclustering = "2C", #M
VSclusterName = dataset$clutch, #M
VSsampler = "Observer", #M
VSnumberTotal = "",
VSnumberSampled = "",
VSselectionProb = "",
VSinclusionProb = "",
VSselectionMethod = "SRSWOR", #M
VSunitName = 1:nrow(VS_base),#M
VSselectionMethodCluster = "SRSWOR",
VSnumberTotalClusters = "",
VSnumberSampledClusters = "",
VSselectionProbCluster = "",
VSinclusionProbCluster = "",
VSsampled = "Y",#M
VSreasonNotSampled = "",
VSnonResponseCollected = "Y",
VSauxiliaryVariableTotal = "",
VSauxiliaryVariableValue = "",
VSauxiliaryVariableName = "",
VSauxiliaryVariableUnit = "",
stringsAsFactors=FALSE
)
# units within cluster
VS_df$VSnumberSampled<-VS_base$n
VS_df$VSnumberTotal<-dataset$csize
VS_df$VSselectionProb<-""
VS_df$VSinclusionProb<-""
VS_df$VSselectionMethod<-"SRSWOR"
# clusters
VS_df$VSnumberTotalClusters<-"" # not known see page 58
VS_df$VSnumberSampledClusters<-184
VS_df$VSselectionMethodCluster<-"SRSWOR"
VS_df$VSselectionProbCluster<-""
VS_df$VSinclusionProbCluster<-"" # not known see page 58
#====FT===========
# 1 FTid [M] - int
# 2 OSid [M/O] - int
# 3 VSid [M/O] - int
# 4 VDid [M] - int
# 5 SDid [M/O] - int
# 6 FOid [M/O] - int
# 7 TEid [M/O] - int
# 8 FTrecordType [M] - string
# 9 FTencryptedVesselCode [M] - StringLength100
# 10 FTsequenceNumber [M] - int
# 11 FTstratification [DV,M] - YesNoFields
# 12 FTstratumName [DV,M] - StringLength100
# 13 FTclustering [DV,M] - Clustering
# 14 FTclusterName [DV,M] - StringLength100
# 15 FTsampler [O] - Sampler
# 16 FTsamplingType [M] - SamplingContext
# 17 FTnumberOfHaulsOrSets [M/O] - IntZeroToMax
# 18 FTdepartureLocation [M/O] - Harbour_LOCODE
# 19 FTdepartureDate [M/O] - Date
# 20 FTdepartureTime [M/O] - StringLength60
# 21 FTarrivalLocation [M] - Harbour_LOCODE
# 22 FTarrivalDate [M] - Date
# 23 FTarrivalTime [M/O] - StringLength60
# 24 FTnumberTotal [DV,O] - int
# 25 FTnumberSampled [DV,O] - int
# 26 FTselectionProb [DV,O] - Decimal0-1
# 27 FTinclusionProb [DV,O] - Decimal0-1
# 28 FTselectionMethod [DV,M] - SelectionMethod
# 29 FTunitName [DV,M] - StringLength100
# 30 FTselectionMethodCluster [DV,O] - SelectionMethod
# 31 FTnumberTotalClusters [DV,O] - int
# 32 FTnumberSampledClusters [DV,O] - int
# 33 FTselectionProbCluster [DV,O] - Decimal0-1
# 34 FTinclusionProbCluster [DV,O] - Decimal0-1
# 35 FTsampled [DV,M] - YesNoFields
# 36 FTreasonNotSampled [DV,O] - ReasonForNotSampling
# 37 FTnonResponseCollected [DV,O] - YesNoFields
# 38 FTauxiliaryVariableTotal [DV,O] - DecimalPrec3
# 39 FTauxiliaryVariableValue [DV,O] - DecimalPrec3
# 40 FTauxiliaryVariableName [DV,O] - AuxiliaryVariableName
# 41 FTauxiliaryVariableUnit [DV,O] - MUNIT
FT_df <- data.frame(
FTid = dataset$VSid,#[M] - int
OSid = "",# [M/O] - int
VSid = dataset$VSid, #[M/O]
VDid = "", #[M] - int
SDid = "", #[M/O] - int
FOid = "", #[M/O] - int
TEid = "", #[M/O] - int
FTrecordType='FT', #[M] - string
FTencryptedVesselCode = VS_base$VSencryptedVesselCode, #[M]
FTsequenceNumber = as.integer(1:nrow(dataset)), #[M] - string
FTstratification = "N", #[DV,M] - RS_Stratification
FTstratumName = "U", #[DV,M] - string
FTclustering = "N", #[DV,M] - RS_Clustering
FTclusterName = "U", #[DV,M] - string
FTsampler = "Observer", #[M] - RS_Sampler
FTsamplingType = "AtSea" , #[M] - RS_SamplingType
FTnumberOfHaulsOrSets = 1, #[O] - int
FTdepartureLocation="ZWHWN", #[O] - Harbour_LOCODE
FTdepartureDate=seq(from = as.Date("1965-01-01", format='%Y-%m-%d'), by=1, length.out=nrow(dataset)), #[M/O] - date
FTdepartureTime="", #[O] - time
FTarrivalLocation = "ZWHWN", #[M] - Harbour_LOCODE
FTarrivalDate=seq(from = as.Date("1965-01-01", format='%Y-%m-%d'), by=1, length.out=nrow(dataset)), #[M] - date
FTarrivalTime="", #[O] - time
FTnumberTotal= 1, #[DV,O] - int
FTnumberSampled=1, #[DV,O] - int
FTselectionProb=1, #[DV,O] - DecimalPrec10
FTinclusionProb=1, #[DV,O] - DecimalPrec10
FTselectionMethod="CENSUS", #[DV,M] - RS_SelectionMethod
FTunitName = VS_base$VSencryptedVesselCode, #[DV,M] - string
FTselectionMethodCluster="", #[DV,O] - RS_SelectionMethod
FTnumberTotalClusters="", #[DV,O] - int
FTnumberSampledClusters="", #[DV,O] - int
FTselectionProbCluster="", #[DV,O] - DecimalPrec10
FTinclusionProbCluster="", #[DV,O] - DecimalPrec10
FTsampled="Y", #[DV,M] - YesNoFields
FTreasonNotSampled= "", #[DV,O] - RS_ReasonForNotSampling
FTnonResponseCollected = "N",
FTauxiliaryVariableTotal = "",
FTauxiliaryVariableValue = "",
FTauxiliaryVariableName = "",
FTauxiliaryVariableUnit = "",
stringsAsFactors=FALSE
)
#====FO===========
# 1 FOid [M] - int
# 2 FTid [M/O] - int
# 3 SDid [M/O] - int
# 4 FOrecordType [M] - string
# 5 FOstratification [DV,M] - YesNoFields
# 6 FOsequenceNumber [M] - int
# 7 FOstratumName [DV,M] - StringLength100
# 8 FOclustering [DV,M] - Clustering
# 9 FOclusterName [DV,M] - StringLength100
# 10 FOsampler [O] - Sampler
# 11 FOaggregationLevel [M] - AggregationLevel
# 12 FOvalidity [M] - ValidityFlag
# 13 FOcatchReg [M] - CatchRegistration
# 14 FOstartDate [O] - Date
# 15 FOstartTime [O] - Time
# 16 FOendDate [M] - Date
# 17 FOendTime [M/O] - Time
# 18 FOduration [M/O] - int
# 19 FOdurationSource [M] - DurationSource
# 20 FOhandlingTime [O] - int
# 21 FOstartLat [O] - Decimal-90.000000-90.000000
# 22 FOstartLon [O] - Decimal-180.000000-180.000000
# 23 FOstopLat [O] - Decimal-90.000000-90.000000
# 24 FOstopLon [O] - Decimal-180.000000-180.000000
# 25 FOexclusiveEconomicZoneIndicator [O] - ISO_3166
# 26 FOarea [M] - ICES_Area
# 27 FOrectangle [O] - StatRec
# 28 FOfisheriesManagementUnit [O] - AreaNonFAO
# 29 FOgsaSubarea [M] - Areas_GFCM_GSA
# 30 FOjurisdictionArea [O] - JurisdictionArea
