Commit 01168185 authored by Irucka Embry's avatar Irucka Embry
Browse files

Various improvements for next release

parent f19f0958
File mode changed from 100644 to 100755
Package: vaers
Title: US Vaccine Adverse Event Reporting System (VAERS) Data for 1990 -
Present
Version: 1.0.4
Depends: R (>= 2.14.1)
Suggests: vaersND, data.table (>= 1.9.4), dplyr, rpivotTable, knitr, rmarkdown,
devtools
Version: 1.0.6
Depends: R (>= 3.5.0)
Suggests: install.load, dplyr, data.table (>= 1.10.2), pivottabler,
knitr, rmarkdown, anytime, vaersND
Additional_repositories: https://gitlab.com/iembry/vaersND
Author: Irucka Embry [aut, cre]
Maintainer: Irucka Embry <iembry@ecoccs.com>
Description: US VAERS data for 1990 - 06/14/2016. To install the
Description: US VAERS data for 1990 - 3/19/2021. To install the
Suggested 'vaersND' package, use the following R code:
'devtools::install_git("https://gitlab.com/iembry/vaersND.git",
build_vignettes = TRUE)'. "VAERS is a national vaccine
safety surveillance program co-sponsored by the US Centers for Disease
Control and Prevention (CDC) and the US Food and Drug Administration (FDA).
VAERS is a post-marketing safety surveillance program, collecting
information about adverse events (possible side effects) that occur after
the administration of vaccines licensed for use in the United States." For
more information about the data, visit <https://vaers.hhs.gov/index>. For
information about vaccination/immunization hazards, visit
<http://www.questionuniverse.com/rethink.html/#vaccine>.
build_vignettes = TRUE)'. "The Vaccine Adverse Event Reporting System
(VAERS) is a national early warning system to detect possible safety
problems in U.S.-licensed vaccines. VAERS is co-managed by the Centers
for Disease Control and Prevention (CDC) and the U.S. Food and Drug
Administration (FDA)." For more information about the data, visit
<https://vaers.hhs.gov/>. For information about
vaccination/immunization hazards, visit
<https://www.questionuniverse.com/rethink.html#vaccine>,
<https://www.ecoccs.com/healing.html#vaccines>,
<https://www.questionuniverse.com/rethink_current_crisis.html#cov_vaccin>.
URL: https://gitlab.com/iembry/vaers
BugReports: https://gitlab.com/iembry/vaers/issues
License: CC0
LazyData: true
License: CC0 | file LICENSE
Language: en-US
Encoding: UTF-8
RoxygenNote: 5.0.1
LazyData: true
VignetteBuilder: knitr
RoxygenNote: 7.1.1
......@@ -113,4 +113,4 @@ Affirmer's express Statement of Purpose.
CC0 or use of the Work.
For more information, please see
<http://creativecommons.org/publicdomain/zero/1.0/>
<https://creativecommons.org/publicdomain/zero/1.0/>
File mode changed from 100644 to 100755
# vaers 1.0.4
# vaers 1.0.6
* Updated source data and examples. Revised the README, LICENSE, and the DESCRIPTION files. Removed the DISCLAIMER file.
# vaers 1.0.5
* Updated source data
# vaers 1.0.4
* Added installation notes for `vaersND` in Description field in DESCRIPTION file as pointed out by Uwe Ligges
......
#' US Vaccine Adverse Event Reporting System (VAERS) data for 1990 - Present
#'
#' A table containing the data from the VAERS-1 form.
#' A table containing "a detailed description of the data provided in each
#' field of the VAERSDATA.CSV file. The first two fields in this table are the
#' only fields of the dataset not derived from the the VAERS-1 form."
#'
#' @format A data.table data frame with 499,246 rows and 29 variables:
#'
#'
#' @format A data.table data frame with 747726 rows and 35 variables
#' \describe{
#' \item{VAERS_ID}{VAERS Identification Number}
#' \item{RECVDATE}{Date report was received}
......@@ -10,7 +14,8 @@
#' \item{AGE_YRS}{Box 4: Age in Years}
#' \item{CAGE_YR}{Age of patient in years calculated by (vax_date- birthdate)*}
#' \item{CAGE_MO}{Age of patient in months calculated by (vax_date- birthdate).
