filterbyoccpFAERS {extractFAERS}R Documentation

Filter extracted FAERS data by reporter occupation

Description

Filter extracted FAERS data by reporter occupation

Usage

filter_by_occp_FAERS(
  workingdir = NULL,
  temp_dir = NULL,
  occpextract = NULL,
  savetoRData = FALSE
)

Arguments

workingdir

Character vector. The directory containing decompressed FAERS ASCII folders.

temp_dir

Internal parameter used only when extract1PSFAERS is called internally. Do not modify.

occpextract

Character vector. Specifies the occupation types to extract. Defaults to c("MD", "HP", "PH", "OT").

savetoRData

Logical. Determines whether to save F_COREDATA_1PS_PROF.RData in the working directory. Must be set to TRUE if filter_by_occu_FAERS is used independently.

Details

This package includes example data files in extdata:

Value

A list containing six data frames, containing formatted FAERS data after selecting single-drug cases and filtering reports based on reporter occupation. Can be used by time_to_day_FAERS() to standardize time units.

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
)


[Package extractFAERS version 0.1.4 Index]