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Create covariates

Source: R/createCovariates.R
createCovariates.Rd

Function to create covariates. Discrete, continuous and/or from an external file. This function acts as a wrapper for the functions : createContinuousCovariates, createDiscreteCovariates, createDiscreteCovariates and createTimeVaryingCovariates

Usage

createCovariates(
  subjects,
  conNames = NULL,
  conMean,
  conCov,
  conRange = NULL,
  conDigits,
  conMaxDraws = 100,
  disNames = NULL,
  disValues,
  disProbs,
  disProbArray,
  extNames = NULL,
  extFile,
  extSubset,
  extRefCol,
  extSameRow = TRUE,
  extDataId = idCol,
  workingPath = getwd(),
  timeNames = NULL,
  timeMean,
  timeCov,
  timeRange = NULL,
  timeCol = getEctdColName("Time"),
  timePeriod,
  idCol = getEctdColName("Subject"),
  seed = .deriveFromMasterSeed()
)

Arguments

subjects

(Required) Subjects for which to create covariates

conNames, conMean, conCov, conRange, conDigits, conMaxDraws

(Optional) Arguments for the createContinuousCovariates function. The createContinuousCovariates function is not called if these arguments are not provided

disNames, disValues, disProbs, disProbArray

(Optional) Arguments for the createDiscreteCovariates function. The createDiscreteCovariates function is not called if these arguments are not provided

extNames, extFile, extSubset, extRefCol, extSameRow, extDataId

(Optional) Arguments for the createExternalCovariates function. The createExternalCovariates function is not called if these arguments are not provided

workingPath

(Optional) Working directory from which to import covariate data. By default, the current working directory is used

timeNames, timeMean, timeCov, timeRange, timeCol, timePeriod

(Optional) Arguments for the createTimeVaryingCovariates function. The createTimeVaryingCovariates function is not called if these arguments are not provided

idCol

(Optional) Name of the subject column. Must be a valid R name (See validNames) and not be found in anyone of conNames, extNames or disNames. "SUBJ" is used by default

seed

(Optional) Random seed to use by all the lower-level functions. By default, this is derived from the current random seed

Value

Data frame merging the results from the lower-level functions : createContinuousCovariates, createDiscreteCovariates, createExternalCovariates and createTimeVaryingCovariates

Details

According to the presence of each "names" argument, the function calls lower-level functions to generate covariates. For example, if conNames is given, the function will attempt to generate covariates from a continuous distribution using the createContinuousCovariates function.

If no names is given, a data frame containing only the subject column will be created.

If createTimeVaryingCovariates is invoked, the additional TIME column will be included in the output data.

Arguments are systematically passed to lower-level function according to a name convention. For example, the conRange argument is passed to createContinuousCovariates as the range argument, the extFile is passed to the createExternalCovariates as the file argument, ...

Warning

The function will generate an error if there is any duplicated names between conNames, extNames, disNames, timeNames and idCol.

See also

createContinuousCovariates, createDiscreteCovariates, createTimeVaryingCovariates and createExternalCovariates for details about each source of covariate and examples.

Author

Mike K Smith mstoolkit@googlemail.com

Examples



  ## unit tests for the covariates component of the MSToolkit package
  if (FALSE) {
    file.show( system.file( "Runit", "runit.data.covariates.R", package = "MSToolkit") )

    wPath <- system.file( "Runit", "data", "createCovariates", package = "MSToolkit")
    dAll <- createCovariates( 30,
      conNames = "X,Y", conMean = "0,0" , conCov = "1,0,1", conRange = "-1<X<1",  # continuous
      disNames = "P1,P2", disValues = "1,2#3,5,6" , disProbs = ".5,.5#.3,.3,.4",  # discrete
      extNames = "X1", extFile = "testCovariates.csv", workingPath = wPath )      # external

    dAllwithtime <- createCovariates( 30,
      conNames = "X,Y", conMean = "0,0" , conCov = "1,0,1", conRange = "-1<X<1", # continuous
      disNames = "P1,P2", disValues = "1,2#3,5,6" , disProbs = ".5,.5#.3,.3,.4", # discrete
      timeNames = "T1,T2", timeMean = list(1:3, 1:3), timeCov = list(1, 1:3),    # time-varying
      timePeriod = 1:3, extNames = "X1", extFile = "testCovariates.csv",         # external
      workingPath = wPath )
 }