#' * The values for this variable range from 0 to <1.}
#' * The values for this variable range from (.0, .1, .2, .3, .4, .5, .6,
#' .7, .8, .9, 1)}
#' \item{SEX}{Box 5: Sex}
#' \item{RPT_DATE}{Box 6: Date Form Completed}
#' \item{SYMPTOM_TEXT}{Box 7: Reported symptom text}
......@@ -28,27 +33,33 @@
#' \item{NUMDAYS}{Number of days (Onset date - Vax. Date)}
#' \item{LAB_DATA}{Box 12: Diagnostic laboratory data}
#' \item{V_ADMINBY}{Box 15: Vaccines Administered at (PUB=Public, PVT=Private,
#' OTH=Other, MIL=Military)}
#' OTH=Other, MIL=Military) PHM=Pharmacy or drug store,
#' SCH=School/student health clinic, SEN=Nursing home or senior living
#' facility, WRK=Workplace clinic, UNK=Unknown}
#' \item{V_FUNDBY}{Box 16: Vaccines purchased with (PUB=Public, PVT=Private,
#' OTH=Other, MIL=Military) funds}
#' OTH=Other, MIL=Military) funds UNK=Unknown}
#' \item{OTHER_MEDS}{Box 17: Other Medications}
#' \item{CUR_ILL}{Box 18: Current Illnesses}
#' \item{HISTORY}{Box 19: Pre-existing physician diagnosed allergies, birth
#' defects, medical conditions}
#' \item{PRIOR_VAX}{Box 21: Prior Vaccination Event information}
#' \item{SPLTTYPE}{Box 24: Manufacturer Number}
#' \item{FORM_VERS}{1 for VAERS form 1.0; 2 for VAERS form 2.0}
#' \item{TODAYS_DATE}{Box 7: Today's Date}
#' \item{BIRTH_DEFECT}{Box 21 (Result or outcome): Congenital anomaly or birth
#' defect ('Y' - Yes)}
#' \item{OFC_VISIT}{Box 21 (Result or outcome): Doctor or other healthcare
#' professional office/clinic visit ('Y' - Yes)}
#' \item{ER_ED_VISIT}{{Box 21 (Result or outcome): Emergency room or emergency
#' department visit ('Y' - Yes)}
#' \item{ALLERGIES}{{Box 10 (Allergies to medications, food, or other products)}
#' }
#'
#'
#' @references
#' US Centers for Disease Control and Prevention (CDC) and the US Food and Drug Administration (FDA) Vaccine Adverse Event Reporting System (VAERS) \url{https://vaers.hhs.gov/index} and \url{https://vaers.hhs.gov/data/READMEJanuary2015.pdf}.
#' US Centers for Disease Control and Prevention (CDC) and the US Food and Drug Administration (FDA) Vaccine Adverse Event Reporting System (VAERS) \url{https://vaers.hhs.gov/} and \url{https://vaers.hhs.gov/docs/VAERSDataUseGuide_November2020.pdf}.
#'
#'
#'
#' @docType data
#' @name vaers_data
#' @usage vaers_data
#' @examples
#' library(data.table)
#' vaers_data
NULL
"vaers_data"
#> [1] "vaers_data"
#' US Vaccine Adverse Event Reporting System (VAERS) symptom data for 1990 -
#' Present
#'
#' A table containing the "adverse event coded terms utilizing the MedDRA
#' A table containing "the adverse event coded terms utilizing the MedDRA
#' dictionary. Coders will search for specific terms in boxes 7 and 12 and code
#' them to a searchable and consistent MedDRA term; note that terms are
#' included in the .csv file in alphabetical order. There can be an unlimited
......@@ -12,12 +12,12 @@
#'
#'
#'
#' @format A data.table data frame with 609,001 rows and 11 variables:
#' @format A data.table data frame with 915638 rows and 11 variables
#' \describe{
#' \item{VAERS_ID}{VAERS Identification Number}
#' \item{SYMPTOM1}{Adverse Event MedDRA Term 1}
#' \item{SYMPTOMVERSION1}{MedDRA dictionary version number 1}
#' \item{SYMPTOM2}{Adverse Event MedDRA Term 1}
#' \item{SYMPTOM2}{Adverse Event MedDRA Term 2}
#' \item{SYMPTOMVERSION2}{MedDRA dictionary version number 2}
#' \item{SYMPTOM3}{Adverse Event MedDRA Term 3}
#' \item{SYMPTOMVERSION3}{MedDRA dictionary version number 3}
......@@ -29,14 +29,10 @@
#'
#'
#' @references
#' US Centers for Disease Control and Prevention (CDC) and the US Food and Drug Administration (FDA) Vaccine Adverse Event Reporting System (VAERS) \url{https://vaers.hhs.gov/index} and \url{https://vaers.hhs.gov/data/READMEJanuary2015.pdf}.