# 31 FOfishingDepth [O] - int
# 32 FOwaterDepth [O] - int
# 33 FOnationalFishingActivity [O] - NationalFishingActivity
# 34 FOmetier5 [O] - Metier5_FishingActivity
# 35 FOmetier6 [M] - Metier6_FishingActivity
# 36 FOgear [M] - GearType
# 37 FOmeshSize [O] - int
# 38 FOselectionDevice [O] - SelectionDevice
# 39 FOselectionDeviceMeshSize [O] - int
# 40 FOtargetSpecies [O] - TargetSpecies
# 41 FOincidentalByCatchMitigationDeviceFirst [M] - BycatchMitigationDevice
# 42 FOincidentalByCatchMitigationDeviceTargetFirst [M] - BycatchMitigationDeviceTarget
# 43 FOincidentalByCatchMitigationDeviceSecond [M] - BycatchMitigationDevice
# 44 FOincidentalByCatchMitigationDeviceTargetSecond [M] - BycatchMitigationDeviceTarget
# 45 FOgearDimensions [O] - int
# 46 FOobservationCode [M] - ObservationCode
# 47 FOnumberTotal [DV,O] - int
# 48 FOnumberSampled [DV,O] - int
# 49 FOselectionProb [DV,O] - Decimal0.0000000000000001-1
# 50 FOinclusionProb [DV,O] - Decimal0.0000000000000001-1
# 51 FOselectionMethod [DV,M] - SelectionMethod
# 52 FOunitName [DV,M] - StringLength100
# 53 FOselectionMethodCluster [DV,O] - SelectionMethod
# 54 FOnumberTotalClusters [DV,O] - int
# 55 FOnumberSampledClusters [DV,O] - int
# 56 FOselectionProbCluster [DV,O] - Decimal0.0000000000000001-1
# 57 FOinclusionProbCluster [DV,O] - Decimal0.0000000000000001-1
# 58 FOsampled [DV,M] - YesNoFields
# 59 FOreasonNotSampled [DV,O] - ReasonForNotSampling
# 60 FOnonResponseCollected [DV,O] - YesNoFields
# 61 FOauxiliaryVariableTotal [DV,O] - DecimalPrec3
# 62 FOauxiliaryVariableValue [DV,O] - DecimalPrec3
# 63 FOauxiliaryVariableName [DV,O] - AuxiliaryVariableName
# 64 FOauxiliaryVariableUnit [DV,O] - MUNIT
FO_df <- data.frame(
FOid = dataset$VSid,
FTid = dataset$VSid,
SDid = "",
FOrecordType = "FO",#M
FOstratification = "N",#M
FOsequenceNumber = as.integer(1:nrow(dataset)),#M
FOstratumName = "U",#M
FOclustering = "N",#M
FOclusterName = "U",#M
FOsampler = "Observer",
FOaggregationLevel = "H",#M
FOvalidity = "V",#M
FOcatchReg = "Lan",#M
FOstartDate = as.Date(FT_df$FTdepartureDate, format='%Y-%m-%d'),
FOstartTime = "",
FOendDate = as.Date(FT_df$FTdepartureDate, format='%Y-%m-%d'),#M
FOendTime ="",#M
FOduration = 60, #M ATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT!!!!
FOdurationSource = "Crew",
FOhandlingTime = "",
FOstartLat="", # ATT!
FOstartLon="", # ATT!
FOstopLat="",
FOstopLon="",
FOexclusiveEconomicZoneIndicator = "", #
FOarea = "27.3.a.21", #M
FOrectangle = "",
FOfisheriesManagementUnit = "",
FOgsaSubarea = "NotApplicable", #M
FOjurisdictionArea = "",
FOfishingDepth = "",
FOwaterDepth = "",
FOnationalFishingActivity = "",
FOmetier5 = "",
FOmetier6 = "OTT_CRU_70-89_2_35",#M
FOgear = "OTT",#M
FOmeshSize = "",
FOselectionDevice = "",
FOselectionDeviceMeshSize = "",
FOtargetSpecies = "",
FOincidentalByCatchMitigationDeviceFirst = "NotRecorded",#M
FOincidentalByCatchMitigationDeviceTargetFirst = "NotApplicable",# [M]
FOincidentalByCatchMitigationDeviceSecond = "NotRecorded",#M
FOincidentalByCatchMitigationDeviceTargetSecond = "NotApplicable",#M
FOgearDimensions = "",
FOobservationCode = 'So', #M
FOnumberTotal = 1,
FOnumberSampled = 1,
FOselectionProb = 1,
FOinclusionProb = 1,
FOselectionMethod = "CENSUS", #M
FOunitName = VS_df$VSid, #M
FOselectionMethodCluster = "",
FOnumberTotalClusters = "",
FOnumberSampledClusters = "",
FOselectionProbCluster = "",
FOinclusionProbCluster = "",
FOsampled = "Y", #M
FOreasonNotSampled = "",
FOnonResponseCollected = "N",
FOauxiliaryVariableTotal = "",
FOauxiliaryVariableValue = "",
FOauxiliaryVariableName = "",
FOauxiliaryVariableUnit = "",
stringsAsFactors=FALSE
)
#===SS============
# 1 SSid [] - int
# 2 LEid [M/O] - int
# 3 FOid [M/O] - int
# 4 FTid [M/O] - int
# 5 OSid [M/O] - int
# 6 TEid [M/O] - int
# 7 SLid [M] - int
# 8 SSrecordType [M] - string
# 9 SSsequenceNumber [M] - int
# 10 SSstratification [DV,M] - YesNoFields
# 11 SSstratumName [DV,M] - StringLength100
# 12 SSclustering [DV,M] - Clustering
# 13 SSclusterName [DV,M] - StringLength100
# 14 SSobservationActivityType [DV,M] - ObservationActivityType
# 15 SScatchFraction [M] - CatchFraction
# 16 SSobservationType [DV,M] - ObservationMethod
# 17 SSsampler [O] - Sampler
# 18 SSspeciesListName [M] - StringLength100
# 19 SSuseForCalculateZero [M] - YesNoFields
# 20 SStimeTotal [O] - int
# 21 SStimeSampled [O] - int
# 22 SSnumberTotal [DV,O] - int
# 23 SSnumberSampled [DV,O] - int
# 24 SSselectionProb [DV,O] - Decimal0.0000000000000001-1
# 25 SSinclusionProb [DV,O] - Decimal0.0000000000000001-1
# 26 SSselectionMethod [DV,M] - SelectionMethod
# 27 SSunitName [DV,M] - StringLength100
# 28 SSselectionMethodCluster [DV,O] - SelectionMethod
# 29 SSnumberTotalClusters [DV,O] - int
# 30 SSnumberSampledClusters [DV,O] - int
# 31 SSselectionProbCluster [DV,O] - Decimal0.0000000000000001-1
# 32 SSinclusionProbCluster [DV,O] - Decimal0.0000000000000001-1
# 33 SSsampled [DV,M] - YesNoFields
# 34 SSreasonNotSampled [DV,O] - ReasonForNotSampling
# 35 SSnonResponseCollected [DV,O] - YesNoFields
# 36 SSauxiliaryVariableTotal [DV,O] - DecimalPrec3
# 37 SSauxiliaryVariableValue [DV,O] - DecimalPrec3
# 38 SSauxiliaryVariableName [DV,O] - AuxiliaryVariableName
# 39 SSauxiliaryVariableUnit [DV,O] - MUNIT
SS_df<-data.frame(
SSid = dataset$VSid,
LEid = "",
FOid = dataset$VSid,
FTid = "",
OSid = "",
TEid = "",
SLid = "",
SSrecordType = "SS", #M
SSsequenceNumber = as.integer(dataset$VSid), #M
SSstratification = "N", #M
SSstratumName = "U", #M
SSclustering = "N", #M
SSclusterName = "U", #M
SSobservationActivityType = "Sort", #M
SScatchFraction = "Lan", #M
