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Use bioconductor-faers to download and parse FAERS quarterly data files for the years [years] and quarters [quarters]
Required inputs
[years]
[quarters]
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SKILL.md
name: bioconductor-faersdescription: The FDA Adverse Event Reporting System (FAERS) is a database used for the spontaneous reporting of adverse events and medication errors related to human drugs and therapeutic biological products. faers pacakge serves as the interface between the FAERS database and R. Furthermore, faers pacakge offers a standardized approach for performing pharmacovigilance analysis.when_to_use: Use when: The FDA Adverse Event Reporting System (FAERS) is a database used for the spontaneous reporting of adverse events and me; FAERS-Pharmacovigilance. Not for: Requires R ≥ 3.5.0 and Bioconductor ≥ 3.16user-invocable: false
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.