#' US Centers for Disease Control and Prevention (CDC) and the US Food and Drug Administration (FDA) Vaccine Adverse Event Reporting System (VAERS) \url{https://vaers.hhs.gov/} and \url{https://vaers.hhs.gov/docs/VAERSDataUseGuide_November2020.pdf}.
#'
#'
#'
#' @docType data
#' @name vaers_symptoms
#' @usage vaers_symptoms
#' @examples
#' library(data.table)
#' vaers_symptoms
NULL
#'
"vaers_symptoms"
#> [1] "vaers_symptoms"
#' US Vaccine Adverse Event Reporting System (VAERS) vaccine data for 1990 -
#' Present
#'
#' A table containing the "remaining vaccine information (e.g., vaccine name,
#' A table containing "the remaining vaccine information (e.g., vaccine name,
#' manufacturer, lot number, route, site, and number of previous doses
#' administered), for each of the vaccines listed in Box 13 of the VAERS form.
#' There is a matching record in this file with the VAERSDATA file identified
......@@ -9,13 +9,13 @@
#'
#'
#'
#' @format A data.table data frame with 804,941 rows and 8 variables:
#' @format A data.table data frame with 1112702 rows and 9 variables
#' \describe{
#' \item{VAERS_ID}{VAERS Identification Number}
#' \item{VAX_TYPE}{Administered Vaccine Type}
#' \item{VAX_MANU}{Vaccine Manufacturer}
#' \item{VAX_LOT}{Manufacturer's Vaccine Lot}
#' \item{VAX_DOSE}{Number of previous doses administered}
#' \item{VAX_DOSE_SERIES}{Dose number in series}
#' \item{VAX_ROUTE}{Vaccination Route}
#' \item{VAX_SITE}{Vaccination Site}
#' \item{VAX_NAME}{Vaccination Name}
......@@ -23,14 +23,10 @@
#'
#'
#' @references
#' US Centers for Disease Control and Prevention (CDC) and the US Food and Drug Administration (FDA) Vaccine Adverse Event Reporting System (VAERS) \url{https://vaers.hhs.gov/index} and \url{https://vaers.hhs.gov/data/READMEJanuary2015.pdf}.
#' US Centers for Disease Control and Prevention (CDC) and the US Food and Drug Administration (FDA) Vaccine Adverse Event Reporting System (VAERS) \url{https://vaers.hhs.gov/} and \url{https://vaers.hhs.gov/docs/VAERSDataUseGuide_November2020.pdf}.
#'
#'
#'
#' @docType data
#' @name vaers_vax
#' @usage vaers_vax
#' @examples
#' library(data.table)
#' vaers_vax
NULL
#'
"vaers_vax"
#> [1] "vaers_vax"
#' @details
#' vaers: US Vaccine Adverse Event Reporting System (VAERS)
#'
#' vaers provides the US Vaccine Adverse Event Reporting System
#' (VAERS) data for 1990 - Present. "VAERS is a national vaccine safety
#' surveillance program co-sponsored by the US Centers for Disease Control
#' and Prevention (CDC) and the US Food and Drug Administration (FDA). VAERS
#' is a post-marketing safety surveillance program, collecting information
#' about adverse events (possible side effects) that occur after the
#' administration of vaccines licensed for use in the United States."
#' (VAERS) data for 1990 - Present. "The Vaccine Adverse Event Reporting System
#' (VAERS) is a national early warning system to detect possible safety problems
#' in U.S.-licensed vaccines. VAERS is co-managed by the Centers for Disease
#' Control and Prevention (CDC) and the U.S. Food and Drug Administration (FDA)."
#' For more information about the data, visit \url{https://vaers.hhs.gov/}. For
#' information about vaccination/immunization hazards, visit
#' \url{https://www.questionuniverse.com/rethink.html#vaccine},
#' \url{https://www.ecoccs.com/healing.html#vaccines},
#' \url{https://www.questionuniverse.com/rethink_current_crisis.html#cov_vaccin}.
