getSubjRoute: Extract the set of animals of the specified route of...

In sendigR: Enable Cross-Study Analysis of 'CDISC' 'SEND' Datasets

Extract the set of animals of the specified route of administration - or just add actual route of administration for each animal.

Description

Returns a data table with the set of animals included in the animalList matching the route of administration specified in the routeFilter.
If the routeFilter is empty (null, na or empty string) - all rows from animalList are returned with an additional populated ROUTE column.

Usage

getSubjRoute(
  dbToken,
  animalList,
  routeFilter = NULL,
  exclusively = FALSE,
  matchAll = FALSE,
  inclUncertain = FALSE,
  noFilterReportUncertain = TRUE
)

Arguments

dbToken	Mandatory Token for the open database connection (see initEnvironment).
animalList	Mandatory, data.table. A table with the list of animals to process. The table must include at least columns named 'STUDYID' and 'USUBJID'.
routeFilter	Optional, character. The route of administration value(s) to use as criterion for filtering of the input data table. It can be a single string, a vector or a list of multiple strings.
exclusively	Mandatory if routeFilter is non empty, boolean. TRUE: Include animals only for studies with no other routes then included in routeFilter. FALSE: Include animals for all studies with route matching routeFilter.
matchAll	Mandatory if routeFilter is non empty, boolean. TRUE: Include animals only for studies with route(s) matching all values in routeFilter. FALSE: Include animals for all studies with route matching at least one value in routeFilter.
inclUncertain	Mandatory if routeFilter is non empty, boolean,. Indicates whether animals for which the route cannot be confidently identified shall be included or not in the output data table.
noFilterReportUncertain	Mandatory if routeFilter is empty, boolean Only relevant if the routeFilter is empty. Indicates if the reason should be included if the route cannot be confidently decided for an animal.

Details

The route of administration per animal are identified by a hierarchical lookup in these domains

• EX - If a distinct not empty EXROUTE value is found for animal, this is included in the output.
  

• TS - if a distinct TS parameter 'ROUTE' value exists for the study, this is included in the output.
  

The comparison of route values is done case insensitive and trimmed for leading/trailing blanks.

If input parameter inclUncertain=TRUE, uncertain animals are included in the output set. These uncertain situations are identified and reported (in column UNCERTAIN_MSG):

• TS parameter ROUTE is missing for study and no EX rows contain a EXROUTE value for the animal

• The selected EXROUTE or TS parameter ROUTE value is invalid (not CT value - CDISC SEND code list ROUTE)

• Multiple EXROUTE values have been found for the animal

• Multiple TS parameter ROUTE values are registered for study but no EX rows contain a EXROUTE value for the animal

• The found EXROUTE value for animal is not included in the TS parameter ROUTE value(s) registered for study

The same checks are performed and reported in column NOT_VALID_MSG if routeFilter is empty and noFilterReportUncertain=TRUE.

Value

The function returns a data.table with columns:

• STUDYID (character)

• Additional columns contained in the animalList table

• ROUTE (character)
  The value is always returned in uppercase and trimmed for leading/trailing blanks.

• UNCERTAIN_MSG (character)
  Included when parameter inclUncertain=TRUE.
  In case the ROUTE cannot be confidently matched during the filtering of data, the column contains an indication of the reason.
  Is NA for rows where ROUTE can be confidently matched.
  A non-empty UNCERTAIN_MSG value generated by this function is merged with non-empty UNCERTAIN_MSG values which may exist in the input set of animals specified in animalList - separated by '|'.

• NOT_VALID_MSG (character)
  Included when parameter noFilterReportUncertain=TRUE.
  In case the ROUTE cannot be confidently decided, the column contains an indication of the reason.
  Is NA for rows where the ROUTE can be confidently decided.
  A non-empty NOT_VALID_MSG value generated by this function is merged with non-empty NOT_VALID_MSG values which may exist in the input set of animals animalList - separated by '|'.

Examples

## Not run: 
# Extract animals administered oral or oral gavage plus uncertain animals
getSubjRoute(dbToken, controlAnimals,
             routeFilter = c('ORAL', 'ORAL GAVAGE'),
             inclUncertain = TRUE)
# Extract animals administered oral or oral gavage.
# Do only include studies which include both route values
getSubjRoute(dbToken, controlAnimals,
             routeFilter = c('ORAL', 'ORAL GAVAGE'),
             matchAll = TRUE)
# Extract animals administered subcutaneous.
# Include only animals from studies which do not contain other route values
getSubjRoute(dbToken, controlAnimals,
             routeFilter = 'subcutaneous',
             exclusively = TRUE)
# No filtering, just add ROUTE - do not include messages when
# these values cannot be confidently found
getSubjRoute(dbToken, controlAnimals,
             noFilterReportUncertain = FALSE)

## End(Not run)

sendigR documentation built on Aug. 18, 2022, 9:07 a.m.