SSobservationType = "Volume", #M
SSsampler = "Observer", #M
SSspeciesListName = project_name_outputs, #M
SSuseForCalculateZero = "N", #M
SStimeTotal = "",
SStimeSampled = "",
SSnumberTotal = 1,
SSnumberSampled = 1,
SSselectionProb = 1,
SSinclusionProb = 1,
SSselectionMethod = "CENSUS",
SSunitName = dataset$VSid,
SSselectionMethodCluster = "",
SSnumberTotalClusters = "",
SSnumberSampledClusters = "",
SSselectionProbCluster = "",
SSinclusionProbCluster = "",
SSsampled = "Y", #M,
SSreasonNotSampled = "",
SSnonResponseCollected = "N",
SSauxiliaryVariableTotal = "",
SSauxiliaryVariableValue = "",
SSauxiliaryVariableName = "",
SSauxiliaryVariableUnit = "",
stringsAsFactors=FALSE
)
#====SA===========
# 1 SAid [] - int
# 2 SSid [] - int
# 3 SArecordType [M] - string
# 4 SAsequenceNumber [M] - int
# 5 SAparentSequenceNumber [O] - int
# 6 SAstratification [DV,M] - YesNoFields
# 7 SAstratumName [DV,M] - StringLength100
# 8 SAspeciesCode [M] - SpecWoRMS
# 9 SAspeciesCodeFAO [O] - SpecASFIS
# 10 SAstateOfProcessing [M] - StateOfProcessing
# 11 SApresentation [M] - ProductPresentation
# 12 SAspecimensState [M] - SpecimensState
# 13 SAcatchCategory [M] - CatchCategory
# 14 SAlandingCategory [O] - LandingCategory
# 15 SAcommSizeCatScale [O] - CommercialSizeCategoryScale
# 16 SAcommSizeCat [O] - CommercialSizeCategory
# 17 SAsex [M] - SEXCO
# 18 SAexclusiveEconomicZoneIndicator [O] - ISO_3166
# 19 SAarea [O] - ICES_Area
# 20 SArectangle [O] - StatRec
# 21 SAfisheriesManagementUnit [O] - AreaNonFAO
# 22 SAgsaSubarea [M] - Areas_GFCM_GSA
# 23 SAjurisdictionArea [O] - JurisdictionArea
# 24 SAnationalFishingActivity [O] - NationalFishingActivity
# 25 SAmetier5 [O] - Metier5_FishingActivity
# 26 SAmetier6 [O] - Metier6_FishingActivity
# 27 SAgear [O] - GearType
# 28 SAmeshSize [O] - int
# 29 SAselectionDevice [O] - SelectionDevice
# 30 SAselectionDeviceMeshSize [O] - int
# 31 SAunitType [M] - SamplingUnit
# 32 SAtotalWeightLive [O] - int
# 33 SAsampleWeightLive [O] - int
# 34 SAnumberTotal [DV,O] - Decimal0.1-999999999
# 35 SAnumberSampled [DV,O] - Decimal0.1-999999999
# 36 SAselectionProb [DV,O] - Decimal0-1
# 37 SAinclusionProb [DV,O] - Decimal0-1
# 38 SAselectionMethod [DV,M] - SelectionMethod
# 39 SAunitName [DV,M] - StringLength100
# 40 SAlowerHierarchy [M/O] - LowerHierarchy
# 41 SAsampler [O] - Sampler
# 42 SAsampled [DV,M] - YesNoFields
# 43 SAreasonNotSampled [DV,O] - ReasonForNotSampling
# 44 SAnonResponseCollected [DV,O] - YesNoFields
# 45 SAreasonNotSampledFM [DV,O] - ReasonForNotSampling
# 46 SAreasonNotSampledBV [DV,O] - ReasonForNotSampling
# 47 SAtotalWeightMeasured [O] - int
# 48 SAsampleWeightMeasured [O] - int
# 49 SAconversionFactorMeasLive [O] - Decimal0.900-10
# 50 SAauxiliaryVariableTotal [DV,O] - DecimalPrec3
# 51 SAauxiliaryVariableValue [DV,O] - DecimalPrec3
# 52 SAauxiliaryVariableName [DV,O] - AuxiliaryVariableName
# 53 SAauxiliaryVariableUnit [DV,O] - MUNIT
SA_df<-data.frame(
SAid = 1:nrow(dataset),
SSid = dataset$VSid,
SArecordType = "SA", #M
SAsequenceNumber = dataset$VSid, #M
SAparentSequenceNumber = "",
SAstratification = "N", #M
SAstratumName = "U", #M
SAspeciesCode = 107254, #M
SAspeciesCodeFAO = "NEP",
SAstateOfProcessing = "FRE", #M
SApresentation = "WHL", #M
SAspecimensState = "DeadOrZeroProbSurvival", #M
SAcatchCategory = "Lan", #M
SAlandingCategory = "",
SAcommSizeCatScale = "",
SAcommSizeCat = "",
SAsex = "U", #M
SAexclusiveEconomicZoneIndicator = "",
SAarea = "",
SArectangle = "",
SAfisheriesManagementUnit = "",
SAgsaSubarea = "NotApplicable", #M
SAjurisdictionArea = "",
SAnationalFishingActivity = "",
SAmetier5 = "",
SAmetier6 = "",
SAgear = "",
SAmeshSize = "",
SAselectionDevice = "",
SAselectionDeviceMeshSize = "",
SAunitType = "Box", #M
SAtotalWeightLive = "",
SAsampleWeightLive = "",
SAnumberTotal = 1,
SAnumberSampled = 1,
SAselectionProb = 1,
SAinclusionProb = 1,
SAselectionMethod = "CENSUS", #M
SAunitName = dataset$VSid, #M
SAlowerHierarchy = "D",
SAsampler = "Observer",
SAsampled = "N", #M
SAreasonNotSampled = "",
SAnonResponseCollected = "N",
SAreasonNotSampledFM = "",
SAreasonNotSampledBV = "",
SAtotalWeightMeasured = dataset[[target_var]]*100000000, # *100000000 to meet type required (integer)
SAsampleWeightMeasured = dataset[[target_var]]*100000000, # *100000000 to meet type required (integer)
SAconversionFactorMeasLive = 1,
SAauxiliaryVariableTotal = "",
SAauxiliaryVariableValue = "",
SAauxiliaryVariableName = "",
SAauxiliaryVariableUnit = "",
stringsAsFactors=FALSE
)
#====Builds final format===========
RDBESlist = list(DE = DE_df,SD = SD_df, VS = VS_df, FT = FT_df, FO = FO_df, SS = SS_df, SA = SA_df)
#id table
a<-merge(DE_df["DEid"],SD_df[c("DEid","SDid")])
a<-merge(a, VS_df[c("SDid","VSid")], all.x=T)
a<-merge(a, FT_df[c("VSid","FTid")], all.x=T)
a<-merge(a, FO_df[c("FTid","FOid")], all.x=T)
a<-merge(a, SS_df[c("FOid","SSid")], all.x=T)
a<-merge(a, SA_df[c("SSid","SAid")], all.x=T)
# reorder columns
a<-a[c("DEid","SDid","VSid","FTid","FOid","SSid","SAid")]
# reorder rows
a<-data.table(a)
a<-a[order(DEid,SDid,VSid,FTid,FOid,SSid,SAid),]
a$DEindex=apply(a[,1:which(colnames(a)=="DEid")],1,paste, collapse="_")
a$SDindex=apply(a[,1:which(colnames(a)=="SDid")],1,paste, collapse="_")
a$VSindex=apply(a[,1:which(colnames(a)=="VSid")],1,paste, collapse="_")
a$FTindex=apply(a[,1:which(colnames(a)=="FTid")],1,paste, collapse="_")
a$FOindex=apply(a[,1:which(colnames(a)=="FOid")],1,paste, collapse="_")
a$SSindex=apply(a[,1:which(colnames(a)=="SSid")],1,paste, collapse="_")
a$SAindex=apply(a[,1:which(colnames(a)=="SAid")],1,paste, collapse="_")
key<-c(a$DEindex[match(DE_df$DEid,a$DEid)],