#'
#' @source VAERS \url{https://vaers.hhs.gov/index}
#' @source VAERS \url{https://vaers.hhs.gov/about.html}
#'
#'
#' @docType package
#' @name vaers
NULL
#' @keywords internal
"_PACKAGE"
#> [1] "_PACKAGE"
File mode changed from 100644 to 100755
# vaers
US Vaccine Adverse Event Reporting System (VAERS) data for 1990 - Present. "VAERS is a national vaccine safety surveillance program co-sponsored by the US Centers for Disease Control and Prevention (CDC) and the US Food and Drug Administration (FDA). VAERS is a post-marketing safety surveillance program, collecting information about adverse events (possible side effects) that occur after the administration of vaccines licensed for use in the United States." Source: [VAERS](https://vaers.hhs.gov/index).
US Vaccine Adverse Event Reporting System (VAERS) data for 1990 - Present.
For information about vaccination/immunization hazards, visit [http://www.questionuniverse.com/rethink.html/#vaccine](http://www.questionuniverse.com/rethink.html/#vaccine).
"Established in 1990, the Vaccine Adverse Event Reporting System (VAERS) is a national early warning system to detect possible safety problems in U.S.-licensed vaccines. VAERS is co-managed by the Centers for Disease Control and Prevention (CDC) and the U.S. Food and Drug Administration (FDA). VAERS accepts and analyzes reports of adverse events (possible side effects) after a person has received a vaccination. Anyone can report an adverse event to VAERS. Healthcare professionals are required to report certain adverse events and vaccine manufacturers are required to report all adverse events that come to their attention.
Due to the large size of the raw data sets, they have not been included in this package. Also, the data sets are presented as is, they have not been cleaned up.
VAERS is a passive reporting system, meaning it relies on individuals to send in reports of their experiences to CDC and FDA. VAERS is not designed to determine if a vaccine caused a health problem, but is especially useful for detecting unusual or unexpected patterns of adverse event reporting that might indicate a possible safety problem with a vaccine. This way, VAERS can provide CDC and FDA with valuable information that additional work and evaluation is necessary to further assess a possible safety concern." Source: [VAERS](https://vaers.hhs.gov/about.html).
For information about vaccination/immunization hazards, visit [https://www.questionuniverse.com/rethink.html#vaccine](https://www.questionuniverse.com/rethink.html/#vaccine), [https://www.ecoccs.com/healing.html#vaccines](https://www.ecoccs.com/healing.html#vaccines), and [https://www.questionuniverse.com/rethink_current_crisis.html#cov_vaccin](https://www.questionuniverse.com/rethink_current_crisis.html#cov_vaccin).
The data sets are presented as is i.e., they have not been cleaned up.
......@@ -18,81 +23,81 @@ devtools::install_git("https://gitlab.com/iembry/vaers.git")
# Examples
```R
library(vaers)
library(data.table)
library(dplyr)
library(rpivotTable)
install.load::load_package("vaers", "dplyr", "data.table", "pivottabler")
# load needed packages using the load_package function from the install.load package (it is assumed that you have already installed these packages)
## load vaers_data
data(vaers_data)
setkey(vaers_data, VAERS_ID)
# How many reports for each sex?
count(vaers_data, SEX)
# Identify the VAERS_IDs for males only.
setkey(vaers_data, VAERS_ID)
vaers_data[SEX == "M"][, 1, with = FALSE]
# Create a pivot table of this data.
rpivotTable(vaers_data)
# Create a pivot table of this data based on SEX and if they DIED
qpvt(vaers_data, "SEX", "DIED", "n()")
## load vaers_symptoms
data(vaers_symptoms)
# How many reports of autism for SYMPTOM1?
setkey(vaers_symptoms, VAERS_ID)
# How many reports of autism for SYMPTOM1?
nrow(vaers_symptoms[SYMPTOM1 == "Autism"])
# Create a pivot table of this data.
rpivotTable(vaers_symptoms)
## load vaers_vax
data(vaers_vax)
setkey(vaers_vax, VAERS_ID)
# What are the counts for each of the VAX_TYPEs?
count(vaers_vax, VAX_TYPE)
# How many reports of MMR as the VAX_TYPE?
nrow(vaers_vax[VAX_TYPE == "MMR"])
# Create a pivot table of this data.
rpivotTable(vaers_vax)
```
# How many reports of COVID19 as the VAX_TYPE?
nrow(vaers_vax[VAX_TYPE == "COVID19"])
# VAERS Data Disclaimer
[https://vaers.hhs.gov/data/data](https://vaers.hhs.gov/data/data) which redirects to [https://vaers.hhs.gov/data/index](https://vaers.hhs.gov/data/index) (The content below is from this second URL and is current as of 2 February 2016):
"VAERS Data
Guide to Interpreting VAERS Case Report Information
# How many people have died from COVID19 vaccine?
data_vax <- vaers_data[vaers_vax]
When evaluating data from VAERS, it is important to note that for any reported event, no cause-and-effect relationship has been established. Reports of all possible associations between vaccines and adverse events (possible side effects) are filed in VAERS. Therefore, VAERS collects data on any adverse event following vaccination, be it coincidental or truly caused by a vaccine. The report of an adverse event to VAERS is not documentation that a vaccine caused the event.
