This document shows how to take the output from doEstimationForAllStrata() and format it into the InterCatch format. This is done by using the function exportEstimationResultsToInterCatchFormat() in the RDBEScore package.
# load an example dataset
# H1 directory
dirH1 <- "../tests/testthat/h1_v_20250211/"
fixProbs <- function(myH1RawObject){
# Edit our data so that we have SRSWOR on each level and calculate the probs
myH1RawObject[["VS"]]$VSselectMeth <- "SRSWOR"
myH1RawObject[["VS"]]$VSincProb <- myH1RawObject[["VS"]]$VSnumSamp / myH1RawObject[["VS"]]$VSnumTotal
myH1RawObject[["VS"]]$VSselProb <- 1/myH1RawObject[["VS"]]$VSnumTotal
myH1RawObject[["FT"]]$FTselectMeth <- "SRSWOR"
myH1RawObject[["FT"]]$FTincProb <- myH1RawObject[["FT"]]$FTnumSamp / myH1RawObject[["FT"]]$FTnumTotal
myH1RawObject[["FT"]]$FTselProb <- 1/myH1RawObject[["FT"]]$FTnumTotal
myH1RawObject[["FO"]]$FOselectMeth <- "SRSWOR"
myH1RawObject[["FO"]]$FOincProb <- myH1RawObject[["FO"]]$FOnumSamp / myH1RawObject[["FO"]]$FOnumTotal
myH1RawObject[["FO"]]$FOselProb <- 1/myH1RawObject[["FO"]]$FOnumTotal
myH1RawObject[["SS"]]$SSselectMeth <- "SRSWOR"
myH1RawObject[["SS"]]$SSincProb <- myH1RawObject[["SS"]]$SSnumSamp / myH1RawObject[["SS"]]$SSnumTotal
myH1RawObject[["SS"]]$SSselProb <- 1/myH1RawObject[["SS"]]$SSnumTotal
myH1RawObject[["SA"]]$SAselectMeth <- "SRSWOR"
myH1RawObject[["SA"]]$SAincProb <- myH1RawObject[["SA"]]$SAnumSamp / myH1RawObject[["SA"]]$SAnumTotal
myH1RawObject[["SA"]]$SAselProb <- 1/myH1RawObject[["SA"]]$SAnumTotal
# Update our test data with some random sample measurements (it didn't include these)
# set the random seed
set.seed(1234)
myH1RawObject[['SA']]$SAsampWtLive <- round(runif(n=nrow(myH1RawObject[['SA']]),min = 1, max = 100))
myH1RawObject[['SA']]$SAsampWtMes <- round(runif(n=nrow(myH1RawObject[['SA']]),min = 1, max = 100))
myH1RawObject
}
## Step 1) load and prepare some test data
myH1RawObject <- createRDBESDataObject(input = dirH1)
#Filter our data for WGRDBES-EST TEST 1, 1965, H1
myCatchFraction <- "Lan"
mySpecies <- 1019159
myFields <- c("DEyear","DEhierarchy","DEsampScheme","DEstratumName","SAspeCode","SScatchFra")
myValues <- c(1965,1,"National Routine","DE_stratum1_H1",mySpecies,myCatchFraction)
myH1RawObject <- filterRDBESDataObject(myH1RawObject,
fieldsToFilter = myFields,
valuesToFilter = myValues )
myH1RawObject <- findAndKillOrphans(myH1RawObject)
myH1 <- fixProbs(myH1RawObject)
# Get our estimated values for the PSU
psuEstimates <- myStrataResults[myStrataResults$recType == "VS",]