a$SDindex[match(SD_df$SDid,a$SDid)],
a$VSindex[match(VS_df$VSid,a$VSid)],
a$FTindex[match(FT_df$FTid,a$FTid)],
a$FOindex[match(FO_df$FOid,a$FOid)],
a$SSindex[match(SS_df$SSid,a$SSid)],
a$SAindex[match(SA_df$SAid,a$SAid)]
)
# file production
Oldscipen<-.Options$scipen
options(scipen=500)
#remove all id
for (i in names(RDBESlist))
{
RDBESlist[[i]][which(grepl(colnames(RDBESlist[[i]]),pat="[A-Z]id"))]<-NULL
}
#===Save============
dir_outputs<-paste0(base_dir_outputs,"/",
project_name_outputs,"/")
dir.create(dir_outputs, recursive=T, showWarnings=FALSE)
filename_output_CS <- paste0("H1.csv")
filename_output_SL <- paste0("HSL.csv")
filename_output_VD <- paste0("HVD.csv")
lapply(RDBESlist, function(x, filename1 = paste0(dir_outputs,filename_output_CS)){
if("DErecordType" %in% colnames(x)){
write.table(x, file = filename1, append = FALSE, quote = FALSE, sep = ",",
eol = "\n", na = "NA", dec = ".", row.names = FALSE,
col.names = FALSE, qmethod = c("escape", "double"))
} else {
write.table(x, file = filename1, append = TRUE, quote = FALSE, sep = ",",
eol = "\n", na = "NA", dec = ".", row.names = FALSE,
col.names = FALSE, qmethod = c("escape", "double"))
}
})
b<-read.table(file=paste0(dir_outputs,filename_output_CS), header=F, sep=";")
b<-cbind(key,b)
b<-b[order(as.character(b$key), decreasing=FALSE),]
b<-b[!is.na(key),]
b$key<-NULL
b$V1<-as.character(b$V1)
# saves CS output
write.table(b$V1, file=paste0(dir_outputs,filename_output_CS), col.names=FALSE, row.names = FALSE, quote=FALSE,sep=",")
# -----Builds and saves dummySL-----------------
SL_base$SLspeciesListName<-project_name_outputs
SL_base$SLyear<-DEyear
SL_base$SLinstitute<-SDinstitution
# saves SL output
write.table(SL_base, file=paste0(dir_outputs,filename_output_SL), col.names=FALSE, row.names = FALSE, quote=FALSE,sep=",")
# -----Builds and saves dummyVD-----------------
# saves VD output
VD_base$VDyear<-DEyear
write.table(VD_base, file=paste0(dir_outputs,filename_output_VD), col.names=FALSE, row.names = FALSE, quote=FALSE,sep=",")
# -----Clean SL after dowload-----------------
# cleans excess of SL rows frequently present in download
# note:
# since it is an example - nicer to do here, fixing directly data input to scripts than patching it over multiple scripts later
# since example data are very simple, a simple select is done on specieaListName - this may not be sufficient in some minor cases
filename_download <- "2022_10_14_090838.zip"
unzip(paste0(dir_outputs, filename_download), exdir = paste0(dir_outputs,"tmp"))
# reads file to be fixed, fixes it and saves it back overwriting
tmp<-fread(paste0(dir_outputs,"tmp/SpeciesList.csv"))
tmp<-tmp[SLspeciesListName==project_name_outputs,]
write.csv(tmp, file=paste0(dir_outputs,"tmp/SpeciesList.csv"), quote=F, row.names=F)
# re-zips the file, puts it in final dir and deletes tmp dir
library(zip)
zip::zip(zipfile = paste0(project_name_outputs,".zip"), files =paste0(dir_outputs,"tmp/",dir(paste0(dir_outputs,"tmp"))), mode="cherry-pick")
unlink(paste0(dir_outputs,"tmp"), force=T, recursive = T)
ices-tools-dev/icesRDBES documentation built on April 17, 2025, 1:58 p.m.
R Package Documentation
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#======Prepares textbook data SDAResources::coots as H1 upload file===========
# Info:
# ?coots
# design is 2-stage cluster sampling with clusters of unequal sizes and Npsu not known
# clusters are clustches of eggs (nests) with at least 2 eggs.
# In each cluster, the volume of two eggs is measured
# clusters (psu) are unequal sized. In each cluster, 2 eggs are selected (ssus) and measured.
# total number of psus is not known (a drawback in this example). It is assumed very large (fpc negligible)
# table(coots$clutch)
# target variable is volume [others are available]
# how this example is placed in RDBES
# 1 DE row with DEstratumName == "Pckg_SDAResources_coots_H1"
# 1 child SD row
# 368 child rows in VS (the 368 eggs/psus observed)
# each associated to its cluster (clutch)
# VSnumberTotalClusters is not known (see page 59)
# VSnumberTotal is csize
# tables FT, FO, SS are just 1:1 links to the final data (in SA)
# in SA each volume is a SAsampleWeightMeasured
# ATT volumes are *100000000 to meet type requirement (integer)
rm(list=ls())
library(data.table)
# load textbook data
library(SDAResources)
data(coots)
dataset<-coots
target_var<-"volume"
# name your project (will be used in filenames for CS, SL and VD)
project_name_outputs <- "WGRDBES-EST_TEST_1_Pckg_SDAResources_coots_H1"
# select a year for upload
DEyear<-1965
SDinstitution <- 4484
DEsamplingScheme<-"WGRDBES-EST TEST 1"
DEstratumName <- "Pckg_SDAResources_coots_H1"
project_name_outputs <- gsub(" ","_", paste0(DEsamplingScheme,"_", DEstratumName))
baseDir <- "./data-raw/exampleData/TextBookExamples/"
baseDir <- ""
VD_base <- readRDS(paste0(baseDir,"aux_TextBookExamples/VD_base.rds"))
SL_base <- readRDS(paste0(baseDir,"aux_TextBookExamples/SL_base.rds"))
#nameof the directory where the outputs are saved currently
base_dir_outputs <- paste0(baseDir,"BuiltUploads")
if(!file.exists(base_dir_outputs)) dir.create(base_dir_outputs, recursive=T, showWarnings=FALSE)
#========Outline of Hierarchy 1================
# Design
# Sampling details
# Vessel Selection
# Fishing Trip
# Fishing Operation
# Species Selection
# Sample
# Length
# Biological variables
#===DE============