VAERS data contains coincidental events and those truly caused by vaccines.
More than 10 million vaccines per year are given to children less than 1 year old, usually between 2 and 6 months of age. At this age, infants are at greatest risk for certain medical adverse events, including high fevers, seizures, and sudden infant death syndrome (SIDS). Some infants will experience these medical events shortly after a vaccination by coincidence.
These coincidences make it difficult to know whether a particular adverse event resulted from a medical condition or from a vaccination. Therefore, vaccine providers are encouraged to report all adverse events following vaccination, whether or not they believe the vaccination was the cause.
nrow(data_vax[VAX_TYPE == "COVID19"][DIED == "Y"])
```
Please read the following statement on the limits of VAERS data. You MUST click on the box below to access the VAERS database.
When reviewing data from VAERS, please keep in mind the following limitations:
VAERS is a passive reporting system, meaning that reports about adverse events are not automatically collected, but require a report to be filed to VAERS. VAERS reports can be submitted voluntarily by anyone, including healthcare providers, patients, or family members. Reports vary in quality and completeness. They often lack details and sometimes can have information that contains errors.
"Underreporting" is one of the main limitations of passive surveillance systems, including VAERS. The term, underreporting refers to the fact that VAERS receives reports for only a small fraction of actual adverse events. The degree of underreporting varies widely. As an example, a great many of the millions of vaccinations administered each year by injection cause soreness, but relatively few of these episodes lead to a VAERS report. Physicians and patients understand that minor side effects of vaccinations often include this kind of discomfort, as well as low fevers. On the other hand, more serious and unexpected medical events are probably more likely to be reported than minor ones, especially when they occur soon after vaccination, even if they may be coincidental and related to other causes.
# VAERS Data Disclaimer
[https://vaers.hhs.gov/data.html](https://vaers.hhs.gov/data.html) (The content below is from this URL and is current as of 28 March 2021):
A report to VAERS generally does not prove that the identified vaccine(s) caused the adverse event described. It only confirms that the reported event occurred sometime after vaccine was given. No proof that the event was caused by the vaccine is required in order for VAERS to accept the report. VAERS accepts all reports without judging whether the event was caused by the vaccine.
"VAERS accepts reports of adverse events and reactions that occur following vaccination. Healthcare providers, vaccine manufacturers, and the public can submit reports to the system. While very important in monitoring vaccine safety, VAERS reports alone cannot be used to determine if a vaccine caused or contributed to an adverse event or illness. The reports may contain information that is incomplete, inaccurate, coincidental, or unverifiable. In large part, reports to VAERS are voluntary, which means they are subject to biases. This creates specific limitations on how the data can be used scientifically. Data from VAERS reports should always be interpreted with these limitations in mind.
DISCLAIMER: Please note that VAERS staff follow-up on all serious and other selected adverse event reports to obtain additional medical, laboratory, and/or autopsy records to help understand the concern raised. However, in general coding terms in VAERS do not change based on the information received during the follow-up process. VAERS data should be used with caution as numbers and conditions do not reflect data collected during follow-up. Note that the inclusion of events in VAERS data does not imply causality.
The strengths of VAERS are that it is national in scope and can quickly provide an early warning of a safety problem with a vaccine. As part of CDC and FDA’s multi-system approach to post-licensure vaccine safety monitoring, VAERS is designed to rapidly detect unusual or unexpected patterns of adverse events, also known as “safety signals.” If a safety signal is found in VAERS, further studies can be done in safety systems such as the CDC’s Vaccine Safety Datalink (VSD) or the Clinical Immunization Safety Assessment (CISA) project. These systems do not have the same scientific limitations as VAERS, and can better assess health risks and possible connections between adverse events and a vaccine.
For more information, please call the VAERS Information Line toll-free at (800) 822-7967 or e-mail to [info@vaers.org](info@vaers.org).
Key considerations and limitations of VAERS data:
I have read and understand the preceding statement."
