Wrapper for several IQRdataGENERAL cleaning functions
clean_IQRdataGENERAL.Rd
This functions performs several cleaning operations in the following order:
Set the BLLOQ handling method, using the function
blloq_IQRdataGENERAL
.Set user defined records to IGNORE, using the function
setIGNORErecords_IQRdataGENERAL
.Remove missing observation records with missing TIME, using the function
rmMissingTIMEobsRecords_IQRdataGENERAL
.Set missing observation records with missing DV to IGNORE, using the function
setMissingDVobsRecordsIGNORE_IQRdataGENERAL
.Remove user defined subjects, using the function
rmSubjects_IQRdataGENERAL
.Remove non-dose and non-observation records, using the function
rmNonTask_IQRdataGENERAL
.Remove placebo subjects, using the function
rmPLACEBO_IQRdataGENERAL
. The removal of placebo subjects is optional and can be changed by a input flag.Removal of subjects without observations, using the function
rmNOobsSUB_IQRdataGENERAL
.Removal of dose records with AMT=0, using the function
rmAMT0_IQRdataGENERAL
.Removal of ignored record (MDV=1), using the function
rmIGNOREd_IQRdataGENERAL
.Imputation of missing covariates, using the function
covImpute_IQRdataGENERAL
.Removal of doses post last observation, using the function
rmDosePostLastObs_IQRdataGENERAL
. A path name can be provided. If it is, then protocols of the changes are written to log files in the IQRoutputTable format.
clean_IQRdataGENERAL( data, methodBLLOQ = "M1", records = NULL, subjects = NULL, FLAGrmPlacebo = FALSE, FLAGrmIGNOREDrecords = FALSE, FLAGrmDosePostLastObs = FALSE, continuousCovs = NULL, categoricalCovs = NULL, pathname = NULL )
Arguments
data | IQRdataGENERAL object |
---|---|
methodBLLOQ | Character string, determining the method to use. Allowed are: "M1","M3","M4","M5","M6", and "M7". If NULL then not done. |
records | List with reason for ignoring as fieldnames (in quotes)
and value as a scalar or vector with the IXGDFs
Example: |
subjects | List with reason for removal as fieldnames (in quotes)
and value as a scalar or vector with the USUBJIDs
Example: |
FLAGrmPlacebo | If TRUE then placebo subjects are removed from the data. If FALSE they are kept |
FLAGrmIGNOREDrecords | If TRUE then MDV=1 records are removed. If FALSE then not removed. |
FLAGrmDosePostLastObs | If TRUE then dose records post last observation in each individual are removed. |
continuousCovs |
In case covariate columns contain
|
categoricalCovs | In case covariate columns contain |
pathname | Pathname to where to write the log files |
Value
"Cleaned" IQRdataGENERAL object
See also
Other IQRdataGeneral:
+.IQRdataGENERAL()
,
IQRcalcTAD()
,
IQRdataGENERAL()
,
IQRexpandADDLII()
,
IQRloadCSVdata()
,
IQRsaveCSVdata()
,
addIndivRegressors_IQRdataGENERAL()
,
addLabel_IQRdataGENERAL()
,
attributes0()
,
blloqInfo_IQRdataGENERAL()
,
blloq_IQRdataGENERAL()
,
check_IQRdataGENERAL()
,
combine_IQRdataGENERAL()
,
convertCat2Text()
,
covImpute_IQRdataGENERAL()
,
date2dateday_IQRdataProgramming()
,
date2datetime_IQRdataProgramming()
,
date2time_IQRdataProgramming()
,
exportDEFINE_IQRdataGENERAL()
,
exportDEFINEpdf_IQRdataGENERAL()
,
exportSYS_IQRdataGENERAL()
,
export_IQRdataGENERAL()
,
getLabels_dataframe()
