Description Usage Arguments Details Value Author(s) See Also Examples
That function is iteratively called from analyzeRep
to analyze
a replicate dataset at each step defined by the interims.
1 2 3 4 5 6 7 8 9 10 11 | performAnalysis(analysisCode,
doses,
data,
software = c("R", "SAS"),
includeRows = NULL,
interimCol = getEctdColName("Interim"),
doseCol = getEctdColName("Dose"),
seed = .deriveFromMasterSeed(),
workingPath = getwd(),
cleanUp = TRUE,
tempSasDir = tempdir())
|
analysisCode |
(Required) Analysis code: An R function, a reference to an external R script, or a reference to an external SAS script |
doses |
(Required) Vector of doses for which estimates are expected |
data |
(Required) Input dataset on which to perform analysis |
software |
(Optional) Software for analysis: "R" or "SAS" (default is "R") |
includeRows |
(Optional) 2 column matrix specifying interims and doses to include in analysis. By default, no subsets are applied |
interimCol |
Interim flag column name |
doseCol |
Dose column name |
seed |
(Optional) Random number generation seed. By default, this is derived from the current random seed |
workingPath |
(Optional) Working directory for the analysis. The default is the current working directory |
cleanUp |
(Optional) Logical: Should we remove the files that have been passed in and out of SAS? |
tempSasDir |
Temporary Sas Directory |
The function tries to perform the analysis contained in the analysisCode
against the
data
.
The analysis code specified is either an external file containing code (SAS and R), or an R
function (R only).
If software is set to "SAS" the analysis code is assumed to be a reference to an external SAS
script. The SAS code must accept a single dataset called work.infile, and create an output
dataset called work.outfile. The work.outfile dataset must be a valid "Micro Evaluation"
structure as specified in the help file for checkMicroFormat
.
If the software is "R", the analysis code input must be either an R function or an R script.
The R analysis code must also return a valid "Micro Evaluatoin" structure as specified in
function checkMicroFormat
The function should output a valid "Micro Evaluation" data structure as specified in the
checkMicroFormat
help file.
Mike K Smith mstoolkit@googlemail.com
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 | ## Not run:
# Emax example
anaCode <- function(data){
with( data, {
uniDoses <- sort( unique(DOSE))
outDf <- data.frame( DOSE = uniDoses,
MEAN = tapply(RESP, DOSE, mean) ,
SE = tapply(RESP, DOSE, sd ) )
outDf$LOWER <- outDf$MEAN - 2 * outDf$SE
outDf$UPPER <- outDf$MEAN + 2 * outDf$SE
outDf$N <- table(DOSE)[ as.character(uniDoses) ]
outDf
})
}
# example data
exData <- system.file( "Runit", "data", "analyseRep", "ReplicateData", "replicate0001.csv",
package = "MSToolkit")
out <- performAnalysis(anaCode, data = exData, doses = c(0, 5, 25, 50, 100) )
checkMicroFormat( out ) # Check the format of the return structure
## End(Not run)
|
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