*Vaccine providers are encouraged to report any clinically significant health problem following vaccination to VAERS, whether or not they believe the vaccine was the cause.
Reports may include incomplete, inaccurate, coincidental and unverified information.
*The number of reports alone cannot be interpreted or used to reach conclusions about the existence, severity, frequency, or rates of problems associated with vaccines.
*VAERS data is limited to vaccine adverse event reports received between 1990 and the most recent date for which data are available.
*VAERS data do not represent all known safety information for a vaccine and should be interpreted in the context of other scientific information."
# source 1
# r - Convert column classes in data.table - Stack Overflow answered by Matt Dowle on Dec 27 2013. See \url{http://stackoverflow.com/questions/7813578/convert-column-classes-in-data-table}.
# r - Convert column classes in data.table - Stack Overflow answered by Matt Dowle on Dec 27 2013. See \url{https://stackoverflow.com/questions/7813578/convert-column-classes-in-data-table}.
# Data source \url{https://vaers.hhs.gov/data/index}
......@@ -11,41 +11,49 @@
# r - 'embedded nul in string' with fread (tried all other method still couldn't solve)
library(data.table)
library("data.table")
library("anytime")
# Vax
vax <- list.files(path = "/vaers_data/raw/", pattern = "vax", full.names = TRUE, ignore.case = TRUE)
vaers_vax <- lapply(vax, fread, colClasses = "character")
vaers_vax <- rbindlist(vaers_vax)
vaers_vax <- lapply(vax, fread, colClasses = "character", na.strings = getOption("datatable.na.strings", c("NA", "", "N/A")))
vaers_vax <- rbindlist(vaers_vax, fill = TRUE)
# changing column to numeric class
change_class1 <- "VAX_DOSE"
change_class1 <- c("VAX_DOSE", "VAX_DOSE_SERIES")
for (col in change_class1) set(vaers_vax, j = col, value = as.numeric(vaers_vax[[col]])) # Source 1
save(vaers_vax, file = "/data/vaers_vax.RData", compress = "xz")
save(vaers_vax, file = "/vaers/data/vaers_vax.RData", compress = "xz")
# Symptoms
symptoms <- list.files(path = "/vaers_data/raw/", pattern = "symptoms", full.names = TRUE, ignore.case = TRUE)
vaers_symptoms <- lapply(symptoms, fread, colClasses = "character")
vaers_symptoms <- lapply(symptoms, fread, colClasses = "character", na.strings = getOption("datatable.na.strings", c("NA", "", "N/A")))
vaers_symptoms <- rbindlist(vaers_symptoms)
change_class2 <- c("SYMPTOMVERSION1", "SYMPTOMVERSION2", "SYMPTOMVERSION3", "SYMPTOMVERSION4", "SYMPTOMVERSION5")
for (col in change_class2) set(vaers_symptoms, j = col, value = as.numeric(vaers_symptoms[[col]])) # Source 1
save(vaers_symptoms, file = "/data/vaers_symptoms.RData", compress = "xz")
save(vaers_symptoms, file = "/vaers/data/vaers_symptoms.RData", compress = "xz")
# Data
data <- list.files(path = "/vaers_data/raw/", pattern = "data", full.names = TRUE, ignore.case = TRUE)
vaers_data <- lapply(data, fread, colClasses = "character")
vaers_data <- rbindlist(vaers_data)
vaers_data <- lapply(data, fread, colClasses = "character", na.strings = getOption("datatable.na.strings", c("NA", "", "N/A")))
vaers_data <- rbindlist(vaers_data, fill = TRUE)
change_class <- c("RECVDATE", "RPT_DATE", "DATEDIED", "VAX_DATE", "ONSET_DATE")
for (col in change_class) set(vaers_data, j = col, value = anydate(vaers_data[[col]])) # Source 1
change_class3 <- c("AGE_YRS", "CAGE_YR", "CAGE_MO", "HOSPDAYS", "NUMDAYS")
for (col in change_class3) set(vaers_data, j = col, value = as.numeric(vaers_data[[col]])) # Source 1
change_class4 <- c("RECVDATE", "RPT_DATE", "DATEDIED", "VAX_DATE", "ONSET_DATE")
for (col in change_class4) set(vaers_data, j = col, value = as.POSIXct(vaers_data[[col]], format = "%m/%d/%Y")) # Source 1
save(vaers_data, file = "/data/vaers_data.RData", compress = "xz")
save(vaers_data, file = "/vaers/data/vaers_data.RData", compress = "xz")
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VAERS Data Disclaimer
https://vaers.hhs.gov/data/data which redirects to https://vaers.hhs.gov/data/index (The content below is from this second URL and is current as of 2 February 2016):
"VAERS Data
Guide to Interpreting VAERS Case Report Information
When evaluating data from VAERS, it is important to note that for any reported event, no cause-and-effect relationship has been established. Reports of all possible associations between vaccines and adverse events (possible side effects) are filed in VAERS. Therefore, VAERS collects data on any adverse event following vaccination, be it coincidental or truly caused by a vaccine. The report of an adverse event to VAERS is not documentation that a vaccine caused the event.