,
getNAcolNLME_IQRdataGENERAL()
,
handleSameTimeObs_IQRdataGENERAL()
,
is_IQRdataGENERAL()
,
loadATRinfo_csvData()
,
loadAttributeFile()
,
load_IQRdataGENERAL()
,
mapCategoricalCovariate_IQRnlmeProject()
,
mapCategoricalCovariate_csvData()
,
mapContinuousCovariate_IQRnlmeProject()
,
mapContinuousCovariate_csvData()
,
mutateCov_IQRdataGENERAL()
,
obfuscate_IQRdataGENERAL()
,
plot.IQRdataGENERAL()
,
plotCorCat_IQRdataGENERAL()
,
plotCorCovCat_IQRdataGENERAL()
,
plotCorCov_IQRdataGENERAL()
,
plotCovDistribution_IQRdataGENERAL()
,
plotDoseSchedule_IQRdataGENERAL()
,
plotIndiv_IQRdataGENERAL()
,
plotRange_IQRdataGENERAL()
,
plotSampleSchedule_IQRdataGENERAL()
,
plotSpaghetti_IQRdataGENERAL()
,
print.IQRdataGENERAL()
,
removeCommata_dataframe()
,
rmAMT0_IQRdataGENERAL()
,
rmDosePostLastObs_IQRdataGENERAL()
,
rmIGNOREd_IQRdataGENERAL()
,
rmMissingTIMEobsRecords_IQRdataGENERAL()
,
rmNOobsSUB_IQRdataGENERAL()
,
rmNonTask_IQRdataGENERAL()
,
rmPLACEBO_IQRdataGENERAL()
,
rmSubjects_IQRdataGENERAL()
,
setIGNORErecords_IQRdataGENERAL()
,
setMissingDVobsRecordsIGNORE_IQRdataGENERAL()
,
subset.IQRdataGENERAL()
,
summary.IQRdataGENERAL()
,
summaryCat_IQRdataGENERAL()
,
summaryCov_IQRdataGENERAL()
,
summaryObservations_IQRdataGENERAL()
,
transformObs_IQRdataGENERAL()
,
unlabel_dataframe()
Other IQRdataGeneral:
+.IQRdataGENERAL()
,
IQRcalcTAD()
,
IQRdataGENERAL()
,
IQRexpandADDLII()
,
IQRloadCSVdata()
,
IQRsaveCSVdata()
,
addIndivRegressors_IQRdataGENERAL()
,
addLabel_IQRdataGENERAL()
,
attributes0()
,
blloqInfo_IQRdataGENERAL()
,
blloq_IQRdataGENERAL()
,
check_IQRdataGENERAL()
,
combine_IQRdataGENERAL()
,
convertCat2Text()
,
covImpute_IQRdataGENERAL()
,
date2dateday_IQRdataProgramming()
,
date2datetime_IQRdataProgramming()
,
date2time_IQRdataProgramming()
,
exportDEFINE_IQRdataGENERAL()
,
exportDEFINEpdf_IQRdataGENERAL()
,
exportSYS_IQRdataGENERAL()
,
export_IQRdataGENERAL()
,
getLabels_dataframe()
,
getNAcolNLME_IQRdataGENERAL()
,
handleSameTimeObs_IQRdataGENERAL()
,
is_IQRdataGENERAL()
,
loadATRinfo_csvData()
,
loadAttributeFile()
,
load_IQRdataGENERAL()
,
mapCategoricalCovariate_IQRnlmeProject()
,
mapCategoricalCovariate_csvData()
,
mapContinuousCovariate_IQRnlmeProject()
,
mapContinuousCovariate_csvData()
,
mutateCov_IQRdataGENERAL()
,
obfuscate_IQRdataGENERAL()
,
plot.IQRdataGENERAL()
,
plotCorCat_IQRdataGENERAL()
,
plotCorCovCat_IQRdataGENERAL()
,
plotCorCov_IQRdataGENERAL()
,
plotCovDistribution_IQRdataGENERAL()
,
plotDoseSchedule_IQRdataGENERAL()
,
plotIndiv_IQRdataGENERAL()
,
plotRange_IQRdataGENERAL()
,
plotSampleSchedule_IQRdataGENERAL()
,
plotSpaghetti_IQRdataGENERAL()
,
print.IQRdataGENERAL()
,
removeCommata_dataframe()
,
rmAMT0_IQRdataGENERAL()
,
rmDosePostLastObs_IQRdataGENERAL()
,
rmIGNOREd_IQRdataGENERAL()
,
rmMissingTIMEobsRecords_IQRdataGENERAL()
,
rmNOobsSUB_IQRdataGENERAL()
,
rmNonTask_IQRdataGENERAL()
,
rmPLACEBO_IQRdataGENERAL()
,
rmSubjects_IQRdataGENERAL()
,
setIGNORErecords_IQRdataGENERAL()
,
setMissingDVobsRecordsIGNORE_IQRdataGENERAL()
,
subset.IQRdataGENERAL()
,
summary.IQRdataGENERAL()
,
summaryCat_IQRdataGENERAL()
,
summaryCov_IQRdataGENERAL()
,
summaryObservations_IQRdataGENERAL()
,
transformObs_IQRdataGENERAL()
,
unlabel_dataframe()