createCovariates: Create covariates
In MSToolkit: The MSToolkit library for clinical trial design

Description Usage Arguments Details Value Warning Author(s) See Also Examples

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

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())

`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
`timeNames,timeMean,timeCov,timeRange,timeCol,timePeriod`	(Optional) Arguments for the `createTimeVaryingCovariates` function. The `createTimeVaryingCovariates` 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
`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

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, ...

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

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

Mike K Smith mstoolkit@googlemail.com

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

  ## unit tests for the covariates component of the MSToolkit package 
  ## Not run: 
    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 )        
 
## End(Not run)