VAERS data contains coincidental events and those truly caused by vaccines.
More than 10 million vaccines per year are given to children less than 1 year old, usually between 2 and 6 months of age. At this age, infants are at greatest risk for certain medical adverse events, including high fevers, seizures, and sudden infant death syndrome (SIDS). Some infants will experience these medical events shortly after a vaccination by coincidence.
These coincidences make it difficult to know whether a particular adverse event resulted from a medical condition or from a vaccination. Therefore, vaccine providers are encouraged to report all adverse events following vaccination, whether or not they believe the vaccination was the cause.
Please read the following statement on the limits of VAERS data. You MUST click on the box below to access the VAERS database.
When reviewing data from VAERS, please keep in mind the following limitations:
VAERS is a passive reporting system, meaning that reports about adverse events are not automatically collected, but require a report to be filed to VAERS. VAERS reports can be submitted voluntarily by anyone, including healthcare providers, patients, or family members. Reports vary in quality and completeness. They often lack details and sometimes can have information that contains errors.
"Underreporting" is one of the main limitations of passive surveillance systems, including VAERS. The term, underreporting refers to the fact that VAERS receives reports for only a small fraction of actual adverse events. The degree of underreporting varies widely. As an example, a great many of the millions of vaccinations administered each year by injection cause soreness, but relatively few of these episodes lead to a VAERS report. Physicians and patients understand that minor side effects of vaccinations often include this kind of discomfort, as well as low fevers. On the other hand, more serious and unexpected medical events are probably more likely to be reported than minor ones, especially when they occur soon after vaccination, even if they may be coincidental and related to other causes.
A report to VAERS generally does not prove that the identified vaccine(s) caused the adverse event described. It only confirms that the reported event occurred sometime after vaccine was given. No proof that the event was caused by the vaccine is required in order for VAERS to accept the report. VAERS accepts all reports without judging whether the event was caused by the vaccine.
DISCLAIMER: Please note that VAERS staff follow-up on all serious and other selected adverse event reports to obtain additional medical, laboratory, and/or autopsy records to help understand the concern raised. However, in general coding terms in VAERS do not change based on the information received during the follow-up process. VAERS data should be used with caution as numbers and conditions do not reflect data collected during follow-up. Note that the inclusion of events in VAERS data does not imply causality.
For more information, please call the VAERS Information Line toll-free at (800) 822-7967 or e-mail to info@vaers.org.
I have read and understand the preceding statement."
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/vaers.R
\docType{package}
\name{vaers-package}
\alias{vaers}
\alias{vaers-package}
\title{vaers: US Vaccine Adverse Event Reporting System (VAERS) Data for 1990 -
Present}
\source{
VAERS \url{https://vaers.hhs.gov/about.html}
}
\description{
US VAERS data for 1990 - 3/19/2021. To install the
Suggested 'vaersND' package, use the following R code:
'devtools::install_git("https://gitlab.com/iembry/vaersND.git",
build_vignettes = TRUE)'. "The Vaccine Adverse Event Reporting System
(VAERS) is a national early warning system to detect possible safety
problems in U.S.-licensed vaccines. VAERS is co-managed by the Centers
for Disease Control and Prevention (CDC) and the U.S. Food and Drug
Administration (FDA)." For more information about the data, visit
<https://vaers.hhs.gov/>. For information about
vaccination/immunization hazards, visit
<https://www.questionuniverse.com/rethink.html#vaccine>,
<https://www.ecoccs.com/healing.html#vaccines>,
<https://www.questionuniverse.com/rethink_current_crisis.html#cov_vaccin>.
}
\details{
vaers: US Vaccine Adverse Event Reporting System (VAERS)
vaers provides the US Vaccine Adverse Event Reporting System
(VAERS) data for 1990 - Present. "The Vaccine Adverse Event Reporting System
(VAERS) is a national early warning system to detect possible safety problems
in U.S.-licensed vaccines. VAERS is co-managed by the Centers for Disease
Control and Prevention (CDC) and the U.S. Food and Drug Administration (FDA)."
