timetodayFAERS: Change all time units to days in the data filtered by...

In extractFAERS: Extract Data from FAERS Database

Change all time units to days in the data filtered by filter_by_occu_FAERS(). This function converts age and time units in the data to days, and processes occupation and reaction data.

Description

Change all time units to days in the data filtered by filter_by_occu_FAERS(). This function converts age and time units in the data to days, and processes occupation and reaction data.

Usage

time_to_day_FAERS(workingdir = NULL, usexistRData = FALSE, filteres = NULL)

Arguments

workingdir	Directory containing F_COREDATA_1PS_PROF.RData.
usexistRData	Logical. Specifies whether to use F_COREDATA_1PS_PROF.RData in the working directory for calculations. Must be set to TRUE and workingdir must be provided if time_to_day_FAERS is used independently.
filteres	Filtered results for changing time units. Used only when extract1PSFAERS is called internally. Set to NULL if time_to_day_FAERS is used separately.

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 path of the processed file "F_COREDATA_1PS_PROF_STU.RData", which can be used for further analysis

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
)

extractFAERS documentation built on June 8, 2025, 10:28 a.m.