# safety_vaccine
[](https://codeocean.com/capsule/7deeac37-cbb7-4969-ad30-dcb2f423fc47/tree)
DOI: https://doi.org/10.24433/CO.6387836.v1
Takefuji Y. Set Operations in Python for Translational Medicine. International Journal of Translational Medicine. 2022; 2(2):174-185.
https://doi.org/10.3390/ijtm2020015
The latest data of VAERS (Vaccine Adverse Event Reporting System) dataset is
available at:
https://vaers.hhs.gov/eSubDownload/index.jsp?fn=2021VAERSData.zip
effectiveness of vaccination status
https://data.cdc.gov/api/views/3rge-nu2a/rows.csv?accessType=DOWNLOAD
vuv.py is for calculating vaccine effectiveness on mortality between fully vaccinated and unvaccinated.
vuc.py is for calculating vaccine effectiveness on infection between fully vaccinated and unvaccinated.
vuc3.py is for calculating vaccine effectiveness on infection and death between fully vaccinated and unvaccinated by vaccine product.
vuc4.py is for calculating bivalent vaccine effectiveness on infection between fully vaccinated and unvaccinated by age group.
# set operations
vaers.py shows a good example of intersection operation.
set(A).intersection(B)
set(A).symmetric_difference(B)
set(A).difference(B)
set(A).union(B)
<pre>
set([1,2,5]).symmetric_difference([1,2,9,4,8,9])
{4, 5, 8, 9}
set([1,2,5]).difference([1,2,9,4,8,9])
{5}
set([1,2,5]).intersection([1,2,9,4,8,9])
{1, 2}
set([1,2,5]).union([1,2,9,4,8,9])
{1, 2, 4, 5, 8, 9}
</pre>
The following figure shows what is intersection operation.
<img src="https://github.com/y-takefuji/safety_vaccine/raw/main/set.jpg" width=700 height=560 >
# How to install vaers
On WSL on Windows, MacOS, or Linux operating systems:
$ pip install vaers
On Windows 11 or 10:
$ pip install vaers --force-reinstall --no-cache-dir --no-binary :all:
# How to run vaers
$ vaers
or
$ vaers 2022
# How to run vaers.py
<pre>
0. Download 2021VAERSData.zip
1. Unzip 2021VAERSData.zip file
2. Run vaers.py program
$ python vaers.py
total instances: 677514
total deaths 8926
NOVIDs instances: 1202
NOVIDs deaths: 4
NOV death per instance 0.003328
MODERNA+PFIZER: 905
MODERNA+PFIZER death: 4
MODERNA+PFIZER death per instance: 0.00442
MODERNAIDs instances: 299195
MODERNA deaths 3648
MODERNA 0.012193
PFIZERIDs instances: 283061
PFIZER deaths 3969
PFIZER 0.014022
</pre>
# How to run pfizerAge.py to generate a pfizer.csv file.
<pre>
$ python pfizerAge.py
</pre>
# How to run modernaAge.py to generate a moderna.csv file.
<pre>
$ python modernaAge.py
</pre>
# How to calculate safety thresholds of PFIZER and MODERNA vaccines by age
<pre>
$ python deathperinstance.py
</pre>
# Subtraction operation
set(A).difference(B)
# Union operation
set(A).union(B)
# Symmetric difference (ExclusiveOR)
set(A).symmetric_difference(B)
Raw data
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"description": "# safety_vaccine \n[](https://codeocean.com/capsule/7deeac37-cbb7-4969-ad30-dcb2f423fc47/tree)\n\nDOI: https://doi.org/10.24433/CO.6387836.v1\n\nTakefuji Y. Set Operations in Python for Translational Medicine. International Journal of Translational Medicine. 2022; 2(2):174-185. \nhttps://doi.org/10.3390/ijtm2020015 \n\nThe latest data of VAERS (Vaccine Adverse Event Reporting System) dataset is \navailable at:\n\nhttps://vaers.hhs.gov/eSubDownload/index.jsp?fn=2021VAERSData.zip\n\neffectiveness of vaccination status\n\nhttps://data.cdc.gov/api/views/3rge-nu2a/rows.csv?accessType=DOWNLOAD\n\nvuv.py is for calculating vaccine effectiveness on mortality between fully vaccinated and unvaccinated.\n\nvuc.py is for calculating vaccine effectiveness on infection between fully vaccinated and unvaccinated.\n\nvuc3.py is for calculating vaccine effectiveness on infection and death between fully vaccinated and unvaccinated by vaccine product.\n\nvuc4.py is for calculating bivalent vaccine effectiveness on infection between fully vaccinated and unvaccinated by age group.\n\n# set operations\nvaers.py shows a good example of intersection operation. \n\nset(A).intersection(B)\n\nset(A).symmetric_difference(B)\n\nset(A).difference(B)\n\nset(A).union(B)\n<pre>\n set([1,2,5]).symmetric_difference([1,2,9,4,8,9])\n {4, 5, 8, 9}\n \n set([1,2,5]).difference([1,2,9,4,8,9])\n {5}\n \n set([1,2,5]).intersection([1,2,9,4,8,9])\n {1, 2}\n \n set([1,2,5]).union([1,2,9,4,8,9])\n {1, 2, 4, 5, 8, 9}\n</pre>\nThe following figure shows what is intersection operation.\n\n<img src=\"https://github.com/y-takefuji/safety_vaccine/raw/main/set.jpg\" width=700 height=560 >\n\n# How to install vaers\nOn WSL on Windows, MacOS, or Linux operating systems:\n\n$ pip install vaers\n\nOn Windows 11 or 10:\n\n$ pip install vaers --force-reinstall --no-cache-dir --no-binary :all:\n\n# How to run vaers\n$ vaers\n\nor\n\n$ vaers 2022\n\n\n# How to run vaers.py\n\n<pre>\n0. Download 2021VAERSData.zip\n1. Unzip 2021VAERSData.zip file\n2. Run vaers.py program\n$ python vaers.py\ntotal instances: 677514\ntotal deaths 8926\nNOVIDs instances: 1202\nNOVIDs deaths: 4\nNOV death per instance 0.003328\nMODERNA+PFIZER: 905\nMODERNA+PFIZER death: 4\nMODERNA+PFIZER death per instance: 0.00442\nMODERNAIDs instances: 299195\nMODERNA deaths 3648\nMODERNA 0.012193\nPFIZERIDs instances: 283061\nPFIZER deaths 3969\nPFIZER 0.014022\n</pre>\n# How to run pfizerAge.py to generate a pfizer.csv file.\n<pre>\n$ python pfizerAge.py\n</pre>\n\n# How to run modernaAge.py to generate a moderna.csv file.\n<pre>\n$ python modernaAge.py\n</pre>\n\n# How to calculate safety thresholds of PFIZER and MODERNA vaccines by age\n<pre>\n$ python deathperinstance.py\n</pre>\n\n# Subtraction operation\n\nset(A).difference(B)\n\n# Union operation\n\nset(A).union(B)\n\n# Symmetric difference (ExclusiveOR)\n\nset(A).symmetric_difference(B)\n\n\n\n",
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