# 1 DEid [] - int
# 2 DErecordType [M] - string
# 3 DEsamplingScheme [M] - SamplingScheme
# 4 DEsamplingSchemeType [M] - SamplingSchemeType
# 5 DEyear [M] - Year
# 6 DEstratumName [M] - StringLength100
# 7 DEhierarchyCorrect [M] - YesNoFields
# 8 DEhierarchy [M] - RDBESUpperHierarchy
# 9 DEsampled [DV,M] - YesNoFields
# 10 DEreasonNotSampled [DV,O] - ReasonForNotSampling
# 11 DEnonResponseCollected [DV,O] - YesNoFields
# 12 DEauxiliaryVariableTotal [DV,O] - DecimalPrec3
# 13 DEauxiliaryVariableValue [DV,O] - DecimalPrec3
# 14 DEauxiliaryVariableName [DV,O] - AuxiliaryVariableName
# 15 DEauxiliaryVariableUnit[DV,O]-MUNIT
DE_df_base<-expand.grid(DEyear=DEyear,
DEstratumName="U",stringsAsFactors=F)
DE_df<-data.frame(
DEid = 1:nrow(DE_df_base),
DErecordType = "DE",
DEsamplingScheme = DEsamplingScheme,
DEsamplingSchemeType = "NatRouCF",
DEyear = as.integer(DEyear),
DEstratumName = DEstratumName,
DEhierarchyCorrect = "Y",
DEhierarchy = 1,
DEsampled = "Y",
DEreasonNotSampled = "",
DEnonResponseCollected = "Y",
DEauxiliaryVariableTotal = "",
DEauxiliaryVariableValue = "",
DEauxiliaryVariableName = "",
DEauxiliaryVariableUnit = "",
stringsAsFactors=FALSE
)
#===SD============
# x
# 1 SDid [M] - int
# 2 DEid [M] - int
# 3 SDrecordType [M] - string
# 4 SDcountry [M] - ISO_3166
# 5 SDinstitution [M] - EDMO
SD_df<-data.frame(
SDid=DE_df$DEid,
DEid=DE_df$DEid,
SDrecordType="SD",
SDcountry="ZW",
SDinstitution=as.integer(SDinstitution),
stringsAsFactors=FALSE
)
#===VS============
# x
# 1 VSid [M] - int
# 2 SDid [M] - int
# 3 VDid [M] - int
# 4 TEid [M/O] - int
# 5 VSrecordType [M] - string
# 6 VSsequenceNumber [M] - int
# 7 VSencryptedVesselCode [M] - StringLength100
# 8 VSstratification [DV,M] - YesNoFields
# 9 VSstratumName [DV,M] - StringLength100
# 10 VSclustering [DV,M] - Clustering
# 11 VSclusterName [DV,M] - StringLength100
# 12 VSsampler [O] - Sampler
# 13 VSnumberTotal [DV,O] - int
# 14 VSnumberSampled [DV,O] - int
# 15 VSselectionProb [DV,O] - Decimal0.0000000000000001-1
# 16 VSinclusionProb [DV,O] - Decimal0.0000000000000001-1
# 17 VSselectionMethod [DV,M] - SelectionMethod
# 18 VSunitName [DV,M] - StringLength100
# 19 VSselectionMethodCluster [DV,O] - SelectionMethod
# 20 VSnumberTotalClusters [DV,O] - int
# 21 VSnumberSampledClusters [DV,O] - int
# 22 VSselectionProbCluster [DV,O] - Decimal0.0000000000000001-1
# 23 VSinclusionProbCluster [DV,O] - Decimal0.0000000000000001-1
# 24 VSsampled [DV,M] - YesNoFields
# 25 VSreasonNotSampled [DV,O] - ReasonForNotSampling
# 26 VSnonResponseCollected [DV,O] - YesNoFields
# 27 VSauxiliaryVariableTotal [DV,O] - DecimalPrec3
# 28 VSauxiliaryVariableValue [DV,O] - DecimalPrec3
# 29 VSauxiliaryVariableName [DV,O] - AuxiliaryVariableName
# 30 VSauxiliaryVariableUnit [DV,O] - MUNIT
#check_All_fields("VS")
# adds VSid to dataset
dataset$VSid <- 1:nrow(dataset)
VS_base<-as.data.table(dataset)[,list(N="",n=.N),clutch]
# creates a dummyVD and adds dataset
# restricts VD_base to what is needed
VD_base <- VD_base[1:nrow(VS_base),]
VS_base$VSencryptedVesselCode<-VD_base$VDencryptedVesselCode
# should be 0
test<-sum(duplicated(VS_base$VSencryptedVesselCode))==0
if(!test) stop( "duplicated VSencryptedVesselCode")
VS_df <- data.frame(
VSid = dataset$VSid,
SDid = as.integer(1),
VDid = "",
TEid = "",
VSrecordType = 'VS',
VSsequenceNumber = rep(1:2,184),# M
VSencryptedVesselCode = VS_base$VSencryptedVesselCode, #M
VSstratification = "N",
VSstratumName = "U", #M
VSclustering = "2C", #M
VSclusterName = dataset$clutch, #M
VSsampler = "Observer", #M
VSnumberTotal = "",
VSnumberSampled = "",
VSselectionProb = "",
VSinclusionProb = "",
VSselectionMethod = "SRSWOR", #M
VSunitName = 1:nrow(VS_base),#M
VSselectionMethodCluster = "SRSWOR",
VSnumberTotalClusters = "",
VSnumberSampledClusters = "",
VSselectionProbCluster = "",
VSinclusionProbCluster = "",
VSsampled = "Y",#M
VSreasonNotSampled = "",
VSnonResponseCollected = "Y",
VSauxiliaryVariableTotal = "",
VSauxiliaryVariableValue = "",
VSauxiliaryVariableName = "",
VSauxiliaryVariableUnit = "",
stringsAsFactors=FALSE
)
# units within cluster
VS_df$VSnumberSampled<-VS_base$n
VS_df$VSnumberTotal<-dataset$csize
VS_df$VSselectionProb<-""
VS_df$VSinclusionProb<-""
VS_df$VSselectionMethod<-"SRSWOR"
# clusters
VS_df$VSnumberTotalClusters<-"" # not known see page 58
VS_df$VSnumberSampledClusters<-184
VS_df$VSselectionMethodCluster<-"SRSWOR"
VS_df$VSselectionProbCluster<-""
VS_df$VSinclusionProbCluster<-"" # not known see page 58
#====FT===========
# 1 FTid [M] - int
# 2 OSid [M/O] - int
# 3 VSid [M/O] - int
# 4 VDid [M] - int
# 5 SDid [M/O] - int
# 6 FOid [M/O] - int
# 7 TEid [M/O] - int
# 8 FTrecordType [M] - string
# 9 FTencryptedVesselCode [M] - StringLength100
# 10 FTsequenceNumber [M] - int
# 11 FTstratification [DV,M] - YesNoFields
# 12 FTstratumName [DV,M] - StringLength100
# 13 FTclustering [DV,M] - Clustering
# 14 FTclusterName [DV,M] - StringLength100
# 15 FTsampler [O] - Sampler
# 16 FTsamplingType [M] - SamplingContext
# 17 FTnumberOfHaulsOrSets [M/O] - IntZeroToMax
# 18 FTdepartureLocation [M/O] - Harbour_LOCODE
# 19 FTdepartureDate [M/O] - Date
# 20 FTdepartureTime [M/O] - StringLength60
# 21 FTarrivalLocation [M] - Harbour_LOCODE
# 22 FTarrivalDate [M] - Date
# 23 FTarrivalTime [M/O] - StringLength60
# 24 FTnumberTotal [DV,O] - int
# 25 FTnumberSampled [DV,O] - int
# 26 FTselectionProb [DV,O] - Decimal0-1
# 27 FTinclusionProb [DV,O] - Decimal0-1
# 28 FTselectionMethod [DV,M] - SelectionMethod
# 29 FTunitName [DV,M] - StringLength100
# 30 FTselectionMethodCluster [DV,O] - SelectionMethod
# 31 FTnumberTotalClusters [DV,O] - int
# 32 FTnumberSampledClusters [DV,O] - int
# 33 FTselectionProbCluster [DV,O] - Decimal0-1
# 34 FTinclusionProbCluster [DV,O] - Decimal0-1
# 35 FTsampled [DV,M] - YesNoFields
# 36 FTreasonNotSampled [DV,O] - ReasonForNotSampling
# 37 FTnonResponseCollected [DV,O] - YesNoFields
# 38 FTauxiliaryVariableTotal [DV,O] - DecimalPrec3
# 39 FTauxiliaryVariableValue [DV,O] - DecimalPrec3
# 40 FTauxiliaryVariableName [DV,O] - AuxiliaryVariableName
# 41 FTauxiliaryVariableUnit [DV,O] - MUNIT
FT_df <- data.frame(
