faers

Workflows

Standard Workflow

library(faers)

# 1. Check metadata of FAERS
faers_meta(internal = TRUE)

# 2. Download and parse quarterly data files
data2 <- faers(
  c(2004, 2017), 
  c("q1", "q2"), 
  dir = system.file("extdata", package = "faers"), 
  compress_dir = tempdir()
)

# 3. Retrieve specific field data (e.g., demographic data)
demo_data <- faers_get(data2, "demo")

# 4. Load standardized data and retrieve MedDRA hierarchy
data_std <- readRDS(system.file("extdata", "standardized_data.rds", package = "faers"))
meddra_hier <- faers_meddra(data_std, use = "hierarchy")

Input/Output Note: Inputs are year, quarter, and directory paths for FAERS raw data; outputs are standardized FAERS data tables and MedDRA hierarchy mappings.

When to Use

• Accessing and parsing the FDA Adverse Event Reporting System (FAERS) quarterly data files.
• Retrieving specific demographic, drug, or reaction fields using faers_get.
• Standardizing drug and reaction terms to MedDRA terminology using faers_standardize and faers_meddra.

When NOT to Use

• For analyzing clinical trial adverse events that are not part of the FAERS public database.
• For real-time adverse event tracking (FAERS data is released quarterly).

Data Requirements

• Raw FAERS quarterly data files (ASCII or XML format).
• MedDRA terminology files for standardization.

Key Parameters

• internal (FALSE): Logical indicating whether to use internal cached FAERS metadata in faers_meta.
• dir: Directory path where FAERS data files are stored or downloaded.
• compress_dir: Temporary directory for uncompressing downloaded files.
• use ("hierarchy"): Component of MedDRA to retrieve (e.g., "hierarchy" or "SMQ").

Best Practices

• Check FAERS metadata using faers_meta(internal = TRUE) to verify available quarters and file sizes before downloading.
• Use faers_combine to merge multiple quarters of parsed FAERS data into a single object.
• Standardize drug and reaction terms using faers_standardize with a valid MedDRA path to ensure consistent terminology.

Common Pitfalls

• Attempting to run standardization without providing a valid path to uncompressed MedDRA data. Ensure meddra_path is correctly specified.

Alternatives

• openfda: For querying the OpenFDA API directly instead of parsing raw quarterly files.

Citations

• FDA Adverse Event Reporting System (FAERS) documentation.

References

• Homepage: bioconductor.org/packages/faers
• Vignette: https://bioconductor.org/packages/release/bioc/vignettes/faers/inst/doc/FAERS-Pharmacovigilance.html