extractFAERS (version 0.1.4)

extract1PSFAERS: Extract reports with only one drug used from FAERS data

Description

This function processes the FDA Adverse Event Reporting System (FAERS) data to extract reports where only a single drug was administered. Only data after 2014Q3 can be directly extracted with this package

Usage

extract_FAERS_data(
  workingdir = NULL,
  usetempdir = FALSE,
  corenum = NULL,
  startfile = NULL,
  endfile = NULL,
  onlydoextract = FALSE,
  occpextract = NULL
)

Value

A character vector containing the file paths of the processed folders

Arguments

workingdir

Character vector. The directory containing the decompressed FAERS ASCII folders.

usetempdir

Logical. If TRUE, processed files are stored in a temporary directory; otherwise, they are saved in workingdir.

corenum

Numeric. The number of CPU cores to use for parallel processing. Using more cores reduces processing time.

startfile

Numeric. The index of the first file to process in the DRUG and related folders.

endfile

Numeric. The index of the last file to process in the DRUG and related folders.

onlydoextract

Logical. If TRUE, only extracts data without performing additional combination or filtering steps.

occpextract

Character vector. Specifies the occupation categories for data extraction. Defaults to c("MD", "HP", "PH", "OT").

Details

This package includes example data files in extdata:

• faers_ascii_2015q1_example.zip: Example dataset 1.

• faers_ascii_2015q2_example.zip: Example dataset 2.

• faers_ascii_2015q3_example.zip: Example dataset 3.

• faers_ascii_2015q4_example.zip: Example dataset 4.

• Use system.file("extdata",package = "extractFAERS") to access the folder contain example zip files.

Examples

# Example_1 Perform FAERS data preprocessing in one step and
# generate `F_COREDATA_1PS_PROF_STU.RData` in a temporary folder.
# In practice, it is recommended to set `usetempdir = FALSE` and specify `workingdir`
# to prevent the processed results in the temporary folder from being automatically deleted.
extract_FAERS_data(
  workingdir = system.file("extdata", package = "extractFAERS"),
  usetempdir = TRUE,
  corenum = 2,
  startfile = 1,
  endfile = 4,
  onlydoextract = FALSE,
  occpextract = NULL
)

# Example_2 Stepwise FAERS data preprocessing
# Setting `onlydoextract = TRUE` extracts only single-drug cases and organizes file paths.
# The processed file paths are saved in a temporary directory.
extractfaerspath <- extract_FAERS_data(
  workingdir = system.file("extdata", package = "extractFAERS"),
  usetempdir = TRUE,
  corenum = 2,
  startfile = 1,
  endfile = 4,
  onlydoextract = TRUE,
  occpextract = NULL
)
print(extractfaerspath)

# Filter data based on reporter occupation
# By default, only reports from healthcare professionals
# (e.g., physicians, pharmacists) are retained.
faers1psprofdata <- filter_by_occp_FAERS(
  workingdir = extractfaerspath,
  occpextract = NULL,
  savetoRData = TRUE
)

# Standardize time units to days
# This ensures consistency in the dataset and facilitates analysis of adverse reactions
# based on patient age.
time_to_day_FAERS(
workingdir = extractfaerspath,
usexistRData = TRUE,
filteres = NULL
)