Extract data from a subject level domain.

Extracts and returns all rows from the specified domain for the set of subjects included in animalList.

Usage

getSubjData(dbToken, animalList, domain, colList = NULL)

Arguments

dbToken: Mandatory
Token for the open database connection (see initEnvironment).
animalList: Mandatory, data.table.
A table with the list of animals to be included in the output data.
The table must include at least columns named 'STUDYID' and 'USUBJID'.
domain: Mandatory, character, not case sensitive.
The name of the domain table to extract data from.
The name must be a subject level domain - i.e. a table including a 'USUBJID' column.
colList: Optional, character, not case sensitive.
The list of columns to be extracted from the specified domain table.
It can be a single string, a vector or a list of multiple strings.

Value

The function returns a data.table with all the rows for the animals included in animalList.

If no columns have been specified in colList, all the columns in the table colList are included.

If a list of columns have been specified in colList, these are included. In addition, a set of columns are always included, whether they are included in colList or not:

To ensure each row can be uniquely identified:
- DOMAIN
- STUDYID
- USUBJID
- POOLID (if it exists)
- domainSEQ (if it exists)
For finding tables - to support age calculation and evaluation of study phase:
- domainDTC
- domainDY

The order of the columns are as they are defined for the domain in the SEND IG.

The data table contains both

subject level data - i.e. rows where USUBJID is not empty
if applicable for the domain, pool level data - i.e. rows where POOLID is not empty.
In this case, all pools, which includes any of the subjects included in animalList, are included

Examples

if (FALSE) {
# Extract all columns from DM:
getSubjData(myDbToken, myControlAnimals, 'dm')

# Extract selected columns from LB:
getSubjData(myDbToken, myControlAnimals, 'LB',
            list('LBTESTCD', 'LBCAT',
                 'LBSTRESC', 'LBSTRESN', 'LBSTRESU',
                 'LBSTAT', 'LBREASND',
                 'LBTPT'))
}