FTid = dataset$VSid,#[M] - int
OSid = "",# [M/O] - int
VSid = dataset$VSid, #[M/O]
VDid = "", #[M] - int
SDid = "", #[M/O] - int
FOid = "", #[M/O] - int
TEid = "", #[M/O] - int
FTrecordType='FT', #[M] - string
FTencryptedVesselCode = VS_base$VSencryptedVesselCode, #[M]
FTsequenceNumber = as.integer(1:nrow(dataset)), #[M] - string
FTstratification = "N", #[DV,M] - RS_Stratification
FTstratumName = "U", #[DV,M] - string
FTclustering = "N", #[DV,M] - RS_Clustering
FTclusterName = "U", #[DV,M] - string
FTsampler = "Observer", #[M] - RS_Sampler
FTsamplingType = "AtSea" , #[M] - RS_SamplingType
FTnumberOfHaulsOrSets = 1, #[O] - int
FTdepartureLocation="ZWHWN", #[O] - Harbour_LOCODE
FTdepartureDate=seq(from = as.Date("1965-01-01", format='%Y-%m-%d'), by=1, length.out=nrow(dataset)), #[M/O] - date
FTdepartureTime="", #[O] - time
FTarrivalLocation = "ZWHWN", #[M] - Harbour_LOCODE
FTarrivalDate=seq(from = as.Date("1965-01-01", format='%Y-%m-%d'), by=1, length.out=nrow(dataset)), #[M] - date
FTarrivalTime="", #[O] - time
FTnumberTotal= 1, #[DV,O] - int
FTnumberSampled=1, #[DV,O] - int
FTselectionProb=1, #[DV,O] - DecimalPrec10
FTinclusionProb=1, #[DV,O] - DecimalPrec10
FTselectionMethod="CENSUS", #[DV,M] - RS_SelectionMethod
FTunitName = VS_base$VSencryptedVesselCode, #[DV,M] - string
FTselectionMethodCluster="", #[DV,O] - RS_SelectionMethod
FTnumberTotalClusters="", #[DV,O] - int
FTnumberSampledClusters="", #[DV,O] - int
FTselectionProbCluster="", #[DV,O] - DecimalPrec10
FTinclusionProbCluster="", #[DV,O] - DecimalPrec10
FTsampled="Y", #[DV,M] - YesNoFields
FTreasonNotSampled= "", #[DV,O] - RS_ReasonForNotSampling
FTnonResponseCollected = "N",
FTauxiliaryVariableTotal = "",
FTauxiliaryVariableValue = "",
FTauxiliaryVariableName = "",
FTauxiliaryVariableUnit = "",
stringsAsFactors=FALSE
)
#====FO===========
# 1 FOid [M] - int
# 2 FTid [M/O] - int
# 3 SDid [M/O] - int
# 4 FOrecordType [M] - string
# 5 FOstratification [DV,M] - YesNoFields
# 6 FOsequenceNumber [M] - int
# 7 FOstratumName [DV,M] - StringLength100
# 8 FOclustering [DV,M] - Clustering
# 9 FOclusterName [DV,M] - StringLength100
# 10 FOsampler [O] - Sampler
# 11 FOaggregationLevel [M] - AggregationLevel
# 12 FOvalidity [M] - ValidityFlag
# 13 FOcatchReg [M] - CatchRegistration
# 14 FOstartDate [O] - Date
# 15 FOstartTime [O] - Time
# 16 FOendDate [M] - Date
# 17 FOendTime [M/O] - Time
# 18 FOduration [M/O] - int
# 19 FOdurationSource [M] - DurationSource
# 20 FOhandlingTime [O] - int
# 21 FOstartLat [O] - Decimal-90.000000-90.000000
# 22 FOstartLon [O] - Decimal-180.000000-180.000000
# 23 FOstopLat [O] - Decimal-90.000000-90.000000
# 24 FOstopLon [O] - Decimal-180.000000-180.000000
# 25 FOexclusiveEconomicZoneIndicator [O] - ISO_3166
# 26 FOarea [M] - ICES_Area
# 27 FOrectangle [O] - StatRec
# 28 FOfisheriesManagementUnit [O] - AreaNonFAO
# 29 FOgsaSubarea [M] - Areas_GFCM_GSA
# 30 FOjurisdictionArea [O] - JurisdictionArea
# 31 FOfishingDepth [O] - int
# 32 FOwaterDepth [O] - int
# 33 FOnationalFishingActivity [O] - NationalFishingActivity
# 34 FOmetier5 [O] - Metier5_FishingActivity
# 35 FOmetier6 [M] - Metier6_FishingActivity
# 36 FOgear [M] - GearType
# 37 FOmeshSize [O] - int
# 38 FOselectionDevice [O] - SelectionDevice
# 39 FOselectionDeviceMeshSize [O] - int
# 40 FOtargetSpecies [O] - TargetSpecies
# 41 FOincidentalByCatchMitigationDeviceFirst [M] - BycatchMitigationDevice
# 42 FOincidentalByCatchMitigationDeviceTargetFirst [M] - BycatchMitigationDeviceTarget
# 43 FOincidentalByCatchMitigationDeviceSecond [M] - BycatchMitigationDevice
# 44 FOincidentalByCatchMitigationDeviceTargetSecond [M] - BycatchMitigationDeviceTarget
# 45 FOgearDimensions [O] - int
# 46 FOobservationCode [M] - ObservationCode
# 47 FOnumberTotal [DV,O] - int
# 48 FOnumberSampled [DV,O] - int
# 49 FOselectionProb [DV,O] - Decimal0.0000000000000001-1
# 50 FOinclusionProb [DV,O] - Decimal0.0000000000000001-1
# 51 FOselectionMethod [DV,M] - SelectionMethod
# 52 FOunitName [DV,M] - StringLength100
# 53 FOselectionMethodCluster [DV,O] - SelectionMethod
# 54 FOnumberTotalClusters [DV,O] - int
# 55 FOnumberSampledClusters [DV,O] - int
# 56 FOselectionProbCluster [DV,O] - Decimal0.0000000000000001-1
# 57 FOinclusionProbCluster [DV,O] - Decimal0.0000000000000001-1
# 58 FOsampled [DV,M] - YesNoFields
# 59 FOreasonNotSampled [DV,O] - ReasonForNotSampling
# 60 FOnonResponseCollected [DV,O] - YesNoFields
# 61 FOauxiliaryVariableTotal [DV,O] - DecimalPrec3
# 62 FOauxiliaryVariableValue [DV,O] - DecimalPrec3
# 63 FOauxiliaryVariableName [DV,O] - AuxiliaryVariableName
# 64 FOauxiliaryVariableUnit [DV,O] - MUNIT
FO_df <- data.frame(
FOid = dataset$VSid,
FTid = dataset$VSid,
SDid = "",
FOrecordType = "FO",#M
FOstratification = "N",#M
FOsequenceNumber = as.integer(1:nrow(dataset)),#M
FOstratumName = "U",#M
FOclustering = "N",#M
FOclusterName = "U",#M
FOsampler = "Observer",
FOaggregationLevel = "H",#M
FOvalidity = "V",#M
FOcatchReg = "Lan",#M
FOstartDate = as.Date(FT_df$FTdepartureDate, format='%Y-%m-%d'),
FOstartTime = "",
FOendDate = as.Date(FT_df$FTdepartureDate, format='%Y-%m-%d'),#M
FOendTime ="",#M
FOduration = 60, #M ATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT!!!!
FOdurationSource = "Crew",
FOhandlingTime = "",
FOstartLat="", # ATT!
FOstartLon="", # ATT!