# This is the data we will export to IC format
dataToOutput <- data.frame(Country = myH1[["SD"]]$SDctry,
Year = myH1[["DE"]]$DEyear,
SeasonType = NA,
Season = NA,
Fleet= NA,
AreaType = "Stratum",
FishingArea = psuEstimates$stratumName,
DepthRange = "NA",
Species = mySpecies ,
Stock = mySpecies,
CatchCategory = substr(myCatchFraction, 1, 1),
ReportingCategory = "A",
Usage = "H",
SamplesOrigin = "O",
UnitCATON = "kg",
CATON = psuEstimates$est.total/1000.0,
varCATON = psuEstimates$var.total/1000000.0,
Sex = "NA",
PlusGroup = "NA",
MeanWeight = -9,
unitMeanWeight = "kg",
unitCANUM = "n",
UnitAgeOrLength = "year",
NumberCaught = -9,
MeanWeight = -9,
CANUMtype = "Age",
AgeLength = c(1,1,1,2,2,2,3,3,3),
NumSamplesAge = c(300,300,300,200,200,200,100,100,100))
tempIC <- exportEstimationResultsToInterCatchFormat(dataToOutput)
print(tempIC)
#> [1] "HI,ZW,1965,NA,NA,NA,Stratum,VS_stratum1,NA,NA,-9,NA"
#> [2] "SI,ZW,1965,NA,NA,NA,Stratum,VS_stratum1,NA,1019159,1019159,L,A,NA,H,O,NA,kg, 4835.556,-9,3006072,NA,NA,NA"
#> [3] "SD,ZW,1965,NA,NA,NA,Stratum,VS_stratum1,NA,1019159,1019159,L,A,NA,Age,1,NA,-9,-9,-9,300,-9,kg,n,year,NA,NA,-9,-9,-9,-9,-9,-9"
#> [4] "SD,ZW,1965,NA,NA,NA,Stratum,VS_stratum1,NA,1019159,1019159,L,A,NA,Age,2,NA,-9,-9,-9,200,-9,kg,n,year,NA,NA,-9,-9,-9,-9,-9,-9"
#> [5] "SD,ZW,1965,NA,NA,NA,Stratum,VS_stratum1,NA,1019159,1019159,L,A,NA,Age,3,NA,-9,-9,-9,100,-9,kg,n,year,NA,NA,-9,-9,-9,-9,-9,-9"
#> [6] "HI,ZW,1965,NA,NA,NA,Stratum,VS_stratum2,NA,NA,-9,NA"
#> [7] "SI,ZW,1965,NA,NA,NA,Stratum,VS_stratum2,NA,1019159,1019159,L,A,NA,H,O,NA,kg,15217.778,-9,8936549,NA,NA,NA"
#> [8] "SD,ZW,1965,NA,NA,NA,Stratum,VS_stratum2,NA,1019159,1019159,L,A,NA,Age,1,NA,-9,-9,-9,300,-9,kg,n,year,NA,NA,-9,-9,-9,-9,-9,-9"
#> [9] "SD,ZW,1965,NA,NA,NA,Stratum,VS_stratum2,NA,1019159,1019159,L,A,NA,Age,2,NA,-9,-9,-9,200,-9,kg,n,year,NA,NA,-9,-9,-9,-9,-9,-9"
#> [10] "SD,ZW,1965,NA,NA,NA,Stratum,VS_stratum2,NA,1019159,1019159,L,A,NA,Age,3,NA,-9,-9,-9,100,-9,kg,n,year,NA,NA,-9,-9,-9,-9,-9,-9"
#> [11] "HI,ZW,1965,NA,NA,NA,Stratum,VS_stratum3,NA,NA,-9,NA"
#> [12] "SI,ZW,1965,NA,NA,NA,Stratum,VS_stratum3,NA,1019159,1019159,L,A,NA,H,O,NA,kg,10311.111,-9,8937750,NA,NA,NA"
#> [13] "SD,ZW,1965,NA,NA,NA,Stratum,VS_stratum3,NA,1019159,1019159,L,A,NA,Age,1,NA,-9,-9,-9,300,-9,kg,n,year,NA,NA,-9,-9,-9,-9,-9,-9"
#> [14] "SD,ZW,1965,NA,NA,NA,Stratum,VS_stratum3,NA,1019159,1019159,L,A,NA,Age,2,NA,-9,-9,-9,200,-9,kg,n,year,NA,NA,-9,-9,-9,-9,-9,-9"
#> [15] "SD,ZW,1965,NA,NA,NA,Stratum,VS_stratum3,NA,1019159,1019159,L,A,NA,Age,3,NA,-9,-9,-9,100,-9,kg,n,year,NA,NA,-9,-9,-9,-9,-9,-9"See also other package vignettes:
#END