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Documentation for `get_repeat_dose_parallel_studyids` Function

Source: vignettes/get_repeat_dose_parallel_studyids.Rmd
get_repeat_dose_parallel_studyids.Rmd

Function Purpose

The get_repeat_dose_parallel_studyids function is designed to retrieve study IDs from a database that correspond to parallel-design studies involving repeat-dose toxicity. It filters the studies based on the specified design and whether the species involved are rats.

Input Parameters

The function accepts the following parameters:

Parameter Description Default Value
path_db The file path to the SQLite database. It must be provided as a valid string. Required
rat_studies A logical flag indicating whether to filter the studies for rats only. Defaults to FALSE. FALSE

Output

The function returns a vector of study IDs that meet the specified criteria. The returned vector contains the following:

  • Study IDs: A list of study IDs that match both the parallel design and repeat-dose toxicity criteria (and rat species, if specified).

Key Steps

  1. Database Existence Check:
    The function first checks if the database file exists at the provided path. If not, an error is raised.

  2. Database Connection:
    The database connection is established using the sendigR package. A connection to the database is initialized using sendigR::initEnvironment().

  3. Retrieve Parallel Study IDs:
    The function uses sendigR::getStudiesSDESIGN() to retrieve all study IDs associated with the parallel design.

  4. Retrieve Repeat-Dose Studies:
    A SQL query is executed via sendigR::genericQuery() to fetch study IDs that are associated with repeat-dose toxicity. This query looks for studies with specific TSPARMCD values related to repeat-dose toxicity.

  5. Intersect Parallel and Repeat-Dose Studies:
    The study IDs obtained from the parallel design and the repeat-dose toxicity studies are intersected to identify common study IDs.

  6. Optionally Filter for Rat Studies:
    If rat_studies = TRUE, the function retrieves study IDs that involve rats as the species. This is done by querying the SPECIES field in the database and filtering based on the presence of “RAT”.

  7. Return Study IDs:
    The final result is a vector of study IDs that meet the filter conditions, including parallel design, repeat-dose toxicity, and optionally, rat species.

Example Usage

```r # Example without filtering for rat studies study_ids <- get_repeat_dose_parallel_studyids(path_db = “path/to/database.sqlite”)

Example with filtering for rat studies

study_ids_rats <- get_repeat_dose_parallel_studyids(path_db = “path/to/database.sqlite”, rat_studies = TRUE)