FOstopLat="",
FOstopLon="",
FOexclusiveEconomicZoneIndicator = "", #
FOarea = "27.3.a.21", #M
FOrectangle = "",
FOfisheriesManagementUnit = "",
FOgsaSubarea = "NotApplicable", #M
FOjurisdictionArea = "",
FOfishingDepth = "",
FOwaterDepth = "",
FOnationalFishingActivity = "",
FOmetier5 = "",
FOmetier6 = "OTT_CRU_70-89_2_35",#M
FOgear = "OTT",#M
FOmeshSize = "",
FOselectionDevice = "",
FOselectionDeviceMeshSize = "",
FOtargetSpecies = "",
FOincidentalByCatchMitigationDeviceFirst = "NotRecorded",#M
FOincidentalByCatchMitigationDeviceTargetFirst = "NotApplicable",# [M]
FOincidentalByCatchMitigationDeviceSecond = "NotRecorded",#M
FOincidentalByCatchMitigationDeviceTargetSecond = "NotApplicable",#M
FOgearDimensions = "",
FOobservationCode = 'So', #M
FOnumberTotal = 1,
FOnumberSampled = 1,
FOselectionProb = 1,
FOinclusionProb = 1,
FOselectionMethod = "CENSUS", #M
FOunitName = VS_df$VSid, #M
FOselectionMethodCluster = "",
FOnumberTotalClusters = "",
FOnumberSampledClusters = "",
FOselectionProbCluster = "",
FOinclusionProbCluster = "",
FOsampled = "Y", #M
FOreasonNotSampled = "",
FOnonResponseCollected = "N",
FOauxiliaryVariableTotal = "",
FOauxiliaryVariableValue = "",
FOauxiliaryVariableName = "",
FOauxiliaryVariableUnit = "",
stringsAsFactors=FALSE
)
#===SS============
# 1 SSid [] - int
# 2 LEid [M/O] - int
# 3 FOid [M/O] - int
# 4 FTid [M/O] - int
# 5 OSid [M/O] - int
# 6 TEid [M/O] - int
# 7 SLid [M] - int
# 8 SSrecordType [M] - string
# 9 SSsequenceNumber [M] - int
# 10 SSstratification [DV,M] - YesNoFields
# 11 SSstratumName [DV,M] - StringLength100
# 12 SSclustering [DV,M] - Clustering
# 13 SSclusterName [DV,M] - StringLength100
# 14 SSobservationActivityType [DV,M] - ObservationActivityType
# 15 SScatchFraction [M] - CatchFraction
# 16 SSobservationType [DV,M] - ObservationMethod
# 17 SSsampler [O] - Sampler
# 18 SSspeciesListName [M] - StringLength100
# 19 SSuseForCalculateZero [M] - YesNoFields
# 20 SStimeTotal [O] - int
# 21 SStimeSampled [O] - int
# 22 SSnumberTotal [DV,O] - int
# 23 SSnumberSampled [DV,O] - int
# 24 SSselectionProb [DV,O] - Decimal0.0000000000000001-1
# 25 SSinclusionProb [DV,O] - Decimal0.0000000000000001-1
# 26 SSselectionMethod [DV,M] - SelectionMethod
# 27 SSunitName [DV,M] - StringLength100
# 28 SSselectionMethodCluster [DV,O] - SelectionMethod
# 29 SSnumberTotalClusters [DV,O] - int
# 30 SSnumberSampledClusters [DV,O] - int
# 31 SSselectionProbCluster [DV,O] - Decimal0.0000000000000001-1
# 32 SSinclusionProbCluster [DV,O] - Decimal0.0000000000000001-1
# 33 SSsampled [DV,M] - YesNoFields
# 34 SSreasonNotSampled [DV,O] - ReasonForNotSampling
# 35 SSnonResponseCollected [DV,O] - YesNoFields
# 36 SSauxiliaryVariableTotal [DV,O] - DecimalPrec3
# 37 SSauxiliaryVariableValue [DV,O] - DecimalPrec3
# 38 SSauxiliaryVariableName [DV,O] - AuxiliaryVariableName
# 39 SSauxiliaryVariableUnit [DV,O] - MUNIT
SS_df<-data.frame(
SSid = dataset$VSid,
LEid = "",
FOid = dataset$VSid,
FTid = "",
OSid = "",
TEid = "",
SLid = "",
SSrecordType = "SS", #M
SSsequenceNumber = as.integer(dataset$VSid), #M
SSstratification = "N", #M
SSstratumName = "U", #M
SSclustering = "N", #M
SSclusterName = "U", #M
SSobservationActivityType = "Sort", #M
SScatchFraction = "Lan", #M
SSobservationType = "Volume", #M
SSsampler = "Observer", #M
SSspeciesListName = project_name_outputs, #M
SSuseForCalculateZero = "N", #M
SStimeTotal = "",
SStimeSampled = "",
SSnumberTotal = 1,
SSnumberSampled = 1,
SSselectionProb = 1,
SSinclusionProb = 1,
SSselectionMethod = "CENSUS",
SSunitName = dataset$VSid,
SSselectionMethodCluster = "",
SSnumberTotalClusters = "",
SSnumberSampledClusters = "",
SSselectionProbCluster = "",
SSinclusionProbCluster = "",
SSsampled = "Y", #M,
SSreasonNotSampled = "",
SSnonResponseCollected = "N",
SSauxiliaryVariableTotal = "",
SSauxiliaryVariableValue = "",
SSauxiliaryVariableName = "",
SSauxiliaryVariableUnit = "",
stringsAsFactors=FALSE
)
#====SA===========
# 1 SAid [] - int
# 2 SSid [] - int
# 3 SArecordType [M] - string
# 4 SAsequenceNumber [M] - int
# 5 SAparentSequenceNumber [O] - int
# 6 SAstratification [DV,M] - YesNoFields
# 7 SAstratumName [DV,M] - StringLength100
# 8 SAspeciesCode [M] - SpecWoRMS
# 9 SAspeciesCodeFAO [O] - SpecASFIS
# 10 SAstateOfProcessing [M] - StateOfProcessing
# 11 SApresentation [M] - ProductPresentation
# 12 SAspecimensState [M] - SpecimensState
# 13 SAcatchCategory [M] - CatchCategory
# 14 SAlandingCategory [O] - LandingCategory
# 15 SAcommSizeCatScale [O] - CommercialSizeCategoryScale
# 16 SAcommSizeCat [O] - CommercialSizeCategory
# 17 SAsex [M] - SEXCO
# 18 SAexclusiveEconomicZoneIndicator [O] - ISO_3166
# 19 SAarea [O] - ICES_Area
# 20 SArectangle [O] - StatRec
# 21 SAfisheriesManagementUnit [O] - AreaNonFAO
# 22 SAgsaSubarea [M] - Areas_GFCM_GSA
# 23 SAjurisdictionArea [O] - JurisdictionArea
# 24 SAnationalFishingActivity [O] - NationalFishingActivity
# 25 SAmetier5 [O] - Metier5_FishingActivity
# 26 SAmetier6 [O] - Metier6_FishingActivity
# 27 SAgear [O] - GearType
# 28 SAmeshSize [O] - int
# 29 SAselectionDevice [O] - SelectionDevice
# 30 SAselectionDeviceMeshSize [O] - int
# 31 SAunitType [M] - SamplingUnit
# 32 SAtotalWeightLive [O] - int
# 33 SAsampleWeightLive [O] - int
# 34 SAnumberTotal [DV,O] - Decimal0.1-999999999
# 35 SAnumberSampled [DV,O] - Decimal0.1-999999999
# 36 SAselectionProb [DV,O] - Decimal0-1
# 37 SAinclusionProb [DV,O] - Decimal0-1
# 38 SAselectionMethod [DV,M] - SelectionMethod
# 39 SAunitName [DV,M] - StringLength100
# 40 SAlowerHierarchy [M/O] - LowerHierarchy
# 41 SAsampler [O] - Sampler
# 42 SAsampled [DV,M] - YesNoFields
# 43 SAreasonNotSampled [DV,O] - ReasonForNotSampling
# 44 SAnonResponseCollected [DV,O] - YesNoFields
# 45 SAreasonNotSampledFM [DV,O] - ReasonForNotSampling
# 46 SAreasonNotSampledBV [DV,O] - ReasonForNotSampling
# 47 SAtotalWeightMeasured [O] - int
# 48 SAsampleWeightMeasured [O] - int
# 49 SAconversionFactorMeasLive [O] - Decimal0.900-10
# 50 SAauxiliaryVariableTotal [DV,O] - DecimalPrec3
# 51 SAauxiliaryVariableValue [DV,O] - DecimalPrec3
# 52 SAauxiliaryVariableName [DV,O] - AuxiliaryVariableName
# 53 SAauxiliaryVariableUnit [DV,O] - MUNIT
SA_df<-data.frame(