For more information about the data, visit \url{https://vaers.hhs.gov/}. For
information about vaccination/immunization hazards, visit
\url{https://www.questionuniverse.com/rethink.html#vaccine},
\url{https://www.ecoccs.com/healing.html#vaccines},
\url{https://www.questionuniverse.com/rethink_current_crisis.html#cov_vaccin}.
}
\seealso{
Useful links:
\itemize{
\item \url{https://gitlab.com/iembry/vaers}
\item Report bugs at \url{https://gitlab.com/iembry/vaers/issues}
}
}
\keyword{internal}
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/vaers.R
\docType{package}
\name{vaers}
\alias{vaers}
\alias{vaers-package}
\title{vaers: US Vaccine Adverse Event Reporting System (VAERS)}
\source{
VAERS \url{https://vaers.hhs.gov/index}
}
\description{
vaers provides the US Vaccine Adverse Event Reporting System
(VAERS) data for 1990 - Present. "VAERS is a national vaccine safety
surveillance program co-sponsored by the US Centers for Disease Control
and Prevention (CDC) and the US Food and Drug Administration (FDA). VAERS
is a post-marketing safety surveillance program, collecting information
about adverse events (possible side effects) that occur after the
administration of vaccines licensed for use in the United States."
}
......@@ -4,53 +4,18 @@
\name{vaers_data}
\alias{vaers_data}
\title{US Vaccine Adverse Event Reporting System (VAERS) data for 1990 - Present}
\format{A data.table data frame with 499,246 rows and 29 variables:
\describe{
\item{VAERS_ID}{VAERS Identification Number}
\item{RECVDATE}{Date report was received}
\item{STATE}{Box 1: State}
\item{AGE_YRS}{Box 4: Age in Years}
\item{CAGE_YR}{Age of patient in years calculated by (vax_date- birthdate)*}
\item{CAGE_MO}{Age of patient in months calculated by (vax_date- birthdate).
* The values for this variable range from 0 to <1.}
\item{SEX}{Box 5: Sex}
\item{RPT_DATE}{Box 6: Date Form Completed}
\item{SYMPTOM_TEXT}{Box 7: Reported symptom text}
\item{DIED}{Box 8a1: Died ('Y' - Yes)}
\item{DATEDIED}{Box 8a2: Date of Death}
\item{L_THREAT}{Box 8b: Life-Threatening Illness ('Y' - Yes)}
\item{ER_VISIT}{Box 8c: Emergency Room or Doctor Visit ('Y' - Yes)}
\item{HOSPITAL}{Box 8d1: Hospitalized ('Y' - Yes)}
\item{HOSPDAYS}{Box 8d2: Number of days Hospitalized}
\item{X_STAY}{Box 8e: Prolonged Hospitalization ('Y' - Yes)}
\item{DISABLE}{Box 8f: Disability ('Y' - Yes)}
\item{RECOVD}{Box 9: Recovered ('Y' - Yes, 'N' - No, 'U' - Unknown)}
\item{VAX_DATE}{Box 10: Vaccination Date}
\item{ONSET_DATE}{Box 11: Adverse Event Onset Date}
\item{NUMDAYS}{Number of days (Onset date - Vax. Date)}
\item{LAB_DATA}{Box 12: Diagnostic laboratory data}
\item{V_ADMINBY}{Box 15: Vaccines Administered at (PUB=Public, PVT=Private,
OTH=Other, MIL=Military)}
\item{V_FUNDBY}{Box 16: Vaccines purchased with (PUB=Public, PVT=Private,
OTH=Other, MIL=Military) funds}
\item{OTHER_MEDS}{Box 17: Other Medications}
\item{CUR_ILL}{Box 18: Current Illnesses}
\item{HISTORY}{Box 19: Pre-existing physician diagnosed allergies, birth
defects, medical conditions}
\item{PRIOR_VAX}{Box 21: Prior Vaccination Event information}
\item{SPLTTYPE}{Box 24: Manufacturer Number}
}}
\format{
}
\usage{
vaers_data
}
\description{
A table containing the data from the VAERS-1 form.
}
\examples{
library(data.table)
vaers_data
A table containing "a detailed description of the data provided in each
field of the VAERSDATA.CSV file. The first two fields in this table are the
only fields of the dataset not derived from the the VAERS-1 form."