extract1PSFAERS {extractFAERS} | R Documentation |
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
)
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 |
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 |
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.
Value
A character vector containing the file paths of the processed folders
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
)