SAid = 1:nrow(dataset),
SSid = dataset$VSid,
SArecordType = "SA", #M
SAsequenceNumber = dataset$VSid, #M
SAparentSequenceNumber = "",
SAstratification = "N", #M
SAstratumName = "U", #M
SAspeciesCode = 107254, #M
SAspeciesCodeFAO = "NEP",
SAstateOfProcessing = "FRE", #M
SApresentation = "WHL", #M
SAspecimensState = "DeadOrZeroProbSurvival", #M
SAcatchCategory = "Lan", #M
SAlandingCategory = "",
SAcommSizeCatScale = "",
SAcommSizeCat = "",
SAsex = "U", #M
SAexclusiveEconomicZoneIndicator = "",
SAarea = "",
SArectangle = "",
SAfisheriesManagementUnit = "",
SAgsaSubarea = "NotApplicable", #M
SAjurisdictionArea = "",
SAnationalFishingActivity = "",
SAmetier5 = "",
SAmetier6 = "",
SAgear = "",
SAmeshSize = "",
SAselectionDevice = "",
SAselectionDeviceMeshSize = "",
SAunitType = "Box", #M
SAtotalWeightLive = "",
SAsampleWeightLive = "",
SAnumberTotal = 1,
SAnumberSampled = 1,
SAselectionProb = 1,
SAinclusionProb = 1,
SAselectionMethod = "CENSUS", #M
SAunitName = dataset$VSid, #M
SAlowerHierarchy = "D",
SAsampler = "Observer",
SAsampled = "N", #M
SAreasonNotSampled = "",
SAnonResponseCollected = "N",
SAreasonNotSampledFM = "",
SAreasonNotSampledBV = "",
SAtotalWeightMeasured = dataset[[target_var]]*100000000, # *100000000 to meet type required (integer)
SAsampleWeightMeasured = dataset[[target_var]]*100000000, # *100000000 to meet type required (integer)
SAconversionFactorMeasLive = 1,
SAauxiliaryVariableTotal = "",
SAauxiliaryVariableValue = "",
SAauxiliaryVariableName = "",
SAauxiliaryVariableUnit = "",
stringsAsFactors=FALSE
)
#====Builds final format===========
RDBESlist = list(DE = DE_df,SD = SD_df, VS = VS_df, FT = FT_df, FO = FO_df, SS = SS_df, SA = SA_df)
#id table
a<-merge(DE_df["DEid"],SD_df[c("DEid","SDid")])
a<-merge(a, VS_df[c("SDid","VSid")], all.x=T)
a<-merge(a, FT_df[c("VSid","FTid")], all.x=T)
a<-merge(a, FO_df[c("FTid","FOid")], all.x=T)
a<-merge(a, SS_df[c("FOid","SSid")], all.x=T)
a<-merge(a, SA_df[c("SSid","SAid")], all.x=T)
# reorder columns
a<-a[c("DEid","SDid","VSid","FTid","FOid","SSid","SAid")]
# reorder rows
a<-data.table(a)
a<-a[order(DEid,SDid,VSid,FTid,FOid,SSid,SAid),]
a$DEindex=apply(a[,1:which(colnames(a)=="DEid")],1,paste, collapse="_")
a$SDindex=apply(a[,1:which(colnames(a)=="SDid")],1,paste, collapse="_")
a$VSindex=apply(a[,1:which(colnames(a)=="VSid")],1,paste, collapse="_")
a$FTindex=apply(a[,1:which(colnames(a)=="FTid")],1,paste, collapse="_")
a$FOindex=apply(a[,1:which(colnames(a)=="FOid")],1,paste, collapse="_")
a$SSindex=apply(a[,1:which(colnames(a)=="SSid")],1,paste, collapse="_")
a$SAindex=apply(a[,1:which(colnames(a)=="SAid")],1,paste, collapse="_")
key<-c(a$DEindex[match(DE_df$DEid,a$DEid)],
a$SDindex[match(SD_df$SDid,a$SDid)],
a$VSindex[match(VS_df$VSid,a$VSid)],
a$FTindex[match(FT_df$FTid,a$FTid)],
a$FOindex[match(FO_df$FOid,a$FOid)],
a$SSindex[match(SS_df$SSid,a$SSid)],
a$SAindex[match(SA_df$SAid,a$SAid)]
)
# file production
Oldscipen<-.Options$scipen
options(scipen=500)
#remove all id
for (i in names(RDBESlist))
{
RDBESlist[[i]][which(grepl(colnames(RDBESlist[[i]]),pat="[A-Z]id"))]<-NULL
}
#===Save============
dir_outputs<-paste0(base_dir_outputs,"/",
project_name_outputs,"/")
dir.create(dir_outputs, recursive=T, showWarnings=FALSE)
filename_output_CS <- paste0("H1.csv")
filename_output_SL <- paste0("HSL.csv")
filename_output_VD <- paste0("HVD.csv")
lapply(RDBESlist, function(x, filename1 = paste0(dir_outputs,filename_output_CS)){
if("DErecordType" %in% colnames(x)){
write.table(x, file = filename1, append = FALSE, quote = FALSE, sep = ",",
eol = "\n", na = "NA", dec = ".", row.names = FALSE,
col.names = FALSE, qmethod = c("escape", "double"))
} else {
write.table(x, file = filename1, append = TRUE, quote = FALSE, sep = ",",
eol = "\n", na = "NA", dec = ".", row.names = FALSE,
col.names = FALSE, qmethod = c("escape", "double"))
}
})
b<-read.table(file=paste0(dir_outputs,filename_output_CS), header=F, sep=";")
b<-cbind(key,b)
b<-b[order(as.character(b$key), decreasing=FALSE),]
b<-b[!is.na(key),]
b$key<-NULL
b$V1<-as.character(b$V1)
# saves CS output
write.table(b$V1, file=paste0(dir_outputs,filename_output_CS), col.names=FALSE, row.names = FALSE, quote=FALSE,sep=",")
# -----Builds and saves dummySL-----------------
SL_base$SLspeciesListName<-project_name_outputs
SL_base$SLyear<-DEyear
SL_base$SLinstitute<-SDinstitution
# saves SL output
write.table(SL_base, file=paste0(dir_outputs,filename_output_SL), col.names=FALSE, row.names = FALSE, quote=FALSE,sep=",")
# -----Builds and saves dummyVD-----------------
# saves VD output
VD_base$VDyear<-DEyear
write.table(VD_base, file=paste0(dir_outputs,filename_output_VD), col.names=FALSE, row.names = FALSE, quote=FALSE,sep=",")
# -----Clean SL after dowload-----------------
# cleans excess of SL rows frequently present in download
# note:
# since it is an example - nicer to do here, fixing directly data input to scripts than patching it over multiple scripts later
# since example data are very simple, a simple select is done on specieaListName - this may not be sufficient in some minor cases
filename_download <- "2022_10_14_090838.zip"
unzip(paste0(dir_outputs, filename_download), exdir = paste0(dir_outputs,"tmp"))
# reads file to be fixed, fixes it and saves it back overwriting
tmp<-fread(paste0(dir_outputs,"tmp/SpeciesList.csv"))
tmp<-tmp[SLspeciesListName==project_name_outputs,]
write.csv(tmp, file=paste0(dir_outputs,"tmp/SpeciesList.csv"), quote=F, row.names=F)
# re-zips the file, puts it in final dir and deletes tmp dir
library(zip)
zip::zip(zipfile = paste0(project_name_outputs,".zip"), files =paste0(dir_outputs,"tmp/",dir(paste0(dir_outputs,"tmp"))), mode="cherry-pick")
unlink(paste0(dir_outputs,"tmp"), force=T, recursive = T)
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