In ices-tools-dev/icesRDBES: Functions for the ICES Regional Database and Estimation System (RDBES)

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
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Introduction

The aim of this document is to illustrate how to calculate zeros and probabilities using the RDBEScore package.

library(RDBEScore)

Load functions from their temporary locations

These should be added to the RDBEScore package which will make this step unnecessary in the future.

# clean the table prefixes of variable names 
#[makes it easier to handle in other functions]
    source("R/removePrefixFromVarNames.R") 
# checks data for some issues related to selection and probabilities, 
# including some features not yet developed 
# [stops need to corrected before probabilities are calculated]
    source("R/runChecksOnSelectionAndProbs.R") 
# modified/improved version of generateProbs developed during WKRDB-EST 1 
# and WKRDB-EST 2 [several new functionalities, warnings, etc]
    source("R/generateProbs.r") 
 # wrapper to "runChecksOnSelectionAndProbs" and "generateProbs"
    source("R/applyGenerateProbs.r")
  source("R/generateZerosUsingSL.r")

Prerequisites

First we'll load some example data from the RDBES and check it's valid. It's a good tip to check your RDBESDataObjects are valid after any manipulations you perform.

getwd()

# H7 test data
load ("data/testDataPreparationFunctions.Rdata")

# Number of rows in each non-null table
unlist(lapply(myH7RawObject, nrow))

validateRDBESDataObject(myH7RawObject, verbose = TRUE)

Check selection and probability values

First we remove the prefixes and then check the selection and probability values for any issues - there are some things we need to fix.

# clean the prefixes [makes it easier to handle in other functions]
myH7RawObject <- removePrefixFromVarNames(myH7RawObject)

class(myH7RawObject)

# checks data for some issues related to selection and probabilities
# note: this function is only exemplified here - 
# in general only applyGenerateProbs will be used as the wrapper also includes
# this function
runChecksOnSelectionAndProbs(myH7RawObject, printStopIssue = FALSE)

First, we'll change the selection methods.

    # changes to selection methods
    myH7RawObject$OS$selectMeth<-"SRSWOR"

    myH7RawObject$SA$stratification<-"N"

    myH7RawObject$SA$selectMeth<-"SRSWOR"

    myH7RawObject$BV$selectMeth<-"SRSWOR"

    runChecksOnSelectionAndProbs(myH7RawObject)

Now the main issues relation to selection methods have been corrected (and documented) but still probabilities cannot be calculated because numTotal are missing.

  myH7PrepObject<-applyGenerateProbs (x = myH7RawObject
                                      , probType = "both"
                                      , overwrite=T
                                      , runInitialProbChecks = FALSE)

We'll fix that now.

    # changes to numTotal
    myH7RawObject$OS$numTotal<-c(3,3,3)
    myH7RawObject$SS$numTotal<-c(1,1,1)
    myH7RawObject$SA$numTotal<-c(20, 10, 5)
    myH7RawObject$BV$numTotal<-c(rep(50, 29*5), rep(200, 95*5), rep(200, 39*5))

    myH7PrepObject<-applyGenerateProbs (x = myH7RawObject
                                        , probType = "both"
                                        , overwrite=T
                                        , runInitialProbChecks = FALSE)

Generate zeroes using SL

Generate true zeroes using the data from the SL table.

  myH7PrepObject2<-generateZerosUsingSL(myH7PrepObject)

# note the solution [dec SAid added to avoid integer that could 
# duplicate other already existing]
    myH7PrepObject2$SA

Finally, let's check our object is still valid. (It won't be until Nuno changes his function code :-) )

  validateRDBESDataObject(myH7PrepObject2, verbose = TRUE)

#END

ices-tools-dev/icesRDBES documentation built on April 17, 2025, 1:58 p.m.